Structure of PDB 3we4 Chain A Binding Site BS02

Receptor Information
>3we4 Chain A (length=287) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIRPECFELLRVLGKGGYGKVFQVRKVTGANTGKIFAMKVLKKAMIVRNA
KDTAHTKAERNILEEVKHPFIVDLIYAFQTGGKLYLILEYLSGGELFMQL
EREGIFMEDTACFYLAEISMALGHLHQKGIIYRDLKPENIMLNHQGHVKL
TDFGLCKESIHDTHTFCGTIEYMAPEILMRSGHNRAVDWWSLGALMYDML
TGAPPFTGENRKKTIDKILKCKLNLPPYLTQEARDLLKKLLKRNAASRLG
AGPGDAGEVQAHPFFRHINWEELLARKVEPPFKPLLQ
Ligand information
Ligand ID5FI
InChIInChI=1S/C19H21F3N6/c1-2-13-10-23-12-24-18(13)28-7-5-27(6-8-28)11-17-25-15-4-3-14(19(20,21)22)9-16(15)26-17/h3-4,9-10,12H,2,5-8,11H2,1H3,(H,25,26)
InChIKeyFBLPQCAQRNSVHB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC(F)(F)c1cc2nc(nc2cc1)CN4CCN(c3ncncc3CC)CC4
CACTVS 3.370
OpenEye OEToolkits 1.7.6		CCc1cncnc1N2CCN(CC2)Cc3[nH]c4ccc(cc4n3)C(F)(F)F
FormulaC19 H21 F3 N6
Name2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole
ChEMBLCHEMBL2134202
DrugBank
ZINCZINC000071773472
PDB chain3we4 Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3we4 Crystal structures of the S6K1 kinase domain in complexes with inhibitors
Resolution1.995 Å
Binding residue
(original residue number in PDB)		K99 G100 G103 V105 A121 K123 L125 E173 Y174 L175 M225 K241
Binding residue
(residue number reindexed from 1)		K15 G16 G19 V21 A37 K39 L41 E89 Y90 L91 M141 K157
Annotation score1
Binding affinityMOAD: ic50=15nM
PDBbind-CN: -logKd/Ki=7.82,IC50=15nM
BindingDB: Ki=20nM,IC50=160nM
Enzymatic activity
Catalytic site (original residue number in PDB) D218 K220 E222 N223 D236 T256
Catalytic site (residue number reindexed from 1) D134 K136 E138 N139 D152 T169
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
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Biological Process
External links
PDB RCSB:3we4, PDBe:3we4, PDBj:3we4
PDBsum3we4
PubMed25078151
UniProtP23443|KS6B1_HUMAN Ribosomal protein S6 kinase beta-1 (Gene Name=RPS6KB1)

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