Structure of PDB 5vdk Chain A Binding Site BS01

Receptor Information
>5vdk Chain A (length=260) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MASRYEKEFLEVEKIGVGEFGTVYKCIKRLDGCVYAIKRSMKTFTELSNE
NSALHEVYAHAVLGHHPHVVRYYSSWAEDDHMIIQNEYCNGGSLQAAISE
NTKSGNHFEEPKLKDILLQISLGLNYIHNSSMVHLDIKPSNIFICHKVMY
KIGDLGHATSINKPKVEEGDSRFLANEILQEDYRHLPKADIFALGLTIAV
AAGAESLPTNGAAWHHIRKGNFPDVPQELSESFSSLLKNMIQPDAEQRPS
AAALARNTVL
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 chain5vdk Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5vdk Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		V220 G221 E222 V226 A239 N289 E290 Y291 C292 G295 F346
Binding residue
(residue number reindexed from 1)		V17 G18 E19 V23 A36 N86 E87 Y88 C89 G92 F143
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.57,Kd=27.0nM
BindingDB: Kd=3.9nM
Enzymatic activity
Catalytic site (original residue number in PDB) D339 K341
Catalytic site (residue number reindexed from 1) D136 K138
Enzyme Commision number 2.7.10.2: non-specific protein-tyrosine 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:5vdk, PDBe:5vdk, PDBj:5vdk
PDBsum5vdk
PubMed28792760
UniProtP0C1S8|WEE2_HUMAN Wee1-like protein kinase 2 (Gene Name=WEE2)

[Back to BioLiP]