Structure of PDB 5vcx Chain A Binding Site BS01

Receptor Information
>5vcx Chain A (length=287) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEV
FKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLE
QAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHL
HSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYM
APELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEF
TAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQ
Ligand information
Ligand IDH8H
InChIInChI=1S/C27H32ClN5O5/c1-32-6-8-33(9-7-32)10-13-35-19-14-21-24(23(15-19)38-18-4-11-34-12-5-18)27(30-16-29-21)31-25-20(28)2-3-22-26(25)37-17-36-22/h2-3,14-16,18H,4-13,17H2,1H3,(H,29,30,31)
InChIKeyOUKYUETWWIPKQR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1CCN(CCOc2cc(OC3CCOCC3)c4c(Nc5c(Cl)ccc6OCOc56)ncnc4c2)CC1
ACDLabs 10.04Clc2ccc1OCOc1c2Nc6ncnc5c6c(OC3CCOCC3)cc(OCCN4CCN(C)CC4)c5
OpenEye OEToolkits 1.7.6CN1CCN(CC1)CCOc2cc3c(c(c2)OC4CCOCC4)c(ncn3)Nc5c(ccc6c5OCO6)Cl
FormulaC27 H32 Cl N5 O5
NameN-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE;
SARACATINIB
ChEMBLCHEMBL217092
DrugBankDB11805
ZINCZINC000024811973
PDB chain5vcx 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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PDB5vcx Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		L116 A137 K139 T187 C190 F240 D251
Binding residue
(residue number reindexed from 1)		L42 A63 K65 T113 C116 F166 D177
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.55,Kd=2817nM
BindingDB: IC50=418nM,Ki=40nM,Kd=2817nM
Enzymatic activity
Catalytic site (original residue number in PDB) D233 K235 N238 D251 D270
Catalytic site (residue number reindexed from 1) D159 K161 N164 D177 D196
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5vcx, PDBe:5vcx, PDBj:5vcx
PDBsum5vcx
PubMed28792760
UniProtQ99640|PMYT1_HUMAN Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (Gene Name=PKMYT1)

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