Structure of PDB 3qd3 Chain A Binding Site BS01

Receptor Information
>3qd3 Chain A (length=279) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIK
ENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKY
IRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQ
ITDFGTAKVLSSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGL
PPFRAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEE
MEGYGPLKAHPFFESVTWENLHQQTPPKL
Ligand information
Ligand ID3Q5
InChIInChI=1S/C22H30N8O2/c1-12-5-7-14(25-21(31)32-22(2,3)4)11-30(12)18-10-16(26-20(24)27-18)13-6-8-15-17(9-13)28-29-19(15)23/h6,8-10,12,14H,5,7,11H2,1-4H3,(H,25,31)(H3,23,28,29)(H2,24,26,27)/t12-,14+/m0/s1
InChIKeyGAMJJHMLLXIWRZ-GXTWGEPZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C[C@H]1CC[C@H](C[N@]1c2cc(nc(n2)N)c3ccc4c(c3)n[nH]c4N)NC(=O)OC(C)(C)C
OpenEye OEToolkits 1.7.0CC1CCC(CN1c2cc(nc(n2)N)c3ccc4c(c3)n[nH]c4N)NC(=O)OC(C)(C)C
CACTVS 3.370C[CH]1CC[CH](CN1c2cc(nc(N)n2)c3ccc4c(N)[nH]nc4c3)NC(=O)OC(C)(C)C
CACTVS 3.370C[C@H]1CC[C@H](CN1c2cc(nc(N)n2)c3ccc4c(N)[nH]nc4c3)NC(=O)OC(C)(C)C
ACDLabs 12.01O=C(OC(C)(C)C)NC4CCC(N(c3nc(nc(c1ccc2c(N)nnc2c1)c3)N)C4)C
FormulaC22 H30 N8 O2
Nametert-butyl {(3R,6S)-1-[2-amino-6-(3-amino-2H-indazol-6-yl)pyrimidin-4-yl]-6-methylpiperidin-3-yl}carbamate
ChEMBLCHEMBL1614776
DrugBank
ZINCZINC000064502326
PDB chain3qd3 Chain A Residue 360 [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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PDB3qd3 Structure-Based Design of Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Inhibitors.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G91 S94 V96 A109 K111 E130 S160 Y161 A162 L212 T222 D223
Binding residue
(residue number reindexed from 1)		G21 S24 V26 A39 K41 E60 S90 Y91 A92 L142 T152 D153
Annotation score1
Binding affinityMOAD: ic50=0.00000001M
PDBbind-CN: -logKd/Ki=8.00,IC50=10nM
BindingDB: IC50=10.0nM
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 T166
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:3qd3, PDBe:3qd3, PDBj:3qd3
PDBsum3qd3
PubMed21341675
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

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