Structure of PDB 5vd0 Chain A Binding Site BS01

Receptor Information
>5vd0 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]
LGTENLYFLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGH
GSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHP
CCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTL
LALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQE
GDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQG
YLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQ
Ligand information
Ligand ID8X7
InChIInChI=1S/C27H32N8O2/c1-5-13-34-25(36)21-18-28-26(29-19-9-11-20(12-10-19)33-16-14-32(4)15-17-33)31-24(21)35(34)23-8-6-7-22(30-23)27(2,3)37/h5-12,18,37H,1,13-17H2,2-4H3,(H,28,29,31)
InChIKeyBKWJAKQVGHWELA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1CCN(CC1)c2ccc(Nc3ncc4C(=O)N(CC=C)N(c5cccc(n5)C(C)(C)O)c4n3)cc2
OpenEye OEToolkits 2.0.6CC(C)(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(cc4)N5CCN(CC5)C)C(=O)N2CC=C)O
ACDLabs 12.01CN5CCN(c1ccc(cc1)Nc2nc3c(cn2)C(=O)N(C\C=C)N3c4nc(C(C)(C)O)ccc4)CC5
FormulaC27 H32 N8 O2
Name1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one
ChEMBLCHEMBL1976040
DrugBankDB11740
ZINCZINC000063539231
PDB chain5vd0 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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PDB5vd0 Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Resolution2.13 Å
Binding residue
(original residue number in PDB)		L116 Y121 V124 K139 T187 C190 G191 P192 F240
Binding residue
(residue number reindexed from 1)		L48 Y53 V56 K71 T119 C122 G123 P124 F172
Annotation score1
Binding affinityMOAD: Kd=324nM
PDBbind-CN: -logKd/Ki=6.49,Kd=324nM
BindingDB: IC50=4940nM,Ki=470nM,Kd=324nM
Enzymatic activity
Catalytic site (original residue number in PDB) D233 K235 N238 D251 D270
Catalytic site (residue number reindexed from 1) D165 K167 N170 D183 D202
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:5vd0, PDBe:5vd0, PDBj:5vd0
PDBsum5vd0
PubMed28792760
UniProtQ99640|PMYT1_HUMAN Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (Gene Name=PKMYT1)

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