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Interactive Exploration of Chemical Space with Scaffold Hunter
Stefan Wetzel, Karsten Klein, Steffen Renner, Daniel Rauh, Tudor I. Oprea, Petra Mutzel, and
Herbert Waldmann*
Dipl.-Chem. S. Wetzel, Dr. S. Renner, Prof. Dr. H. Waldmann
Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, D –
44227 Dortmund, Germany and Chemical Biology, Technical University of Dortmund, D-
44227 Dortmund, Germany, Tel: +49 231 133 2400; Fax: +49 231 133 2499, E-mail:
herbert.waldmann@mpi-dortmund.mpg.de
Dipl.-Inform. K. Klein, Prof. Dr. P. Mutzel
Chair of Algorithm Engineering, Faculty of Computer Sciences, Technical University
Dortmund, Otto-Hahn-Str. 14, D-44227 Dortmund, Germany, Tel: +49 231 755 7700, E-mail:
petra.mutzel@cs.uni-dortmund.de
Dr. Daniel Rauh, Chemical Genomics Centre of the Max-Planck Society, Otto-Hahn-Str. 15,
D-44227 Dortmund, Germany, daniel.rauh@cgc.mpg.de
Prof. Dr. Tudor I. Oprea, University of New Mexico School of Medicine, Division of
Biocomputing, MSC11 6145, Research Incubator Building, Suite 170, 2703 Frontier, NE, 1
University of New Mexico
Albuquerque, NM 87131, United States of America
Supplementary Methods
General: Compounds employed in the pyruvate kinase screen were purchased from ChemDiv
and Aurora Fine Chemicals Ltd. as 10mM solutions in DMSO.1, 2
Supplementary Movies: Supplementary Movies were generated using CamStudio 2.03, with
the Lagrith lossless codec 1.3.15.4 Post processing was done with Adobe Premiere Pro CS3.5
Nature Chemical Biology: doi:10.1038/nchembio.187
Supplementary Movie 1 – Scaffold Hunter – A guided Tour
Supplementary Movie 2 – Exploring Virtual Scaffolds Data sources:
WOMBAT: WOMBAT is a database containing small molecules and their annotated biological
activity extracted from contemporary literature. The 2007.1 version used in this analysis
contains more than 186,000 molecules and 370,000 annotated bioactivities. More information
can be obtained from www.sunsetmolecular.com.
PubChem: PubChem is a database providing information on the biological activities of small
molecules. It is part of the NIH’s moelcular libraries part of the roadmap initiative aiming at
providing researchers with publicly available HTS data sets for biomedical research. As of
February 19th 2009 it contained more than 10.5 million unique chemical structures and over
1300 bioassays. For more information see: http://pubchem.ncbi.nlm.nih.gov/.
For our analysis we used the set of the Pyruvate Kinase Screen (assay id 361). AC50 and log
AC50 values are provided for all compounds. Inactive compounds have values in the range of
2.9 x 10-5 M to 6.7 x 10-3 M and -4.55 to -2.24, respectively.
UniProt: UniProt is a comprehensive web resource for protein data, e.g. sequences and
annotation.6 Its identifier is a well recognized standard to unambiguously identify proteins and
to link protein data from different sources. It can be found at: http://www.uniprot.org/.
Biochemical assays: Lactate dehydrogenase was obtained from USB Corporation, Cleveland,
USA. Pyruvate kinase from Bacillus stearothermophilus, ribose-5-phosphate (R5P), potassium
dihydrogen phosphate, potassium chloride, magnesium sulphate, imidazole and
phosphoenolpyruvic acid monopotassium salt (PEP) were bought from Sigma Aldrich.
Adenosine-5’-diphosphate disodium salt (ADP), � -nicotinamide adenine dinucleotide (NADH)
and DMSO were purchased from Serva Electrophoresis GmbH, Heidelberg, Germany. Sodium
Nature Chemical Biology: doi:10.1038/nchembio.187
pyruvate was purchased from Alfa Aesar GmbH, Germany. All measurements were conducted
in transparent 384 well small volume plates from Greiner with a total volume of 14 � L and
carried out in triplicate using a Tecan infinite M200 plate reader set to absorbance at 340 nm.
Plates were measured for 40 minutes. Pipetting was done using a Caliper Zymark Sciclone
ALH 500 pipetting robot. All measurements were evaluated using Microsoft Excel and IDBS
XLfit. The values reported are the average values and their standard deviation.
Pyruvate kinase assay: The lactate dehydrogenase (LDH) coupled pyruvate kinase assay was
set up according to protocols from PubChem7, 8 and Sigma.9 Firstly, 1 � L of compound solution
in DMSO was dissolved in 49 � L of a solution containing all components except the pyruvate
kinase substrate PEP. Of this mix, 4x7 � L were transferred to the small volume measurement
plate. After incubation for 15 minutes at 30°C, 7 � L of PEP solution were added to each well
and the plate was measured in a continuous kinetics mode. Final assay concentrations were 50
mM imidazole (pH 7.2), 0.6 mM NADH, 0.4 mM ADP, 0.14 nM R5P, 50 mM potassium
chloride, 7mM magnesium sulphate, 0.01% Tween 20, 0.2 U LDH, 0.07 U pyruvate kinase,
0.05% BSA and 2 mM PEP.
The data was treated as described by Inglese et al.8 except for normalization. Activity data were
normalized to a negative control without PEP instead of a negative control with the pyruvate
kinase inhibitor luteolin.8 Compounds with less than 50% or more than 130% activity in the
pyruvate kinase assay were confirmed in a concentration dependent measurement using 11
concentrations with a 2-fold dilution starting at 100 � M. The IC50 values derived from these
experiments are reported together with their standard deviation for three independent
measurements.
Lactate dehydrogenase assay: To rule out false positives by inhibition of the LDH reporter
system, all compounds were screened for possible inhibition of LDH with a protocol adapted
from Sigma-Aldrich.10 For this purpose, 1 � L of compound solution in DMSO was dissolved in
Nature Chemical Biology: doi:10.1038/nchembio.187
49 � L of a solution containing all components except pyruvate. Of this mix, 4x7 � L were
transferred to the small volume measurement plate. After incubation for 15 minutes at 37°C,
7 � L of pyruvate solution were added to each well. Final concentrations in this assay were
38 mM potassium dihydrogen phosphate pH 7.6, 0.9 mM NADH, 0.01% Tween 20, 0.002 U
LDH, 0.05% BSA and 1.2 mM sodium pyruvate.
Database generation and tree construction
“Scaffold Tree Generator“, a separate program, generates the scaffold hierarchy data structure
and database in one step from a standard SD file format. The graphical user interface makes
database generation an easy task, such that Scaffold Hunter can be efficiently and reliably run
also by users with non-expert cheminformatic knowledge. The SDF format is a standard open
file format supported by most chemical drawing programs including ChemDraw (ChemDraw
2006, CambridgeSoft Corporation,www.cambridgesoft.com) and ISISDraw (IsisDraw 2.5,
MDL Information Systems Inc.,www.mdl.com) and used by a wide variety of databases, e.g.,
PubChem and compound vendor catalogues. The process of the database generation is depicted
in Supplementary Figure 1.
Nature Chemical Biology: doi:10.1038/nchembio.187
Supplementary Figure 1: Visualization of the scaffold tree database generation. After scaffold
isolation, all possible parent scaffolds are generated and one parent-child pair is selected. If this
parent scaffold can be deconstructed further, successive pairs are formed using the generated
parent scaffold as a new child, and the resulting branch is generated. Combination of all
branches yields the scaffold tree, which is written to a database. For exploration of gaps in
chemical space, Scaffold Hunter reads the scaffolds from the database that pass the initial user-
defined filter and displays the tree resulting from them. Annotation of bioactivity, for example,
by color shading, identifies promising virtual scaffolds shown in gray.
Scaffold Hunter first reads the scaffold data from an SQL database and automatically constructs
and displays the tree. Chemical structures are mapped on the nodes which are stored in the
database as scalable vector graphics (SVG) images. The branches, which reflect the
substructure relationships between scaffolds, are represented by radial lines whereas concentric
circles in the background mark the hierarchy levels of the tree. Virtual scaffolds are colored in
grey.
Analysis of PubChem with annotation from WOMBAT to identify virtual scaffolds
Nature Chemical Biology: doi:10.1038/nchembio.187
The analysis of PubChem and WOMBAT (see the main text) yielded 60 different targets
present in both PubChem and in the WOMBAT database, corresponding to 199 individual
assays in PubChem (see Supplementary Table 1). Of these 199 assays, in 102 cases
concentration-dependent measurements were carried out and IC50, EC50 or GI50 values were
calculated for 46 different targets. These values represent the concentration at half-maximal
inhibition (IC50), at half-maximal response (EC50), and at half-maximal growth inhibition (GI50),
e.g. in cells. We further analyzed the scaffold tree comprising of all compounds screened on a
particular target (screened at one fixed concentration as well as concentration-dependent). We
then started from the scaffolds representing the active compounds as defined by PubChem and
selected their virtual parents, i.e. scaffolds that are not represent by compounds for which
screening data are available against this particular target in PubChem (see Supplementary Table
2).
Nature Chemical Biology: doi:10.1038/nchembio.187
Supplementary Figure 2: Representative example for a virtual scaffold from a Serotonin 5-
HT1a receptor screen in PubChem, the Murcko families and their corresponding compounds
found in the WOMBAT search. For a complete list of examples, please see Supplementary
Table 3.
Control screen of compounds based on virtual scaffolds from branches of the pyruvate kinase
tree mainly representing inactive compounds
For the control screen we selected and tested 88 compounds from branches where parent and
child scaffolds represent mainly inactive compounds, i.e. they exhibit a mean log AC50 > -2.5.
