Structure of PDB 5vd3 Chain A Binding Site BS01

Receptor Information
>5vd3 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]
DLGTENLYFQQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLG
HGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQH
PCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDT
LLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQ
EGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQ
GYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLR
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 chain5vd3 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vd3 Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		L116 A137 K139 L185 T187 C190 G191 P192 F240
Binding residue
(residue number reindexed from 1)		L49 A70 K72 L118 T120 C123 G124 P125 F173
Annotation score1
Binding affinityMOAD: Kd=2817nM
PDBbind-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) D166 K168 N171 D184 D203
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:5vd3, PDBe:5vd3, PDBj:5vd3
PDBsum5vd3
PubMed28792760
UniProtQ99640|PMYT1_HUMAN Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (Gene Name=PKMYT1)

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