Structure of PDB 5vd1 Chain A Binding Site BS01

Receptor Information
>5vd1 Chain A (length=295) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LGTENLYFQSLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRL
GHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQ
HPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRD
TLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEV
QEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLR
QGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQ
Ligand information
Ligand IDP48
InChIInChI=1S/C25H32N8O/c1-25(2)14-16-15-27-24(29-20(16)22-19(25)21(23(34)26-3)30-32(22)5)28-17-6-8-18(9-7-17)33-12-10-31(4)11-13-33/h6-9,15H,10-14H2,1-5H3,(H,26,34)(H,27,28,29)
InChIKeyRXZMYLDMFYNEIM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CNC(=O)c1nn(C)c2c3nc(Nc4ccc(cc4)N5CCN(C)CC5)ncc3CC(C)(C)c12
ACDLabs 10.04O=C(NC)c3nn(c2c1nc(ncc1CC(c23)(C)C)Nc4ccc(cc4)N5CCN(C)CC5)C
OpenEye OEToolkits 1.6.1CC1(Cc2cnc(nc2-c3c1c(nn3C)C(=O)NC)Nc4ccc(cc4)N5CCN(CC5)C)C
FormulaC25 H32 N8 O
NameN,1,4,4-TETRAMETHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE
ChEMBLCHEMBL564829
DrugBankDB16232
ZINCZINC000053119602
PDB chain5vd1 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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PDB5vd1 Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		L116 Y121 V124 A137 K139 C190 G191 P192 Q196 F240 D251
Binding residue
(residue number reindexed from 1)		L50 Y55 V58 A71 K73 C124 G125 P126 Q130 F174 D185
Annotation score1
Binding affinityMOAD: Kd=990nM
PDBbind-CN: -logKd/Ki=6.00,Kd=990nM
BindingDB: Kd=990nM
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:5vd1, PDBe:5vd1, PDBj:5vd1
PDBsum5vd1
PubMed28792760
UniProtQ99640|PMYT1_HUMAN Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (Gene Name=PKMYT1)

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