The 88 compounds selected represent six different scaffolds and are shown in the
Supplementary Table 7. A screen conducted at 100 � M compound concentration indeed
confirmed that even at this very high concentration in all cases more than 70% of the enzymatic
activity remained. Thus, these compounds are weak pyruvate kinase inhibitors at best.
Nature Chemical Biology: doi:10.1038/nchembio.187
Retrospective analysis of virtual scaffolds from PubChem screens Supplementary Table 1: PubChem Assays whose targets are also present in the WOMBAT11 database.
UniProt Accession Code
Uni Prot Name UniProt Description PubChem Assay ID
PubChem Assay Name
O14920 IKKB_HUMAN Inhibitor of nuclear factor kappa-B kinase subunit
beta 1282 In Vitro Kinase Assay Using Purified Enzyme IKK-beta
O75116 ROC2_HUMAN Rho-associated protein
kinase 2 604
Primary biochemical high-throughput screening assay for inhibitors of Rho kinase 2 (Rhok2)
O75116 ROC2_HUMAN Rho-associated protein
kinase 2 644 Dose-response biochemical assay of inhibitors of Rho kinase 2 (Rock2)
O75116 ROC2_HUMAN Rho-associated protein
kinase 2 791 Dose-response biochemical assay of Rho kinase 2 (Rock2) inhibitors
O95136 EDG5_HUMAN Sphingosine 1-phosphate
receptor 2 729
Primary Cell-Based High-Throughput Screening to Identify Agonists of the Sphingosine 1-phosphate receptor 2 (S1P2)
O95136 EDG5_HUMAN Sphingosine 1-phosphate
receptor 2 736
Primary Cell-Based High-Throughput Screening to Identify Antagonists of the Sphingosine 1-phosphate receptor 2 (S1P2)
O95136 EDG5_HUMAN Sphingosine 1-phosphate
receptor 2 851 Dose Response Cell Based Assay for Antagonists of the S1P2 Receptor
O95136 EDG5_HUMAN Sphingosine 1-phosphate
receptor 2 854 Dose Response Cell Based Assay for Agonists of the S1P2 Receptor
O95136 EDG5_HUMAN Sphingosine 1-phosphate
receptor 2 872
Dose Response Cell Based Assay for Agonists of the S1P2 Receptor of Purchased Analogues
O95136 EDG5_HUMAN Sphingosine 1-phosphate
receptor 2 1232
Dose Response Cell-Based Assay for Agonists of the Sphingosine 1-Phosphate Receptor 2 (S1P2): Purchased Analogues
O95477 ABCA1_HUMAN ATP-binding cassette sub-
family B member 1 377 MDR-1
O96013 PAK4_HUMAN Serine/threonine-protein
kinase PAK 4 389 Compound Screen Assay, Human PAK4
P00352 DHA1_HUMAN Retinal dehydrogenase 1 1030 Concentration-Response Assay for Inhibitors of aldehyde dehydrogenase 1 (ALDH1A1)
P00533 EGFR_HUMAN Epidermal growth factor
receptor 578
Literature data for small-molecule inhibitors of EGF-R_Tyrosine _Kinase_Homo_sapiens
P00734 THRB_HUMAN Prothrombin 1046 Thrombin 1536 HTS
P00734 THRB_HUMAN Prothrombin 1215 Thrombin 1536 HTS Dose Response Confirmation
P00748 FA12_HUMAN Coagulation factor XII 684 Factor XIIa Mixture HTS
P00748 FA12_HUMAN Coagulation factor XII 701 Factor XIIa Single Well HTS
P00748 FA12_HUMAN Coagulation factor XII 716 Factor XIIa Dose Response Confirmation
Nature Chemical Biology: doi:10.1038/nchembio.187
UniProt Accession Code
Uni Prot Name UniProt Description PubChem Assay ID
PubChem Assay Name
P00748 FA12_HUMAN Coagulation factor XII 728 Factor XIIa Dose Response Confirmation from Single Well HTS
P00748 FA12_HUMAN Coagulation factor XII 800 Factor XIIa 1536 HTS
P00748 FA12_HUMAN Coagulation factor XII 852 Factor XIIa 1536 HTS Dose Response Confirmation
P01112 RASH_HUMAN GTPase HRas 759 HTS to identify specific small molecule inhibitors of Ras and Ras-related GTPases specifically Ras wildtype
P01112 RASH_HUMAN GTPase HRas 1335 Multiplexed dose response to identify specific small molecule inhibitors of Ras and Ras-related GTPases specifically Ras wildtype
P01112 RASH_HUMAN GTPase HRas 1341 Multiplexed dose response to identify specific small molecule inhibitors of Ras and Ras-related GTPases specifically Ras activated mutant
P03372 ESR1_HUMAN Estrogen receptor 629 HTS of Estrogen Receptor- alpha Coactivator Binding inhibitors
P03372 ESR1_HUMAN Estrogen receptor 639 HTS of Estrogen Receptor- alpha Coactivator Binding Potentiators
P03372 ESR1_HUMAN Estrogen receptor 694 HTS of LOPAC library for Estrogen Receptor-alpha Coactivator Binding inhibitors
P03372 ESR1_HUMAN Estrogen receptor 713 Estrogen Receptor-alpha Coactivator Binding Inhibitors Dose Response Confirmation
P03372 ESR1_HUMAN Estrogen receptor 737 Estrogen Receptor-alpha Coactivator Binding Potentiators Dose Response Confirmation
P03372 ESR1_HUMAN Estrogen receptor 1078 Estrogen Receptor-alpha Coactivator Binding Inhibitors Reporter Gene Dose Response
P03372 ESR1_HUMAN Estrogen receptor 1079 Estrogen Receptor-alpha Coactivator Binding Inhibitors ELISA Secondary Assay
P03372 ESR1_HUMAN Estrogen receptor 1211 Estrogen Receptor (alpha) binding: Primary Screen
P03372 ESR1_HUMAN Estrogen receptor 1223 Estrogen Receptor (alpha) binding: Dose Response of Primary Screen Assay
P03468 NRAM_IAPUE Neuraminidase 493 Literature data for small-molecule inhibitors of Influenza_A_virus_(A_Puerto_Rico_8_34(H1N1))
P03474 NRAM_INBLE Neuraminidase 489 Literature data for small-molecule inhibitors of Influenza_B_Virus_(B_Lee_40)
P03951 FA11_HUMAN Coagulation factor XI 679 Factor XIa Dose Response Confirmation
P03951 FA11_HUMAN Coagulation factor XI 680 Factor XIa Mixture HTS
P03951 FA11_HUMAN Coagulation factor XI 687 Factor XIa Single Well HTS
P03951 FA11_HUMAN Coagulation factor XI 721 Factor XIa Dose Response Confirmation from Single Well Screen
P03951 FA11_HUMAN Coagulation factor XI 798 Factor XIa 1536 HTS
P03951 FA11_HUMAN Coagulation factor XI 846 Factor XIa 1536 HTS Dose Response Confirmation
P05067 A4_HUMAN Amyloid beta A4 protein 956 Beta amyloid ThS binding assay
P05771 KPCB_HUMAN Protein kinase C beta type 1280 In Vitro Kinase Assay Using Purified Enzyme PKC-beta
P06280 AGAL_HUMAN Alpha-galactosidase A 992 Counterscreen for Glucocerebrosidase Inhibitors: qHTS Assay for Human alpha-Galactosidase at pH 4.5
Nature Chemical Biology: doi:10.1038/nchembio.187
UniProt Accession Code
Uni Prot Name UniProt Description PubChem Assay ID
PubChem Assay Name
P06820 NRAM_IATOK Neuraminidase 490 Literature data for small-molecule inhibitors of Influenza_A_virus_(A_Tokyo_3_67(H2N2))
P07711 CATL_HUMAN cathepsin L1 preproprotein 460 Cathepsin L
P07711 CATL_HUMAN cathepsin L1 preproprotein 825 Cathepsin L dose-response confirmation
P07858 CATB_HUMAN Cathepsin B 453 Cathepsin B
P07858 CATB_HUMAN Cathepsin B 488 Cathepsin B compound mixture screening
P07858 CATB_HUMAN Cathepsin B 523 Cathepsin B Inhibitor Series SAR Study
P07858 CATB_HUMAN Cathepsin B 820 Cathepsin B dose-response confirmation
P07858 CATB_HUMAN Cathepsin B 830 Cathepsin B mixture HTS dose-response confirmation
P08311 CATG_HUMAN Cathepsin G 581 Cathepsin G
P08311 CATG_HUMAN Cathepsin G 832 Cathepsin G dose-response confirmation
P08908 5HT1A_HUMAN 5-hydroxytryptamine
receptor 1A 567
Primary HTS assay for 5-Hydroxytryptamine (Serotonin) Receptor Subtype 1a (5HT1a) agonists
P08908 5HT1A_HUMAN 5-hydroxytryptamine
receptor 1A 612
Primary HTS assay for 5-Hydroxytryptamine (Serotonin) Receptor Subtype 1a (5HT1a) antagonists
P08908 5HT1A_HUMAN 5-hydroxytryptamine
receptor 1A 613
Dose Response assay for 5-Hydroxytryptamine (Serotonin) Receptor Subtype 1a (5HT1a) agonists
P08908 5HT1A_HUMAN 5-hydroxytryptamine
receptor 1A 718
Dose Response assay for agonists of 5-Hydroxytryptamine (Serotonin) Receptor Subtype 1A (5HT1A)
P08908 5HT1A_HUMAN 5-hydroxytryptamine
receptor 1A 755
Dose Response Cell Based Assay for Antagonists of the 5-Hydroxytryptamine Receptor Subtype 1A (5HT1A)
P09871 C1S_HUMAN Complement C1s subcomponent
538 Complement factor C1s
P09871 C1S_HUMAN Complement C1s subcomponent
787 Complement factor C1s IC50 from mixture screen
P09871 C1S_HUMAN Complement C1s subcomponent
829 Complement C1s ELISA
P10415 BCL2_HUMAN Apoptosis regulator Bcl-2 950 Multiplexed high-throughput screen for small molecule regulators of Bcl-2 family protein interactions, specifically Bim-Bcl-2.
