Structure of PDB 4rqk Chain A Binding Site BS02

Receptor Information
>4rqk Chain A (length=286) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENK
VPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRK
IGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITD
FGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIY
QLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATK
RLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT
Ligand information
Ligand IDR1S
InChIInChI=1S/C15H9ClN2O2S3/c16-9-5-6-11-13(7-9)22-15(17-11)18-23(19,20)14-8-21-12-4-2-1-3-10(12)14/h1-8H,(H,17,18)
InChIKeyVLGMTYRMKMVUHJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=S(=O)(c1c2ccccc2sc1)Nc3nc4ccc(Cl)cc4s3
OpenEye OEToolkits 1.7.6c1ccc2c(c1)c(cs2)S(=O)(=O)Nc3nc4ccc(cc4s3)Cl
CACTVS 3.385Clc1ccc2nc(N[S](=O)(=O)c3csc4ccccc34)sc2c1
FormulaC15 H9 Cl N2 O2 S3
NameN-(6-chloro-1,3-benzothiazol-2-yl)-1-benzothiophene-3-sulfonamide
ChEMBLCHEMBL4592040
DrugBank
ZINCZINC000219975175
PDB chain4rqk Chain A Residue 404 [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]
PDB4rqk A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		K115 I118 I119 V127 R131 T148 F149 L155
Binding residue
(residue number reindexed from 1)		K42 I45 I46 V54 R58 T75 F76 L82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.82,Kd=1.5uM
BindingDB: Kd=1500nM
Enzymatic activity
Catalytic site (original residue number in PDB) D205 K207 E209 N210 D223 T245
Catalytic site (residue number reindexed from 1) D132 K134 E136 N137 D150 T172
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:4rqk, PDBe:4rqk, PDBj:4rqk
PDBsum4rqk
PubMed25518860
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

[Back to BioLiP]