Structure of PDB 2pe1 Chain A Binding Site BS01

Receptor Information
>2pe1 Chain A (length=276) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENK
VPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRK
IGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITD
FGTAKVLSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFR
AGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGY
GPLKAHPFFESVTWENLHQQTPPKLT
Ligand information
Ligand ID517
InChIInChI=1S/C15H14N4O2/c1-8(11-3-2-6-17-11)13-10-7-9(18-15(16)21)4-5-12(10)19-14(13)20/h2-8,17H,1H3,(H3,16,18,21)/t8-/m0/s1
InChIKeyKJDBLWKTHMHALD-QMMMGPOBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(c1ccc[nH]1)C2=C3C=C(C=CC3=NC2=O)NC(=O)N
CACTVS 3.341C[CH](c1[nH]ccc1)C2=C3C=C(NC(N)=O)C=CC3=NC2=O
ACDLabs 10.04O=C(N)NC3=CC=1C(=NC(=O)C=1C(c2cccn2)C)C=C3
CACTVS 3.341C[C@@H](c1[nH]ccc1)C2=C3C=C(NC(N)=O)C=CC3=NC2=O
FormulaC15 H14 N4 O2
Name1-{2-OXO-3-[(1R)-1-(1H-PYRROL-2-YL)ETHYL]-2H-INDOL-5-YL}UREA
ChEMBL
DrugBankDB07132
ZINCZINC000016052364
PDB chain2pe1 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

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PDB2pe1 Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 1: Design, synthesis and biological activity.
Resolution2.14 Å
Binding residue
(original residue number in PDB)		L88 A109 K111 Y161 A162 G165 L212 T222 D223
Binding residue
(residue number reindexed from 1)		L15 A36 K38 Y88 A89 G92 L139 T149 D150
Annotation score1
Binding affinityMOAD: ic50=6nM
PDBbind-CN: -logKd/Ki=8.30,IC50=5nM
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 T162
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:2pe1, PDBe:2pe1, PDBj:2pe1
PDBsum2pe1
PubMed17531483
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

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