P10415 BCL2_HUMAN Apoptosis regulator Bcl-2 1328 Multiplexed high-throughput screen for small molecule regulators of Bcl-2 family protein interactions, specifically Bim-Bcl-2
P10635 CPD6_HUMAN Cytochrome P450 2D6 891 qHTS Assay for Inhibitors and Substrates of Cytochrome P450 2D6
P11229 ACM1_HUMAN Muscarinic acetylcholine
receptor M1 626
Discovery of Novel Allosteric Modulators of the M1 Muscarinic Receptor: Agonist Primary Screen
P11229 ACM1_HUMAN Muscarinic acetylcholine
receptor M1 628
Discovery of novel allosteric modulators of the M1 muscarinic receptor: Antagonist Primary Screen
P11229 ACM1_HUMAN Muscarinic acetylcholine
receptor M1 677
Discovery of novel allosteric modulators of the M1 muscarinic receptor: Antagonist Confirmation Screen
Nature Chemical Biology: doi:10.1038/nchembio.187
UniProt Accession Code
Uni Prot Name UniProt Description PubChem Assay ID
PubChem Assay Name
P11229 ACM1_HUMAN Muscarinic acetylcholine
receptor M1 678
Discovery of novel allosteric modulators of the M1 muscarinic receptor: Antagonist Secondary Assay 1
P11229 ACM1_HUMAN Muscarinic acetylcholine
receptor M1 859
Discovery of novel allosteric modulators of the M1 muscarinic receptor: Antagonist Dose-Response Assay
P11229 ACM1_HUMAN Muscarinic acetylcholine
receptor M1 860
Discovery of novel allosteric modulators of the M1 muscarinic receptor: Antagonist Dose-Response Counterscreen
P11229 ACM1_HUMAN Muscarinic acetylcholine
receptor M1 943
qHTS Assay for Antagonists of Acetylcholine Muscarinic M1 Receptor: Kinetic Measurement of Intracellular Calcium Response
P11229 ACM1_HUMAN Muscarinic acetylcholine
receptor M1 944
qHTS Assay for Antagonists of Acetylcholine Muscarinic M1 Receptor: Measurement of IP-One Response
P11309 PIM1_HUMAN Proto-oncogene
serine/threonine-protein kinase Pim-1
393 Compound Screen Assay, Human PIM1
P11712 CPC9_HUMAN Cytochrome P450 2C9 883 qHTS Assay for Inhibitors and Substrates of Cytochrome P450 2C9
P12931 SRC_HUMAN Proto-oncogene tyrosine-
protein kinase Src 363 Literature data for small-molecule inhibitors of Human Src.
P13612 ITA4_HUMAN Integrin alpha-4 528 Allosteric Agonists for the VLA-4 Integrin
P13612 ITA4_HUMAN Integrin alpha-4 529 Allosteric Antagonists for the VLA-4 Integrin
P13612 ITA4_HUMAN Integrin alpha-4 576 Auto-fluorescence of compounds effecting screening of VLA-4 Integrin
P13612 ITA4_HUMAN Integrin alpha-4 702 Dose-Response of Allosteric Antagonists for the VLA-4 Integrin
P13612 ITA4_HUMAN Integrin alpha-4 703 Dose-Response of Allosteric Agonists for the VLA-4 Integrin
P15917 LEF_BACAN Lethal factor 912 qHTS Assay for Anthrax Lethal Toxin Internalization
P15917 LEF_BACAN Lethal factor 942 Confirmation Concentration-Response Assay for Anthrax Lethal Toxin Internalization
P16473 TSHR_HUMAN Thyrotropin receptor 926 qHTS Assay for Agonists of the Thyroid Stimulating Hormone Receptor
P16473 TSHR_HUMAN Thyrotropin receptor 933 Secondary Concentration-Response Assay for Agonists of the Thyroid Stimulating Hormone Receptor: HTRF Activity Detection
P16473 TSHR_HUMAN Thyrotropin receptor 938 qHTS Assay for Agonists of the Thyroid Stimulating Hormone Receptor: Activators of Intracellular cAMP Concentrations in Parental HEK 293
P16473 TSHR_HUMAN Thyrotropin receptor 939 Confirmation Concentration-Response Assay for Agonists of the Thyroid Stimulating Hormone Receptor
P16473 TSHR_HUMAN Thyrotropin receptor 953 Confirmation Concentration-Response Assay for Agonists of the Thyroid Stimulating Hormone Receptor: Activators of Intracellular cAMP Concentrations in Parental HEK 293
P17612 KAPA_HUMAN cAMP-dependent protein kinase catalytic subunit
alpha isoform 1 524
Primary biochemical high-throughput screening assay for inhibitors of protein kinase A (PKA) activity
P17612 KAPA_HUMAN cAMP-dependent protein 548 Dose-response biochemical assay for inhibitors of protein kinase A (PKA)
Nature Chemical Biology: doi:10.1038/nchembio.187
UniProt Accession Code
Uni Prot Name UniProt Description PubChem Assay ID
PubChem Assay Name
kinase catalytic subunit alpha isoform 1
activity
P19838 KBF1_HUMAN Nuclear factor NF-kappa-B
p105 subunit 895
qHTS Assay for Identification of Small Molecule Antagonists for NFkB Signaling Pathway
P19838 KBF1_HUMAN Nuclear factor NF-kappa-B
p105 subunit 928
qHTS Assay for Identification of Small Molecule Agonists for NFkB Signaling Pathway
P21453 EDG1_HUMAN sphingosine-1-phosphate
receptor 1 449
Primary HTS and Confirmation Assays for S1P1 Agonists and Agonism Potentiators
P21453 EDG1_HUMAN Sphingosine 1-phosphate
receptor 1 1044
Primary cell-based high-throughput screening assay to identify agonists of Sphingosine 1-Phosphate receptor 1 (S1P1)
P21453 EDG1_HUMAN Sphingosine 1-phosphate
receptor 1 1248
Dose Response Cell-Based Assay for Agonists of the Sphingosine 1-Phosphate Receptor 1 (S1P1): Purchased Analogues
P21453 EDG1_HUMAN Sphingosine 1-phosphate
receptor 1 1363
Cell-membrane dose response assay to identify antagonists of the Sphingosine 1-Phosphate receptor 1 (S1P1)
P21462 FPR1_HUMAN formylpeptide receptor
(FPR) family 362 Formylpeptide Receptor Ligand Binding Assay
P21462 FPR1_HUMAN formylpeptide receptor
(FPR) family 441
Primary HTS Assay for Formylpeptide Receptor-Like-1 (FPRL1) Ligands and Primary HTS Counter-Screen Assay for Formylpeptide Receptor (FPR) Ligands
P21462 FPR1_HUMAN fMet-Leu-Phe receptor 519 Dose Response Assay for Formylpeptide Receptor (FPR) Ligands and Dose Response Counter-Screen Assay for Formylpeptide-Like-1 (FPRL1) Ligands
P21462 FPR1_HUMAN formylpeptide receptor
(FPR) family 699
Secondary Calcium Response Assay for Formylpeptide Receptor (FPR) Antagonists
P21462 FPR1_HUMAN formylpeptide receptor
(FPR) family 722
Formylpeptide Receptor (FPR) Ligand Structure Activity Relationship (SAR) Analysis : Primary HTS Assay
P21462 FPR1_HUMAN formylpeptide receptor
(FPR) family 724
Formylpeptide Receptor (FPR) Ligand Structure Activity Relationship (SAR) Analysis : Dose Response Assay
P21462 FPR1_HUMAN formylpeptide receptor
(FPR) family 762
Formylpeptide Receptor (FPRL1) Ligand Structure Activity Relationship (SAR) Analysis : FPR Dose Response Counterscreen Assay
P21462 FPR1_HUMAN formylpeptide receptor
(FPR) family 763
Formylpeptide Receptor-Like-1 (FPRL1) Ligand Structure Activity Relationship (SAR) Analysis : FPR Primary HTS Assay Counterscreen
P21462 FPR1_HUMAN fMet-Leu-Phe receptor 805 Assay for Formylpeptide Receptor Family Ligands: Target Formylpeptide Receptor
P21462 FPR1_HUMAN formylpeptide receptor
(FPR) family 863
Formylpeptide Receptor (FPR) Structure Activity Relationship (SAR) Analysis: Secondary Calcium Response Assay for Antagonists
P21728 DRD1_HUMAN D(1) dopamine receptor 641 Allosteric Modulators of D1 Receptors: Primary Screen
P21728 DRD1_HUMAN D(1) dopamine receptor 642 Allosteric Modulators of D1 Receptors: Confirmation Screen
P21728 DRD1_HUMAN D(1) dopamine receptor 646 Allosteric Modulators of D1 Receptors: Secondary Assay 1
P21728 DRD1_HUMAN D(1) dopamine receptor 647 Allosteric Modulators of D1 Receptors: Secondary Assay 2
P21918 DRD5_HUMAN D(1) dopamine receptor 641 Allosteric Modulators of D1 Receptors: Primary Screen
Nature Chemical Biology: doi:10.1038/nchembio.187
UniProt Accession Code
Uni Prot Name UniProt Description PubChem Assay ID
PubChem Assay Name
P21918 DRD5_HUMAN D(1) dopamine receptor 642 Allosteric Modulators of D1 Receptors: Confirmation Screen
P21918 DRD5_HUMAN D(1) dopamine receptor 646 Allosteric Modulators of D1 Receptors: Secondary Assay 1
