Structure of PDB 4a9t Chain A Binding Site BS01

Receptor Information
>4a9t Chain A (length=289) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSVYPKALRDEYIMSKTLGSGEVKLAFERKTCKKVAIKIISKPALNVETE
IEILKKLNHPCIIKIKNFFDAEDYYIVLELMEGGELFDKVVGNKRLKEAT
CKLYFYQMLLAVQYLHENGIIHRDLKPENVLLSSQEEDCLIKITDFGHSK
ILGETSLMRTLCGTPTYLAPEVLVSVGTAGYNRAVDCWSLGVILFICLSG
YPPFSEHRTQVSLKDQITSGKYNFIPEVWAEVSEKALDLVKKLLVVDPKA
RFTTEEALRHPWLQDEDMKRKFQDLLSEENESTALPQVL
Ligand information
Ligand IDA9T
InChIInChI=1S/C27H27ClN4O2/c28-22-6-1-18(2-7-22)16-32-13-11-19(12-14-32)17-34-23-8-3-20(4-9-23)27-30-24-10-5-21(26(29)33)15-25(24)31-27/h1-10,15,19H,11-14,16-17H2,(H2,29,33)(H,30,31)
InChIKeyLKKIDFQBVDANKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc(ccc1CN2CCC(CC2)COc3ccc(cc3)c4[nH]c5ccc(cc5n4)C(=O)N)Cl
ACDLabs 12.01O=C(N)c1cc2nc(nc2cc1)c5ccc(OCC4CCN(Cc3ccc(Cl)cc3)CC4)cc5
CACTVS 3.385NC(=O)c1ccc2[nH]c(nc2c1)c3ccc(OCC4CCN(CC4)Cc5ccc(Cl)cc5)cc3
FormulaC27 H27 Cl N4 O2
Name2-(4-{[1-(4-CHLOROBENZYL)PIPERIDIN-4-YL]METHOXY}PHENYL)-1H-BENZIMIDAZOLE-5-CARBOXAMIDE
ChEMBLCHEMBL251170
DrugBank
ZINCZINC000028960706
PDB chain4a9t Chain A Residue 1514 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4a9t Benzimidazole Inhibitors of the Protein Kinase Chk2: Clarification of the Binding Mode by Flexible Side Chain Docking and Protein-Ligand Crystallography.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		L226 V234 K249 M304 G307 L354 T367 D368 L512
Binding residue
(residue number reindexed from 1)		L18 V23 K38 M81 G84 L131 T144 D145 L289
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.15,IC50=70nM
Enzymatic activity
Catalytic site (original residue number in PDB) D347 K349 N352 D368 T387
Catalytic site (residue number reindexed from 1) D124 K126 N129 D145 T164
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein 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:4a9t, PDBe:4a9t, PDBj:4a9t
PDBsum4a9t
PubMed23058106
UniProtO96017|CHK2_HUMAN Serine/threonine-protein kinase Chk2 (Gene Name=CHEK2)

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