Structure of PDB 3qd0 Chain A Binding Site BS01

Receptor Information
>3qd0 Chain A (length=274) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKEN
KVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIR
KIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQIT
DFGTAKVLSGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRA
GNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYG
PLKAHPFFESVTWENLHQQTPPKL
Ligand information
Ligand ID3Q4
InChIInChI=1S/C24H26N8O/c1-14-7-8-16(23(33)27-17-5-3-2-4-6-17)13-32(14)21-12-19(28-24(26)29-21)15-9-10-18-20(11-15)30-31-22(18)25/h2-6,9-12,14,16H,7-8,13H2,1H3,(H,27,33)(H3,25,30,31)(H2,26,28,29)/t14-,16+/m1/s1
InChIKeyTXXYVBLFLGPQOR-ZBFHGGJFSA-N
SMILES
SoftwareSMILES
CACTVS 3.370C[C@@H]1CC[C@@H](CN1c2cc(nc(N)n2)c3ccc4c(N)[nH]nc4c3)C(=O)Nc5ccccc5
OpenEye OEToolkits 1.7.0CC1CCC(CN1c2cc(nc(n2)N)c3ccc4c(c3)n[nH]c4N)C(=O)Nc5ccccc5
OpenEye OEToolkits 1.7.0C[C@@H]1CC[C@@H](C[N@@]1c2cc(nc(n2)N)c3ccc4c(c3)n[nH]c4N)C(=O)Nc5ccccc5
CACTVS 3.370C[CH]1CC[CH](CN1c2cc(nc(N)n2)c3ccc4c(N)[nH]nc4c3)C(=O)Nc5ccccc5
ACDLabs 12.01O=C(Nc1ccccc1)C5CCC(N(c4nc(nc(c2ccc3c(N)nnc3c2)c4)N)C5)C
FormulaC24 H26 N8 O
Name(3S,6R)-1-[2-amino-6-(3-amino-2H-indazol-6-yl)pyrimidin-4-yl]-6-methyl-N-phenylpiperidine-3-carboxamide
ChEMBLCHEMBL1614775
DrugBank
ZINCZINC000064502325
PDB chain3qd0 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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PDB3qd0 Structure-Based Design of Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Inhibitors.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		V96 A109 K111 Y126 E130 L159 S160 Y161 A162 L212 T222 D223 G225
Binding residue
(residue number reindexed from 1)		V24 A37 K39 Y54 E58 L87 S88 Y89 A90 L140 T150 D151 G153
Annotation score1
Binding affinityMOAD: ic50=3.16nM
PDBbind-CN: -logKd/Ki=8.50,IC50=3.16nM
BindingDB: IC50=333nM
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 T161
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3qd0, PDBe:3qd0, PDBj:3qd0
PDBsum3qd0
PubMed21341675
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

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