P21918 DRD5_HUMAN D(1) dopamine receptor 647 Allosteric Modulators of D1 Receptors: Secondary Assay 2
P21918 DRD5_HUMAN D(1B) dopamine receptor 857 Allosteric Modulators of D1 Receptors: Dose-dependent Counterscreen
P21918 DRD5_HUMAN D(1B) dopamine receptor 858 Allosteric Modulators of D1 Receptors: Dose-dependent Assay
P25774 CATS_HUMAN cathepsin S 501 Cathepsin S
P25774 CATS_HUMAN cathepsin S 831 Cathepsin S dose-response confirmation
P28566 5HT1E_HUMAN 5-hydroxytryptamine
receptor 1E 571
Primary Cell Based High Throughput Screening Assay for Antagonists of the 5-Hydroxytryptamine Receptor Subtype 1E (5HT1E)
P28566 5HT1E_HUMAN 5-hydroxytryptamine
receptor 1E 574
Primary Cell Based High Throughput Screening Assay for Agonists of the 5-Hydroxytryptamine Receptor Subtype 1E (5HT1E)
P28566 5HT1E_HUMAN 5-hydroxytryptamine
receptor 1E 726
Dose Response Cell Based High Throughput Screening Assay for Agonists of the 5-Hydroxytryptamine Receptor Subtype 1E (5HT1E)
P28566 5HT1E_HUMAN 5-hydroxytryptamine
receptor 1E 749
Dose Response Cell Based Assay for Antagonists of the 5-Hydroxytryptamine Receptor Subtype 1E (5HT1E
P28845 DHI1_HUMAN 11-beta-hydroxysteroid
dehydrogenase 1 398 Compound Screen Assay, Human HSD11B1
P29466 I1BC_HUMAN Interleukin-1 beta
convertase 888
Concentration-Response Counterscreen for Redox Active Inhibitors of Caspase-1: Catalase
P29466 I1BC_HUMAN Interleukin-1 beta
convertase 896
Confirmation Concentration-Response Assay for Allosteric/Competitive Inhibitors of Caspase-1
P29466 I1BC_HUMAN Interleukin-1 beta
convertase 900 qHTS Assay for Allosteric/Competitive Inhibitors of Caspase-1
P30305 MPI2_HUMAN cell division cycle 25B
isoform 2 368 Cdc25B Catalytic Domain protein tyrosine phosphatase HTS
P30305 MPI2_HUMAN M-phase inducer phosphatase 2
443 Cdc25B Catalytic Domain Protein Tyrosine Phosphatase Dose Response Confirmation and Secondary Selectivity/Specificity Assay
P30305 MPI2_HUMAN cell division cycle 25B
isoform 2 569
Cdc25B Catalytic Domain Protein Tyrosine Phosphatase HTS Dose Response Confirmation Assay
P30305 MPI2_HUMAN cell division cycle 25B
isoform 2 649
Cdc25B Catalytic Domain Protein Tyrosine Phosphatase Probe Assessment Dose Response assay in 25 mM DTT
P30305 MPI2_HUMAN cell division cycle 25B
isoform 2 650
Cdc25B Catalytic Domain Protein Tyrosine Phosphatase Probe Assessment Dose Response Reproducibility Assay
P30305 MPI2_HUMAN cell division cycle 25B
isoform 2 668
Cdc25B Catalytic Domain Protein Tyrosine Phosphatase Probe Assessment Dose Response assay in the presence of Catalase.
P30305 MPI2_HUMAN cell division cycle 25B
isoform 2 669
Cdc25B Catalytic Domain Protein Tyrosine Phosphatase Probe Assessment Dose Response assay in 25 mM DTT and Catalase.
P30305 MPI2_HUMAN cell division cycle 25B
isoform 2 670
Cdc25B Catalytic Domain Protein Tyrosine Phosphatase Probe Assessment Dose Response assay in the presence of Beta-Mercaptoethanol.
Nature Chemical Biology: doi:10.1038/nchembio.187
UniProt Accession Code
Uni Prot Name UniProt Description PubChem Assay ID
PubChem Assay Name
P30305 MPI2_HUMAN cell division cycle 25B
isoform 2 671
Cdc25B Catalytic Domain Protein Tyrosine Phosphatase Probe Assessment Dose Response assay in the presence of Glutathione.
P30305 MPI2_HUMAN cell division cycle 25B
isoform 2 682
Cdc25B Catalytic Domain Protein Tyrosine Phosphatase Probe Assessment: Compound Dose Dependent Redox Cycling H2O2 Generation in 0.5 mM DTT
P30305 MPI2_HUMAN cell division cycle 25B
isoform 2 683
Cdc25B Catalytic Domain Protein Tyrosine Phosphatase Probe Assessment: Compound Dose Dependent Redox Cycling H2O2 Generation in 1.0 mM DTT
P33261 CPCJ_HUMAN Cytochrome P450 2C19 899 qHTS Assay for Inhibitors and Substrates of Cytochrome P450 2C19
P43116 PE2R2_HUMAN Prostaglandin E2 receptor
EP2 subtype 940 Modulators of the EP2 prostaglandin E2 receptor - Primary Screening
P43116 PE2R2_HUMAN Prostaglandin E2 receptor
EP2 subtype 1080 Modulators of the EP2 prostaglandin EP2 receptor - Primary Counterscreens
P43367 CAN2_PIG Calpain-2 catalytic subunit 478 Calpain activity in endothelial cells
P43367 CAN2_PIG Calpain-2 catalytic subunit 1236 uHTS for Calpain Inhibitors
P49146 NPY2R_HUMAN Neuropeptide Y receptor
type 2 1255
Counterscreen assay for antagonists of neuropeptide Y receptor Y1 (NPY-Y1): Cell-based high throughput assay to measure NPY-Y2 antagonism
P49146 NPY2R_HUMAN Neuropeptide Y receptor
type 2 1257
Cell-based high throughput confirmation assay for antagonists of neuropeptide Y receptor Y2 (NPY-Y2)
P49146 NPY2R_HUMAN Neuropeptide Y receptor
type 2 1272
Dose response cell-based screening assay for antagonists of neuropeptide Y receptor Y2 (NPY-Y2)
P49146 NPY2R_HUMAN Neuropeptide Y receptor
type 2 1278
Dose response counterscreen assay for neuropeptide Y receptor Y1 (NPY-Y1): Cell-based high throughput assay to measure NPY-Y2 antagonism
P49146 NPY2R_HUMAN Neuropeptide Y receptor
type 2 1359
Primary cell-based high-throughput screening assay for potentiators or agonists of NPY-Y2
P49888 SUOE_HUMAN Estrogen sulfotransferase 747 Basic StarGazer Assay on Human SULT1E1
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 619 Fluorescence polarization assay for PLK1 inhibitors
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 693
High throughput fluorescence polarization-based assay to screen for small molecule inhibitors of the Polo box domain (PBD) of Plk1.
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 744 Fluorescence polarization assay for PLK1 confirmation assay
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 756 Fluorescence Polarization assay for Plk1: compound interference assay
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 785 Fluorescence Polarization assay for Plk1: IC50 Dose Response Assay
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 876
Concentration Response Redox Cycling H2O2 Generation assay to characterize small molecule inhibitors identified in the Polo box domain (PBD) of Plk1 Primary HTS.
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 877
Concentration Response fluorescence polarization-based assay to confirm small molecule inhibitors identified in the Polo box domain (PBD) of Plk1
Nature Chemical Biology: doi:10.1038/nchembio.187
UniProt Accession Code
Uni Prot Name UniProt Description PubChem Assay ID
PubChem Assay Name
Primary HTS.
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 936
Concentration Response Redox Cycling H2O2 Generation assay, 1 mM DTT, to characterize small molecule inhibitors identified in the Polo box domain (PBD) of Plk1 Primary HTS.
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 1053
High throughput fluorescence polarization-based assay to screen for small molecule inhibitors of the Polo box domain (PBD) of Plk1 to follow up on purchased Analogs of Selected Hits from the screen.
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 1057
Concentration Response fluorescence polarization-based assay to test PMLSC Chemistry Core synthesized analogs of confirmed hits from the Polo box domain (PBD) of Plk1 Primary HTS.
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 1082
Concentration Response fluorescence polarization-based assay to test PMLSC Chemistry Core synthesized analogs of 861574, a confirmed hit from the Polo box domain (PBD) of Plk1 Primary HTS.
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 1083
Concentration Response fluorescence polarization-based assay to test purchased Analogs of Selected Hits from the Polo box domain (PBD) of Plk1 Primary HTS.
