Structure of PDB 5vcy Chain A Binding Site BS01

Receptor Information
>5vcy Chain A (length=296) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLGTENLYFQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRL
GHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQ
HPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRD
TLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEV
QEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLR
QGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP
Ligand information
Ligand IDDB8
InChIInChI=1S/C26H29Cl2N5O3/c1-32-6-8-33(9-7-32)5-4-10-36-25-13-21-18(11-24(25)35-3)26(17(15-29)16-30-21)31-22-14-23(34-2)20(28)12-19(22)27/h11-14,16H,4-10H2,1-3H3,(H,30,31)
InChIKeyUBPYILGKFZZVDX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370COc1cc(Nc2c(cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc23)C#N)c(Cl)cc1Cl
OpenEye OEToolkits 1.7.2CN1CCN(CC1)CCCOc2cc3c(cc2OC)c(c(cn3)C#N)Nc4cc(c(cc4Cl)Cl)OC
ACDLabs 12.01Clc1c(OC)cc(c(Cl)c1)Nc4c(C#N)cnc3cc(OCCCN2CCN(CC2)C)c(OC)cc34
FormulaC26 H29 Cl2 N5 O3
Name4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile;
Bosutinib
ChEMBLCHEMBL288441
DrugBankDB06616
ZINCZINC000022448983
PDB chain5vcy Chain A Residue 401 [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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PDB5vcy Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Resolution1.56 Å
Binding residue
(original residue number in PDB)		L116 A137 V138 K139 V171 L185 T187 C190 G191 P192 F240
Binding residue
(residue number reindexed from 1)		L50 A71 V72 K73 V105 L119 T121 C124 G125 P126 F174
Annotation score1
Binding affinityMOAD: Kd=270nM
PDBbind-CN: -logKd/Ki=6.57,Kd=270nM
BindingDB: Ki=13nM,IC50=704nM,Kd=350nM
Enzymatic activity
Catalytic site (original residue number in PDB) D233 K235 N238 D251 D270
Catalytic site (residue number reindexed from 1) D167 K169 N172 D185 D204
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:5vcy, PDBe:5vcy, PDBj:5vcy
PDBsum5vcy
PubMed28792760
UniProtQ99640|PMYT1_HUMAN Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (Gene Name=PKMYT1)

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