Structure of PDB 4j53 Chain A Binding Site BS02

Receptor Information
>4j53 Chain A (length=293) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEIPEVLVDPRSRRRYVRGRFLGKGGFAKCFEISDADTKEVFAGKIVPKS
LLLKPHQREKMSMEISIHRSLAHQHVVGFHGFFEDNDFVFVVLELCRRRS
LLELHKRRKALTEPEARYYLRQIVLGCQYLHRNRVIHRDLKLGNLFLNED
LEVKIGDFGLATKVEYDGERKKVLCGTPNYIAPEVLSKKGHSFEVDVWSI
GCIMYTLLVGKPPFETSCLKETYLRIKKNEYSIPKHINPVAASLIQKMLQ
TDPTARPTINELLNDEFFTSGYIPARLPITCLTIPPRFSIAPS
Ligand information
Ligand ID1J4
InChIInChI=1S/C27H34F3N7O3/c1-35-10-8-16(9-11-35)32-24(38)18-12-22(40-3)20(13-19(18)28)33-26-31-14-21-23(34-26)37(17-6-4-5-7-17)15-27(29,30)25(39)36(21)2/h12-14,16-17H,4-11,15H2,1-3H3,(H,32,38)(H,31,33,34)
InChIKeyGWRSATNRNFYMDI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC5(F)C(=O)N(c1c(nc(nc1)Nc3c(OC)cc(C(=O)NC2CCN(C)CC2)c(F)c3)N(C4CCCC4)C5)C
OpenEye OEToolkits 1.7.6CN1CCC(CC1)NC(=O)c2cc(c(cc2F)Nc3ncc4c(n3)N(CC(C(=O)N4C)(F)F)C5CCCC5)OC
CACTVS 3.370COc1cc(c(F)cc1Nc2ncc3N(C)C(=O)C(F)(F)CN(C4CCCC4)c3n2)C(=O)NC5CCN(C)CC5
FormulaC27 H34 F3 N7 O3
Name4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-2-fluoro-5-methoxy-N-(1-methylpiperidin-4-yl)benzamide
ChEMBLCHEMBL2392545
DrugBank
ZINCZINC000043203898
PDB chain4j53 Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4j53 Discovery of TAK-960: An orally available small molecule inhibitor of polo-like kinase 1 (PLK1).
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L59 C67 V114 C133 R136 F183
Binding residue
(residue number reindexed from 1)		L22 C30 V77 C96 R99 F146
Annotation score1
Binding affinityMOAD: ic50=2nM
PDBbind-CN: -logKd/Ki=8.70,IC50=2nM
BindingDB: IC50=2.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) D176 K178 G180 N181 D194 T214
Catalytic site (residue number reindexed from 1) D139 K141 G143 N144 D157 T177
Enzyme Commision number 2.7.11.21: polo 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:4j53, PDBe:4j53, PDBj:4j53
PDBsum4j53
PubMed23664874
UniProtP53350|PLK1_HUMAN Serine/threonine-protein kinase PLK1 (Gene Name=PLK1)

[Back to BioLiP]