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 1264 Fluorescence polarization assay for PLK1 analogues - primary screen repeat
P53350 PLK1_HUMAN Serine/threonine-protein
kinase PLK1 1383 PLK1 counterscreening assay for identified PKD inhibitors
P53779 MK10_HUMAN Mitogen-activated protein
kinase 10 530 JNK3 AlphaScreen Assay
P53779 MK10_HUMAN Mitogen-activated protein
kinase 10 746
Primary biochemical high-throughput screening assay for inhibitors of the c-Jun N-Terminal Kinase 3 (JNK3)
P53779 MK10_HUMAN Mitogen-activated protein
kinase 10 1284
Dose response biochemical screening assay for inhibitors of c-Jun N-Terminal Kinase 3 (JNK3)
P54760 EPHB4_HUMAN Ephrin type-B receptor 4 720 Primary biochemical high-throughput screening assay for antagonists of the interaction between the Eph receptor B4 (EphB4) and its ligand ephrin-B2 via TNYL-RAW peptide probe
P54760 EPHB4_HUMAN Ephrin type-B receptor 4 835 Dose-response biochemical assay for antagonists of the interaction between the Eph receptor B4 (EphB4) and its ligand ephrin-B2 via TNYL-RAW peptide
P55210 ICE7_HUMAN Caspase-7 889 qHTS Assay for Allosteric/Competitive Inhibitors of Caspase-7
P55210 ICE7_HUMAN Caspase-7 897 Confirmation Concentration-Response Assay for Allosteric/Competitive Inhibitors of Caspase-7
Q04759 KPCT_HUMAN Protein kinase C theta type 1283 In Vitro Kinase Assay Using Purified Enzyme PKC-theta
Q05397 FAK1_HUMAN Focal adhesion kinase 1 727 Primary biochemical high-throughput screening assay for inhibitors of Focal Adhesion Kinase (FAK)
Q05397 FAK1_HUMAN Focal adhesion kinase 1 794 Confirmation biochemical assay for inhibitors of Focal Adhesion Kinase (FAK)
Q05397 FAK1_HUMAN Focal adhesion kinase 1 810 Dose-response biochemical assay for inhibitors of Focal Adhesion Kinase
Nature Chemical Biology: doi:10.1038/nchembio.187
UniProt Accession Code
Uni Prot Name UniProt Description PubChem Assay ID
PubChem Assay Name
(FAK)
Q07820 MCL1_HUMAN Induced myeloid leukemia cell differentiation protein
Mcl-1 1009
Multiplexed high-throughput screen for small molecule regulators of Bcl-2 family protein interactions, specifically Bim-Mcl-1
Q07820 MCL1_HUMAN Induced myeloid leukemia cell differentiation protein
Mcl-1 1021 uHTS of Mcl-1/Bid interaction inhibitors
Q07820 MCL1_HUMAN Induced myeloid leukemia cell differentiation protein
Mcl-1 1022 uHTS of Mcl-1/Noxa interaction inhibitors
Q07820 MCL1_HUMAN Induced myeloid leukemia cell differentiation protein
Mcl-1 1329
Multiplexed dose response screen for small molecule regulators of Bcl-2 family protein interactions, specifically Bim-Mcl-1.
Q15139 KPCM_HUMAN Serine/threonine-protein
kinase D1 797 Fluorescence polarization assay for PKD inhibitors
Q15139 KPCM_HUMAN Serine/threonine-protein
kinase D1 1286
Fluorescence polarization assay for PKD inhibitors - repeat of primary screen on hits identified from 140K library primary screen
Q15139 KPCM_HUMAN Serine/threonine-protein
kinase D1 1315
Fluorescence polarization for PKD inhibitors - interference assay (140K library campaign)
Q15139 KPCM_HUMAN Serine/threonine-protein
kinase D1 1342
Fluorescence polarization assay for PKD inhibitiors-interference assay-57K HTS campaign
Q15139 KPCM_HUMAN Serine/threonine-protein
kinase D1 1378 AKT counterscreen of confirmed PKD inhibitors-57K library
Q92731 ESR2_HUMAN Estrogen receptor beta 633 HTS for Estrogen Receptor-beta Coactivator Binding inhibitors
Q92731 ESR2_HUMAN Estrogen receptor beta 733 Estrogen Receptor-beta Coactivator Binding Inhibitors Dose Response Confirmation
Q92731 ESR2_HUMAN Estrogen receptor beta 1060 Estrogen Receptor-beta Coactivator Binding Inhibitors ELISA Secondary Assay
Q92731 ESR2_HUMAN Estrogen receptor beta 1210 Estrogen Receptor (beta) binding: Primary Screen
Q92731 ESR2_HUMAN Estrogen receptor beta 1221 Estrogen Receptor (beta) binding: Dose Response of Primary Screen Assay
Q99500 EDG3_HUMAN sphingosine-1-phosphate
receptor 3 373 S1P3 Agonist Primary HTS and Confirmation Assays
Q99500 EDG3_HUMAN sphingosine-1-phosphate
receptor 3 439 S1P3 Agonist Dose-Response Potency Assay
Q99500 EDG3_HUMAN sphingosine-1-phosphate
receptor 3 484 Dose Response Assay for S1P3 Antagonists
Q99500 EDG3_HUMAN sphingosine-1-phosphate
receptor 3 485 Primary HTS Assay for S1P3 Antagonists
Q99500 EDG3_HUMAN sphingosine-1-phosphate 730 S1P3 Dose Response Assay Counterscreen for 5-
Nature Chemical Biology: doi:10.1038/nchembio.187
UniProt Accession Code
Uni Prot Name UniProt Description PubChem Assay ID
PubChem Assay Name
receptor 3 Hydroxytryptamine(Serotonin) Receptor Subtype 1E Agonists
Q99500 EDG3_HUMAN sphingosine-1-phosphate
receptor 3 776
S1P3 Dose Response Assay Counterscreen for 5-Hydroxytryptamine(Serotonin) Receptor Subtype 1E Antagonists
Q99500 EDG3_HUMAN sphingosine-1-phosphate
receptor 3 1192
Dose Response Cell-Based Assay for Agonists of the Sphingosine 1-Phosphate Receptor 3 (S1P3): Purchased Analogues
Q99527 CML2_HUMAN G-protein coupled estrogen
receptor 1 1212 GPR 30 Binding: Primary Screen
Q99527 CML2_HUMAN G-protein coupled estrogen
receptor 1 1213 CALCIUM_SIGNALING_VIA_GPR30: Primary Screen
Q99527 CML2_HUMAN G-protein coupled estrogen
receptor 1 1224 GPR 30 Binding: Dose Response
Q9P1W9 PIM2_HUMAN Serine/threonine-protein
kinase Pim-2 505 Compound Screen Assay, Human PIM2
Nature Chemical Biology: doi:10.1038/nchembio.187
Supplementary Table 2: Statistics of the analyzed PubChem targets giving the number of compound screened in PubChem, the number of actives found
(exclusively in concentration dependant-manner) and the number of parent scaffolds that are virtual and non-virtual scaffolds in PubChem.
SwissProt ID
SwissProt Name SwissProt Short Description
Cpds screened
in PubChem
Active Compounds
PubChem Virtual
Scaffolds
PubChem Non
Virtual Scaffolds
O75116 ROCK2_HUMAN Rho-associated protein kinase 2 (EC 2.7.11.1) (Rho-associated,
coiled-coil-containing protein kinase 2) (p164 ROCK-2) (Rho kinase 2) [Gene: ROCK2 or KIAA0619] - Homo sapiens (Human)
229 88 11 76
O95136 EDG5_HUMAN
Sphingosine 1-phosphate receptor Edg-5 (S1P receptor Edg-5) (Endothelial differentiation G-protein coupled receptor 5) (Sphingosine
1-phosphate receptor 2) (S1P2) [Gene: EDG5] - Homo sapiens (Human)
202 80 38 41
P00352 AL1A1_HUMAN
Retinal dehydrogenase 1 (EC 1.2.1.36) (RalDH1) (RALDH 1) (Aldehyde dehydrogenase family 1 member A1) (Aldehyde
dehydrogenase, cytosolic) (ALHDII) (ALDH-E1) [Gene: ALDH1A1 or ALDC or ALDH1 or PUMB1] - Homo sapiens (Human)
1238 488 263 131
P00734 THRB_HUMAN
Prothrombin precursor (EC 3.4.21.5) (Coagulation factor II) [Contains: Activation peptide fragment 1; Activation peptide fragment 2;
Thrombin light chain; Thrombin heavy chain] [Gene: F2] - Homo sapiens (Human)
529 235 31 200
P00748 FA12_HUMAN
Coagulation factor XII precursor (EC 3.4.21.38) (Hageman factor) (HAF) [Contains: Coagulation factor XIIa heavy chain; Beta-factor XIIa
part 1; Beta-factor XIIa part 2; Coagulation factor XIIa light chain] [Gene: F12] - Homo sapiens (Human)
774 224 25 196
P01112 RASH_HUMAN GTPase HRas precursor (Transforming protein p21) (p21ras) (H-Ras-1) (c-H-ras) (Ha-Ras) [Gene: HRAS or HRAS1] - Homo sapiens (Human)
634 58 17 39
Nature Chemical Biology: doi:10.1038/nchembio.187
SwissProt ID
SwissProt Name SwissProt Short Description
Cpds screened
in PubChem
Active Compounds
PubChem Virtual
Scaffolds
PubChem Non
Virtual Scaffolds
P03372 ESR1_HUMAN Estrogen receptor (ER) (Estradiol receptor) (ER-alpha) (Nuclear
receptor subfamily 3 group A member 1) [Gene: ESR1 or ESR or NR3A1] - Homo sapiens (Human)
577 296 123 172
