Structure of PDB 2ym7 Chain A Binding Site BS02

Receptor Information
>2ym7 Chain A (length=248) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDWDLVQTLGEVQLAVNRVTEEAVAVKIVNIKKEICINKMLNHENVVKFY
GHRREIQYLFLEYCSGGELFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHG
IGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRERLLNKMCGTLPY
VAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKE
KKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKK
Ligand information
Ligand IDYM7
InChIInChI=1S/C15H18N8/c16-6-12-8-20-15(9-18-12)23-14-5-13(21-10-22-14)19-7-11-1-3-17-4-2-11/h5,8-11,17H,1-4,7H2,(H2,19,20,21,22,23)
InChIKeyLNWARQATROLGJR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01N#Cc1ncc(nc1)Nc3ncnc(NCC2CCNCC2)c3
OpenEye OEToolkits 1.9.2c1c(ncnc1Nc2cnc(cn2)C#N)NCC3CCNCC3
CACTVS 3.385N#Cc1cnc(Nc2cc(NCC3CCNCC3)ncn2)cn1
FormulaC15 H18 N8
Name5-({6-[(piperidin-4-ylmethyl)amino]pyrimidin-4-yl}amino)pyrazine-2-carbonitrile
ChEMBLCHEMBL1928689
DrugBank
ZINCZINC000082153556
PDB chain2ym7 Chain A Residue 1273 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ym7 Structure-Guided Evolution of Potent and Selective Chk1 Inhibitors Through Scaffold Morphing.
Resolution1.81 Å
Binding residue
(original residue number in PDB)		W9 E33 Y71 R74 F83
Binding residue
(residue number reindexed from 1)		W3 E22 Y50 R53 F60
Annotation score1
Binding affinityMOAD: ic50=0.13uM
PDBbind-CN: -logKd/Ki=6.89,IC50=0.13uM
BindingDB: IC50=130nM
Enzymatic activity
Catalytic site (original residue number in PDB) D130 K132 E134 N135 D148 T170
Catalytic site (residue number reindexed from 1) D107 K109 E111 N112 D125 T147
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0000077 DNA damage checkpoint signaling
GO:0006468 protein phosphorylation

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:2ym7, PDBe:2ym7, PDBj:2ym7
PDBsum2ym7
PubMed22111927
UniProtO14757|CHK1_HUMAN Serine/threonine-protein kinase Chk1 (Gene Name=CHEK1)

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