Structure of PDB 3wf5 Chain A Binding Site BS02

Receptor Information
>3wf5 Chain A (length=278) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIRPECFELLRVLGKGGYGKVFQVRKVTGANTGKIFAMKVLKKTKAERNI
LEEVKHPFIVDLIYAFQTGGKLYLILEYLSGGELFMQLEREGIFMEDTAC
FYLAEISMALGHLHQKGIIYRDLKPENIMLNHQGHVKLTDFGLCKESIHD
GTVTHTFCGTIEYMAPEILMRSGHNRAVDWWSLGALMYDMLTGAPPFTGE
NRKKTIDKILKCKLNLPPYLTQEARDLLKKLLKRNAASRLGAGPGDAGEV
QAHPFFRHINWEELLARKVEPPFKPLLQ
Ligand information
Ligand IDFZ8
InChIInChI=1S/C17H17N7/c1-2-4-14-13(3-1)21-15(22-14)11-5-7-24(8-6-11)17-12-9-20-23-16(12)18-10-19-17/h1-4,9-11H,5-8H2,(H,21,22)(H,18,19,20,23)
InChIKeySAOVCWDCHHZCCL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01n1c(c2c(nc1)nnc2)N5CCC(c4nc3ccccc3n4)CC5
OpenEye OEToolkits 1.7.6c1ccc2c(c1)[nH]c(n2)C3CCN(CC3)c4c5cn[nH]c5ncn4
CACTVS 3.385C1CN(CCC1c2[nH]c3ccccc3n2)c4ncnc5[nH]ncc45
FormulaC17 H17 N7
Name4-[4-(1H-benzimidazol-2-yl)piperidin-1-yl]-1H-pyrazolo[3,4-d]pyrimidine
ChEMBL
DrugBank
ZINC
PDB chain3wf5 Chain A Residue 402 [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]
PDB3wf5 Crystal structures of the S6K1 kinase domain in complexes with inhibitors
Resolution2.099 Å
Binding residue
(original residue number in PDB)		K99 G100 V105 A121 E173 L175 K241
Binding residue
(residue number reindexed from 1)		K15 G16 V21 A37 E77 L79 K145
Annotation score1
Binding affinityMOAD: ic50=81nM
PDBbind-CN: -logKd/Ki=7.09,IC50=81nM
Enzymatic activity
Catalytic site (original residue number in PDB) D218 K220 E222 N223 D236 T256
Catalytic site (residue number reindexed from 1) D122 K124 E126 N127 D140 T160
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine 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:3wf5, PDBe:3wf5, PDBj:3wf5
PDBsum3wf5
PubMed25078151
UniProtP23443|KS6B1_HUMAN Ribosomal protein S6 kinase beta-1 (Gene Name=RPS6KB1)

[Back to BioLiP]