P03468 NRAM_I34A1 Neuraminidase (EC 3.2.1.18) [Gene: NA] - Influenza A virus (strain
A/Puerto Rico/8/1934 H1N1) 53 52 14 5
P03474 NRAM_INBLE Neuraminidase (EC 3.2.1.18) [Gene: NA] - Influenza B virus (strain
B/Lee/1940) 96 80 24 10
P03951 FA11_HUMAN
Coagulation factor XI precursor (EC 3.4.21.27) (Plasma thromboplastin antecedent) (PTA) (FXI) [Contains: Coagulation factor XIa heavy
chain; Coagulation factor XIa light chain] [Gene: F11] - Homo sapiens (Human)
379 146 19 125
P06820 NRAM_I67A0 Neuraminidase (EC 3.2.1.18) [Gene: NA] - Influenza A virus (strain
A/Tokyo/3/1967 H2N2) 14 14 6 0
P07858 CATB_HUMAN Cathepsin B precursor (EC 3.4.22.1) (Cathepsin B1) (APP secretase) (APPS) [Contains: Cathepsin B light chain; Cathepsin B heavy chain]
[Gene: CTSB or CPSB] - Homo sapiens (Human) 107 96 27 64
P08311 CATG_HUMAN Cathepsin G precursor (EC 3.4.21.20) (CG) [Gene: CTSG] - Homo
sapiens (Human) 93 71 20 51
P08908 5HT1A_HUMAN 5-hydroxytryptamine receptor 1A (5-HT-1A) (Serotonin receptor 1A) (5-
HT1A) (G-21) [Gene: HTR1A or ADRB2RL1 or ADRBRL1] - Homo sapiens (Human)
431 49 16 32
P10415 BCL2_HUMAN Apoptosis regulator Bcl-2 [Gene: BCL2] - Homo sapiens (Human) 834 9 4 5
P10635 CP2D6_HUMAN Cytochrome P450 2D6 (EC 1.14.14.1) (CYPIID6) (P450-DB1)
(Debrisoquine 4-hydroxylase) [Gene: CYP2D6 or CYP2DL1] - Homo sapiens (Human)
9391 3444 1259 1996
P11229 ACM1_HUMAN Muscarinic acetylcholine receptor M1 [Gene: CHRM1] - Homo sapiens
(Human) 1238 1091 428 496
Nature Chemical Biology: doi:10.1038/nchembio.187
SwissProt ID
SwissProt Name SwissProt Short Description
Cpds screened
in PubChem
Active Compounds
PubChem Virtual
Scaffolds
PubChem Non
Virtual Scaffolds
P11712 CP2C9_HUMAN
Cytochrome P450 2C9 (EC 1.14.13.80) ((R)-limonene 6-monooxygenase) (EC 1.14.13.48) ((S)-limonene 6-monooxygenase) (EC 1.14.13.49) ((S)-limonene 7-monooxygenase) (CYPIIC9) (P450 PB-1) (P450 MP-4/MP-8) (S-mephenytoin 4-hydroxylase) (P-450MP)
[Gene: CYP2C9 or CYP2C10] - Homo sapiens (Human)
9391 2656 964 1554
P12931 SRC_HUMAN Proto-oncogene tyrosine-protein kinase Src (EC 2.7.10.2) (p60-Src) (c-
Src) (pp60c-src) [Gene: SRC or SRC1] - Homo sapiens (Human) 749 592 329 263
P13612 ITA4_HUMAN Integrin alpha-4 precursor (Integrin alpha-IV) (VLA-4) (CD49d antigen)
[Gene: ITGA4 or CD49D] - Homo sapiens (Human) 62 34 16 17
P15917 LEF_BACAN Lethal factor precursor (EC 3.4.24.83) (LF) (Anthrax lethal toxin
endopeptidase component) [Gene: lef or pXO1-107 or BXA0172 or GBAA_pXO1_0172] - Bacillus anthracis
68995 6274 1990 4028
P16473 TSHR_HUMAN Thyrotropin receptor precursor (TSH-R) (Thyroid-stimulating hormone
receptor) [Gene: TSHR or LGR3] - Homo sapiens (Human) 72086 27221 8214 17885
P17612 KAPCA_HUMAN cAMP-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) (PKA C-alpha) [Gene: PRKACA or PKACA] - Homo sapiens (Human)
94 62 21 40
P19838 NFKB1_HUMAN Nuclear factor NF-kappa-B p105 subunit (DNA-binding factor KBF1) (EBP-1) [Contains: Nuclear factor NF-kappa-B p50 subunit] [Gene:
NFKB1] - Homo sapiens (Human) 1238 986 524 278
P21453 EDG1_HUMAN Sphingosine 1-phosphate receptor Edg-1 (Sphingosine 1-phosphate
receptor 1) (S1P1) [Gene: EDG1] - Homo sapiens (Human) 11 6 0 4
Nature Chemical Biology: doi:10.1038/nchembio.187
SwissProt ID
SwissProt Name SwissProt Short Description
Cpds screened
in PubChem
Active Compounds
PubChem Virtual
Scaffolds
PubChem Non
Virtual Scaffolds
P21462 FPR1_HUMAN fMet-Leu-Phe receptor (fMLP receptor) (N-formyl peptide receptor) (FPR) (N-formylpeptide chemoattractant receptor) [Gene: FPR1] -
Homo sapiens (Human) 330 39 15 23
P21918 DRD5_HUMAN D(1B) dopamine receptor (D(5) dopamine receptor) (D1beta dopamine
receptor) [Gene: DRD5 or DRD1B or DRD1L2] - Homo sapiens (Human)
517 324 223 85
P25774 CATS_HUMAN Cathepsin S precursor (EC 3.4.22.27) [Gene: CTSS] - Homo sapiens
(Human) 129 34 12 21
P28566 5HT1E_HUMAN 5-hydroxytryptamine receptor 1E (5-HT-1E) (Serotonin receptor 1E) (5-
HT1E) (S31) [Gene: HTR1E] - Homo sapiens (Human) 95 51 15 36
P29466 CASP1_HUMAN
Caspase-1 precursor (EC 3.4.22.36) (CASP-1) (Interleukin-1 beta convertase) (IL-1BC) (IL-1 beta-converting enzyme) (ICE) (Interleukin-1
beta-converting enzyme) (p45) [Contains: Caspase-1 subunit p20; Caspase-1 subunit p10] [Gene: CASP1 or IL1BC or IL1BCE] - Homo
sapiens (Human)
73922 2892 896 1953
P30305 MPIP2_HUMAN M-phase inducer phosphatase 2 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25B) [Gene: CDC25B or CDC25HU2] - Homo
sapiens (Human) 87 151 58 92
P33261 CP2CJ_HUMAN
Cytochrome P450 2C19 (EC 1.14.13.80) ((R)-limonene 6-monooxygenase) (EC 1.14.13.48) ((S)-limonene 6-monooxygenase)
(EC 1.14.13.49) ((S)-limonene 7-monooxygenase) (CYPIIC19) (P450-11A) (Mephenytoin 4-hydroxylase) (CYPIIC17) (P450-254C) [Gene:
CYP2C19] - Homo sapiens (Human)
9391 3190 1132 1888
P49146 NPY2R_HUMAN Neuropeptide Y receptor type 2 (NPY2-R) (NPY-Y2 receptor) [Gene:
NPY2R] - Homo sapiens (Human) 182 80 18 61
Nature Chemical Biology: doi:10.1038/nchembio.187
SwissProt ID
SwissProt Name SwissProt Short Description
Cpds screened
in PubChem
Active Compounds
PubChem Virtual
Scaffolds
PubChem Non
Virtual Scaffolds
P53350 PLK1_HUMAN Serine/threonine-protein kinase PLK1 (EC 2.7.11.21) (Polo-like kinase
1) (PLK-1) (Serine/threonine-protein kinase 13) (STPK13) [Gene: PLK1 or PLK] - Homo sapiens (Human)
366 141 38 100
P53779 MK10_HUMAN
Mitogen-activated protein kinase 10 (EC 2.7.11.24) (Stress-activated protein kinase JNK3) (c-Jun N-terminal kinase 3) (MAP kinase p49
3F12) [Gene: MAPK10 or JNK3 or JNK3A or PRKM10] - Homo sapiens (Human)
10378 1256 364 717
P54760 EPHB4_HUMAN Ephrin type-B receptor 4 precursor (EC 2.7.10.1) (Tyrosine-protein
kinase receptor HTK) (Tyrosine-protein kinase TYRO11) [Gene: EPHB4 or HTK or TYRO11] - Homo sapiens (Human)
128 5 2 3
P55210 CASP7_HUMAN
Caspase-7 precursor (EC 3.4.22.60) (CASP-7) (ICE-like apoptotic protease 3) (ICE-LAP3) (Apoptotic protease Mch-3) (CMH-1) [Contains:
Caspase-7 subunit p20; Caspase-7 subunit p11] [Gene: CASP7 or MCH3] - Homo sapiens (Human)
73834 2302 688 1593
Q05397 FAK1_HUMAN Focal adhesion kinase 1 (EC 2.7.10.2) (FADK 1) (pp125FAK) (Protein-
tyrosine kinase 2) [Gene: PTK2 or FAK or FAK1] - Homo sapiens (Human)
210 109 57 51
Q07820 MCL1_HUMAN Induced myeloid leukemia cell differentiation protein Mcl-1 (Bcl-2-
related protein EAT/mcl1) (mcl1/EAT) [Gene: MCL1] - Homo sapiens (Human)
834 3 2 1
Q15139 KPCD1_HUMAN Serine/threonine-protein kinase D1 (EC 2.7.11.13) (nPKC-D1) (Protein
kinase D) (Protein kinase C mu type) (nPKC-mu) [Gene: PRKD1 or PKD or PKD1 or PRKCM] - Homo sapiens (Human)
18 17 3 13
Q99500 EDG3_HUMAN
Sphingosine 1-phosphate receptor Edg-3 (S1P receptor Edg-3) (Endothelial differentiation G-protein coupled receptor 3) (Sphingosine
1-phosphate receptor 3) (S1P3) [Gene: EDG3] - Homo sapiens (Human)
367 51 17 34
Nature Chemical Biology: doi:10.1038/nchembio.187
SwissProt ID
SwissProt Name SwissProt Short Description
Cpds screened
in PubChem
Active Compounds
PubChem Virtual
Scaffolds
PubChem Non
Virtual Scaffolds
Q99527 GPER_HUMAN
G-protein coupled estrogen receptor 1 (Membrane estrogen receptor) (mER) (G-protein coupled receptor 30) (Chemokine receptor-like 2) (IL8-related receptor DRY12) (Flow-induced endothelial G-protein
coupled receptor 1) (FEG-1) (Lymphocyte-derived G-protein coupled receptor) (LYGPR) (GPCR-BR) [Gene: GPER or CEPR or CMKRL2 or
DRY12 or GPR30] - Homo sapiens (Human)
10 3 1 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Supplementary Table 3: Data for virtual scaffolds from PubChem present in compounds
described as active against the same molecular target in the WOMBAT database.
