Structure of PDB 4xx9 Chain A Binding Site BS02

Receptor Information
>4xx9 Chain A (length=289) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIK
ENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKY
IRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQ
ITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGC
IIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLD
ATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT
Ligand information
Ligand IDRF4
InChIInChI=1S/C19H20N2O3S/c1-13-6-5-7-14(2)18(13)24-10-11-25-19-20-15-8-3-4-9-16(15)21(19)12-17(22)23/h3-9H,10-12H2,1-2H3,(H,22,23)
InChIKeyZAHFRMHMWCBLOL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1cccc(c1OCCSc2nc3ccccc3n2CC(=O)O)C
ACDLabs 12.01c1(c(c(ccc1)C)OCCSc2nc3c(n2CC(O)=O)cccc3)C
CACTVS 3.385Cc1cccc(C)c1OCCSc2nc3ccccc3n2CC(O)=O
FormulaC19 H20 N2 O3 S
Name(2-{[2-(2,6-dimethylphenoxy)ethyl]sulfanyl}-1H-benzimidazol-1-yl)acetic acid
ChEMBLCHEMBL1439113
DrugBank
ZINCZINC000002051956
PDB chain4xx9 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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PDB4xx9 Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		K76 K115 I118 V127 R131 T148 L155 F157
Binding residue
(residue number reindexed from 1)		K6 K45 I48 V57 R61 T78 L85 F87
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.08,Kd=8.4uM
BindingDB: Kd=8000nM,EC50=2000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D205 K207 E209 N210 D223 T245
Catalytic site (residue number reindexed from 1) D135 K137 E139 N140 D153 T175
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:4xx9, PDBe:4xx9, PDBj:4xx9
PDBsum4xx9
PubMed26443011
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

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