Structure of PDB 4bcg Chain A Binding Site BS01

Receptor Information
>4bcg Chain A (length=313) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEK
EGFPITALREIKILQLLKHENVVNLIEICRTKGSIYLVFDFCEHDLAGLL
SNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLK
LADFGLARAFSLAKNSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWG
AGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELYEK
LELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDF
FWSDPMPSDLKGM
Ligand information
Ligand IDT3C
InChIInChI=1S/C21H24N8S/c1-14-19(30-21(23-2)26-14)18-15(12-22)13-25-20(28-18)27-16-5-3-6-17(11-16)29-9-4-7-24-8-10-29/h3,5-6,11,13,24H,4,7-10H2,1-2H3,(H,23,26)(H,25,27,28)
InChIKeyBKOYUSKBPMSUBK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNc1sc(c(C)n1)c2nc(Nc3cccc(c3)N4CCCNCC4)ncc2C#N
ACDLabs 12.01N#Cc1c(nc(nc1)Nc3cccc(N2CCCNCC2)c3)c4sc(nc4C)NC
OpenEye OEToolkits 1.9.2Cc1c(sc(n1)NC)c2c(cnc(n2)Nc3cccc(c3)N4CCCNCC4)C#N
FormulaC21 H24 N8 S
Name2-[[3-(1,4-diazepan-1-yl)phenyl]amino]-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile
ChEMBLCHEMBL2312185
DrugBank
ZINCZINC000095597277
PDB chain4bcg Chain A Residue 1328 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4bcg Substituted 4-(Thiazol-5-Yl)-2-(Phenylamino)Pyrimidines are Highly Active Cdk9 Inhibitors: Synthesis, X-Ray Crystal Structure, Sar and Anti-Cancer Activities.
Resolution3.085 Å
Binding residue
(original residue number in PDB)		I25 T29 V33 A46 V79 F103 C106 D109 L156 D167
Binding residue
(residue number reindexed from 1)		I19 T23 V27 A40 V73 F89 C92 D95 L142 D153
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.15,Ki=7nM
Enzymatic activity
Catalytic site (original residue number in PDB) D149 K151 A153 N154 D167 S180 T191
Catalytic site (residue number reindexed from 1) D135 K137 A139 N140 D153 S166 T177
Enzyme Commision number 2.7.11.22: cyclin-dependent kinase.
2.7.11.23: [RNA-polymerase]-subunit kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4bcg, PDBe:4bcg, PDBj:4bcg
PDBsum4bcg
PubMed23301767
UniProtP50750|CDK9_HUMAN Cyclin-dependent kinase 9 (Gene Name=CDK9)

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