Entry Target (Swiss Prot ID)
Virtual scaffold from screen in PubChem
Number of scaffold
families found to be active in WOMBAT
Number of compounds
represented by these scaffolds
1 Estrogen
Receptor-alpha (P03372)
9 169
2 Estrogen
Receptor-alpha (P03372)
6 74
3 5-HT Receptor
Subtype 1A (P08908)
4 9
4 5-HT Receptor
Subtype 1A (P08908)
1 2
5 Acetylcholine
Muscarinic M1 Receptor (P11229) 1 1
6 Acetylcholine
Muscarinic M1 Receptor (P11229)
1 1
7 Acetylcholine
Muscarinic M1 Receptor (P11229)
54 131
8 Acetylcholine
Muscarinic M1 Receptor (P11229)
12 25
9 Acetylcholine
Muscarinic M1 Receptor (P11229) 1 1
10 Acetylcholine
Muscarinic M1 Receptor (P11229)
9 98
11 Acetylcholine
Muscarinic M1 Receptor (P11229)
1 1
12
Thyroid Stimulating
Hormone Receptor (P16473)
1 1
13
Allosteric Modulators of D1
Receptors (P21918)
1 1
Nature Chemical Biology: doi:10.1038/nchembio.187
14
Allosteric Modulators of D1
Receptors (P21918)
2 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Supplementary Table 4: Virtual scaffolds from PubChem Screens, corresponding Murcko-
families of actives found in WOMBAT as well as the number of compounds represented by
each Murcko-Family
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
1
P03372 1
2
P03372 4
3
P03372 4
4
P03372 2
5
P03372 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
6
P03372 2
7
P03372 2
8
P03372 2
9
P03372 2
10
P03372 1
11
P03372 1
12
P03372 118
13
P03372 34
14
P03372 1
15
P03372 67
16
P08908 2
17
P08908 3
18
P08908 3
19
P08908 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
20
P08908 1
21
P11229 1
22
P11229 2
23
P11229 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
24
P11229 2
25
P11229 2
26
P11229 2
27
P11229 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
28
P11229 1
29
P11229 3
30
P11229 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
31
P11229 2
32
P11229 4
33
P11229 1
34
P11229 1
35 P11229 1
36
P11229 1
37
P11229 1
38
P11229 48
39
P11229 2
40
P11229 4
41
P11229
42
P11229 1
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
43
P11229 1
44
P11229 1
45
P11229 2
46
P11229 18
47 P11229 9
48
P11229 1
49
P11229 19
50
P11229 1
51
P11229 25
52
P11229 1
53
P11229 1
54
P11229 1
55
P11229 1
56
P11229 1
57
P11229 1
58
P11229 1
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
59
P11229 1
60
P11229 3
61
P11229 1
62
P11229 1
63
P11229 1
64
P11229 1
65
P11229 1
66
P11229 3
67
P11229 1
68
P11229 1
69
P11229 1
70
P11229 1
71
P11229 1
72
P11229 1
73
P11229 1
74
P11229 1
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
75
P11229 1
76 P11229 3
77 P11229 1
78 P11229 1
79
P11229 2
80
P11229 1
81
P11229 1
82
P11229 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
83
P11229 1
84
P11229 2
85
P11229 2
86
P11229 2
87
P11229 2
88
P11229 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
89
P11229 2
90
P11229 2
91
P11229 2
92
P11229 2
93
P11229 2
94
P11229 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
95
P11229 2
296
P11229 2
97
P11229 2
98
P11229 4
99
P11229 2
Nature Chemical Biology: doi:10.1038/nchembio.187
Entry PubChem virtual
scaffold Murcko scaffold of WOMBAT actives
Target Swiss Prot ID
Number of actives
100
P11229 2
101
P16473 1
102
P21918 1
103
P21918 1
104
P21918 1
Nature Chemical Biology: doi:10.1038/nchembio.187
Prospective analysis of the PubChem pyruvate kinase screen and experimental
validation
Supplementary Table 5: Structures and hierarchy level of virtual scaffolds with potent
neighbour scaffolds. The average log AC50 for all the compounds represented by either the
parent or the child scaffold(s) is given as well. The table is sorted by ascending log AC50 of the
child scaffolds and the parent scaffolds. Scaffold selected for compound acquisition and
subsequent experimental screening are marked in green.
Number Structures Scaffold hierarchy level
Avg. log AC50 of parent
scaffold(s)
Avg. log AC50 of child
scaffold(s)
1
3 -2.47 -7.26
2
3 -3.06 -6.79
3
3 -2.47 -6.38
4
2 -2.29 -6.27
5
3 -3.20 -6.13
6
4 -3.64 -6.12
7
3 -2.34 -6.07
8
4 -3.84 -6.07
9
3 -2.37 -6.05
10
4 -5.02 -6.03
11
3 -2.99 -5.94
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structures Scaffold hierarchy level
Avg. log AC50 of parent
scaffold(s)
Avg. log AC50 of child
scaffold(s)
12
3 -3.02 -5.90
13
3 -2.99 -5.84
14
2 -2.36 -5.83
15
4 -5.02 -5.82
16
3 -2.32 -5.73
17
4 -2.79 -5.72
18
4 -5.02 -5.68
19
3 -2.24 -5.66
20
3 -2.32 -5.64
21
2 -2.45 -5.62
22
3 -2.99 -5.61
23
3 -2.37 -5.60
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structures Scaffold hierarchy level
Avg. log AC50 of parent
scaffold(s)
Avg. log AC50 of child
scaffold(s)
24
4 -2.79 -5.56
25
3 -2.34 -5.55
26
3 -2.37 -5.55
27
2 -2.31 -5.50
28
3 -2.32 -5.50
29
2 -2.27 -5.47
30
3 -2.51 -5.46
31
4 -2.24 -5.42
32
2 -2.24 -5.40
33
3 -2.24 -5.38
34
2 -2.26 -5.37
35
3 -2.24 -5.35
36
3 -2.59 -5.35
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structures Scaffold hierarchy level
Avg. log AC50 of parent
scaffold(s)
Avg. log AC50 of child
scaffold(s)
37
4 -2.24 -5.33
38
3 -2.75 -5.33
39
3 -2.24 -5.25
40
3 -2.32 -5.25
41
3 -2.24 -5.24
42
4 -3.16 -5.24
43
3 -2.99 -5.23
44
3 -2.24 -5.22
45
4 -2.59 -5.22
46
3 -2.52 -5.21
47
3 -3.06 -5.21
48
2 -2.40 -5.20
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structures Scaffold hierarchy level
Avg. log AC50 of parent
scaffold(s)
Avg. log AC50 of child
scaffold(s)
49
4 -3.79 -5.19
50
2 -2.24 -5.16
51
3 -2.32 -5.16
52
3 -2.94 -5.16
53
4 -2.24 -5.15
54
2 -2.24 -5.11
55
3 -2.29 -5.09
56
4 -3.39 -5.07
57
3 -2.34 -5.05
58
3 -2.42 -5.05
59
2 -2.24 -5.04
60
3 -2.24 -5.04
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structures Scaffold hierarchy level
Avg. log AC50 of parent
scaffold(s)
Avg. log AC50 of child
scaffold(s)
61
4 -4.30 -5.03
62
3 -2.37 -5.02
63
3 -3.21 -5.02
64
3 -2.75 -5.01
65
4 -4.76 -5.01
Nature Chemical Biology: doi:10.1038/nchembio.187
Supplementary Table 6: Compound structure, vendor compound ID, source and PubChem SID.
