Structure of PDB 3qcs Chain A Binding Site BS01

Receptor Information
>3qcs Chain A (length=277) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKEN
KVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIR
KIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQIT
DFGTAKVLSSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPP
FRAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEME
GYGPLKAHPFFESVTWENLHQQTPPKL
Ligand information
Ligand ID3Q1
InChIInChI=1S/C15H17N7O/c16-14-10-2-1-9(7-12(10)20-21-14)11-8-13(19-15(17)18-11)22-3-5-23-6-4-22/h1-2,7-8H,3-6H2,(H3,16,20,21)(H2,17,18,19)
InChIKeyIBSXLFOFZRSWEZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01n3c(nc(c2ccc1c(N)nnc1c2)cc3N4CCOCC4)N
OpenEye OEToolkits 1.7.0c1cc2c(cc1c3cc(nc(n3)N)N4CCOCC4)n[nH]c2N
CACTVS 3.370Nc1[nH]nc2cc(ccc12)c3cc(nc(N)n3)N4CCOCC4
FormulaC15 H17 N7 O
Name6-[2-amino-6-(morpholin-4-yl)pyrimidin-4-yl]-2H-indazol-3-amine
ChEMBLCHEMBL1614772
DrugBank
ZINCZINC000064502327
PDB chain3qcs Chain A Residue 370 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qcs Structure-Based Design of Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Inhibitors.
Resolution2.487 Å
Binding residue
(original residue number in PDB)		V96 A109 K111 S160 A162 L212 T222 D223
Binding residue
(residue number reindexed from 1)		V24 A37 K39 S88 A90 L140 T150 D151
Annotation score1
Binding affinityMOAD: ic50=0.316uM
PDBbind-CN: -logKd/Ki=6.50,IC50=0.316uM
BindingDB: IC50=316nM
Enzymatic activity
Catalytic site (original residue number in PDB) D205 K207 E209 N210 D223 T245
Catalytic site (residue number reindexed from 1) D133 K135 E137 N138 D151 T164
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:3qcs, PDBe:3qcs, PDBj:3qcs
PDBsum3qcs
PubMed21341675
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

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