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
1
kbsenon-0012203
Aurora Fine Chemicals 57571219
2
kcd-124573 Aurora Fine Chemicals 57571220
3
kcheb-067808
Aurora Fine Chemicals 57571221
4
kcheb-070443
Aurora Fine Chemicals 57571222
5
kcheb-072091
Aurora Fine Chemicals 57571223
6
kcheb-079810
Aurora Fine Chemicals 57571224
7
kcheb-100864
Aurora Fine Chemicals 57571225
8
kuk-303437 Aurora Fine Chemicals 57571226
9
kuk-303461 Aurora Fine Chemicals 57571227
10
kuk-539878 Aurora Fine Chemicals 57571228
11
kuk-544394 Aurora Fine Chemicals 57571229
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
12
kuk-732953 Aurora Fine Chemicals 57571230
13
kuk-744159 Aurora Fine Chemicals 57571231
14
kuk-745624 Aurora Fine Chemicals 57571232
15
kchi-145021
Aurora Fine Chemicals 57571233
16
ken-252537 Aurora Fine Chemicals 57571234
17
ken-255165 Aurora Fine Chemicals 57571235
18
ken-279479 Aurora Fine Chemicals 57571236
19
ken-281857 Aurora Fine Chemicals 57571237
20
ken-281858 Aurora Fine Chemicals 57571238
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
21
ken-289492 Aurora Fine Chemicals 57571239
22
ken-290647 Aurora Fine Chemicals 57571240
23
ken-290648 Aurora Fine Chemicals 57571241
24
ken-333311 Aurora Fine Chemicals 57571242
25
ken-350671 Aurora Fine Chemicals 57571243
26
ken-350759 Aurora Fine Chemicals 57571244
27
ken-464194 Aurora Fine Chemicals 57571245
28
kuk-867448 Aurora Fine Chemicals 57571246
29
kuk-303440 Aurora Fine Chemicals 57571247
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
30
C505-0827 ChemDiv 57571141
31
E676-1525 ChemDiv 57571148
32
E676-1559 ChemDiv 57571149
33
E676-1574 ChemDiv 57571150
34
E676-1627 ChemDiv 57571151
35
E676-1637 ChemDiv 57571152
36
E676-1644 ChemDiv 57571153
37
E676-1645 ChemDiv 57571154
38
E676-4324 ChemDiv 57571155
39
E676-4359 ChemDiv 57571156
40
E676-4364 ChemDiv 57571157
41
E676-4404 ChemDiv 57571158
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
42
E676-4435 ChemDiv 57571159
43
E677-1525 ChemDiv 57571160
44
E677-1565 ChemDiv 57571161
45
G786-0905 ChemDiv 57571164
46
G786-0908 ChemDiv 57571165
47
G786-0909 ChemDiv 57571166
48
G786-0911 ChemDiv 57571167
49
G786-0916 ChemDiv 57571168
50
G786-0919 ChemDiv 57571169
51
7756-0336 ChemDiv 57571205
52
7756-0337 ChemDiv 57571206
53
7756-0340 ChemDiv 57571207
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
54
7756-0761 ChemDiv 57571208
55
7756-0771 ChemDiv 57571209
56
C177-0121 ChemDiv 57571210
57
C184-0754 ChemDiv 57571211
58
C184-0757 ChemDiv 57571212
59
C184-0761 ChemDiv 57571213
60
C184-0762 ChemDiv 57571214
61
C184-0892 ChemDiv 57571215
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
62
C184-0898 ChemDiv 57571216
63
C184-0918 ChemDiv 57571217
64
C239-0716 ChemDiv 57571218
65
D094-0010 ChemDiv 57571142
66
D094-0011 ChemDiv 57571143
67
D094-0013 ChemDiv 57571144
68
D094-0014 ChemDiv 57571145
69
D094-0015 ChemDiv 57571146
70
D094-0016 ChemDiv 57571147
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
71
F019-1236 ChemDiv 57571162
72
F019-1314 ChemDiv 57571163
73
K242-1013 ChemDiv 57571170
74
K242-1015 ChemDiv 57571171
75
K242-1019 ChemDiv 57571172
76
K242-1020 ChemDiv 57571173
77
K242-1021 ChemDiv 57571174
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
78
K242-1037 ChemDiv 57571175
79
K242-1041 ChemDiv 57571176
80
K242-1095 ChemDiv 57571177
81
K242-1096 ChemDiv 57571178
82
K242-1097 ChemDiv 57571179
83
K242-1098 ChemDiv 57571180
84
K242-1099 ChemDiv 57571181
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
85
K242-1100 ChemDiv 57571182
86
K242-1101 ChemDiv 57571183
87
K242-1102 ChemDiv 57571184
88
K242-1103 ChemDiv 57571185
89
K242-1104 ChemDiv 57571186
90
K242-1108 ChemDiv 57571187
91
K242-1109 ChemDiv 57571188
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
92
K242-1110 ChemDiv 57571189
93
K242-1111 ChemDiv 57571190
94
K242-1112 ChemDiv 57571191
95
K242-1119 ChemDiv 57571192
96
K242-1126 ChemDiv 57571193
97
K242-1127 ChemDiv 57571194
98
K242-1128 ChemDiv 57571195
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
99
K242-1129 ChemDiv 57571196
100
K242-1130 ChemDiv 57571197
101
K242-1138 ChemDiv 57571198
102
K242-1139 ChemDiv 57571199
103
K242-1140 ChemDiv 57571200
104
K242-1141 ChemDiv 57571201
105
K242-1142 ChemDiv 57571202
Nature Chemical Biology: doi:10.1038/nchembio.187
Number Structure Virtual scaffold Vendor cpd. ID Source PubChem
SID
106
K242-1143 ChemDiv 57571203
107
K242-1148 ChemDiv 57571204
Supplementary Table 7: Virtual scaffolds identified and selected from the scaffold tree
(generated with Scaffold Hunter) for the pyruvate kinase screen. Number of compounds
purchased for each scaffold.
Num. Virtual
scaffold
Number of compounds
purchased
1 21
2
57
3
14
4
15
Nature Chemical Biology: doi:10.1038/nchembio.187
Supplementary Table 8: Hits identified in the pyruvate kinase assay with an IC50 of 10 � M or
less (PubChem assay id 1687).
Num. Structure PubChem SID Activity type IC50 [µM]
5
57571161 Inhibitor 8.9 +/- 1.1
6
57571143 Inhibitor 2.0 +/- 0.3
7
57571145 Inhibitor 10.5 +/- 1.6
8
57571142 Inhibitor 1.0 +/- 0.1
9
57571146 Inhibitor 1.7 +/- 0.3
10
57571147 Inhibitor 2.2 +/- 0.3
11
57571219 Activator 4.9 +/- 0.6
12
57571225 Activator 5.4 +/- 0.6
13
57571232 Activator 7.6 +/- 0.6
Nature Chemical Biology: doi:10.1038/nchembio.187
Supplementary Table 9: Selected and tested compounds incorporating virtual scaffolds from
mainly inactive branches of the scaffold tree.
No. Structure Virtual Scaffold Vendor Compound Id Producer
1
C240-0044 ChemDiv
2
C358-0046 ChemDiv
3
C240-0169 ChemDiv
4
C358-0169 ChemDiv
5
C358-0091 ChemDiv
6
C289-0037 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
7
C289-0046 ChemDiv
8
C240-0047 ChemDiv
9
C240-0170 ChemDiv
10
C066-2311 ChemDiv
11
C066-2239 ChemDiv
12
C066-2160 ChemDiv
13
C647-0466 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
14
C647-0110 ChemDiv
15
C647-0467 ChemDiv
16
C647-0390 ChemDiv
17
C647-0227 ChemDiv
18
C647-0387 ChemDiv
19
C647-0192 ChemDiv
20
C647-0472 ChemDiv
21
C647-0386 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
22
C647-0347 ChemDiv
23
C647-0345 ChemDiv
24
C647-0268 ChemDiv
25
C647-0468 ChemDiv
26
C647-0351 ChemDiv
27
C647-0426 ChemDiv
28
C647-0108 ChemDiv
29
C647-0187 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
30
C647-0392 ChemDiv
31
C647-0225 ChemDiv
32
C647-0105 ChemDiv
33
C614-0595 ChemDiv
34
C614-0593 ChemDiv
35
C614-0921 ChemDiv
36
C614-0571 ChemDiv
37
C614-0570 ChemDiv
38
C614-0985 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
39
C614-0591 ChemDiv
40
C614-0592 ChemDiv
41
C614-0979 ChemDiv
42
C614-0569 ChemDiv
43
C614-0918 ChemDiv
44
C614-0923 ChemDiv
45
C614-0577 ChemDiv
46
C614-0573 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
47
C614-0920 ChemDiv
48
C614-0917 ChemDiv
49
C614-0913 ChemDiv
50
C614-0910 ChemDiv
51
C614-0578 ChemDiv
52
C614-6013 ChemDiv
53
C614-0572 ChemDiv
54
C614-0589 ChemDiv
55
C614-0933 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
56
C614-0574 ChemDiv
57
C614-0598 ChemDiv
58
C614-0907 ChemDiv
59
C614-0901 ChemDiv
60
C614-0586 ChemDiv
61
C614-0935 ChemDiv
62
C567-0017 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
63
C567-0407 ChemDiv
64
C567-0857 ChemDiv
65
C567-0967 ChemDiv
66
C567-0257 ChemDiv
67
C567-0057 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
68
C567-0467 ChemDiv
69
C567-0767 ChemDiv
70
C567-0107 ChemDiv
71
C567-0447 ChemDiv
72
C594-0015 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
73
C594-0040 ChemDiv
74
C619-0133 ChemDiv
75
C594-0018 ChemDiv
76
C619-0164 ChemDiv
77
C594-0036 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
78
C619-0208 ChemDiv
79
C619-0193 ChemDiv
80
C594-0010 ChemDiv
81
C066-3140 ChemDiv
82
C619-0082 ChemDiv
83
C619-0166 ChemDiv
84
C660-0117 ChemDiv
85
C660-0125 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
No. Structure Virtual Scaffold Vendor Compound Id Producer
86
C619-0202 ChemDiv
87
C594-0021 ChemDiv
88
C594-0076 ChemDiv
Nature Chemical Biology: doi:10.1038/nchembio.187
1. Aurora Fine Chemicals Ltd., Reininghausstr. 49, A-8020 Graz, Austria, E-mail:
aurora@aurorafinechemicals.com,http://www.aurorafinechemicals.com/ 2. ChemDiv Inc., 6605 Nancy Ridge Drive, San Diego, CA 92121 USA,
chemdiv@chemdiv.com,www.chemdiv.com 3. CamCamStudio - Desktop Screen Recorder,http://sourceforge.net/projects/camstudio/ 4. Lagarith Lossless Video Codec,http://lags.leetcode.net/codec.html 5. Adobe Premiere Pro
CS3,http://www.adobe.com/products/premiere/?promoid=121DJGSD_P_US_FP2_PR_MN&tt=P_US_FP2_PR_MN
6. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res. 37, D169-D174 (2009).
7. Pyruvate kinase assay data in PubChem,http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=361&loc=ea_ras
8. Inglese, J. et al. Quantitative high-throughput screening: a titration-based approach that efficiently identifies biological activities in large chemical libraries. Proc. Natl. Acad. Sci. U. S. A. 103, 11473-11478 (2006).
9. Enzymatic Assay of PYRUVATE KINASE (EC 2.7.1.40), Sigma Prod. No. P-1903, Sigma-Aldrich, 2008,http://www.sigmaaldrich.com/sigma/enzyme%20assay/p1903enz.pdf
10. Enzymatic Assay of L-LACTIC DEHYDROGENASE1 (EC 1.1.1.27), Sigma-Aldrich, 2008,http://www.sigmaaldrich.com/sigma/enzyme%20assay/l1254enz.pdf
11. Olah, M. et al. WOMBAT and WOMBAT-PK: bioactivity databases for lead and drug discovery. Chem. Biol. 2, 760-786 (2007).
Nature Chemical Biology: doi:10.1038/nchembio.187