Structure of PDB 3nax Chain A Binding Site BS01

Receptor Information
>3nax Chain A (length=278) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVP
YVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIG
SFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFG
TAKVLSPESKQARAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPF
RAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEG
YGPLKAHPFFESVTWENLHQQTPPKLTA
Ligand information
Ligand IDMP7
InChIInChI=1S/C28H22F2N4O4/c29-21-10-8-17(13-22(21)30)15-34-12-4-7-20(27(34)36)26(35)31-25(18-5-2-1-3-6-18)16-38-19-9-11-23-24(14-19)33-28(37)32-23/h1-14,25H,15-16H2,(H,31,35)(H2,32,33,37)/t25-/m0/s1
InChIKeyGCWCGSPBENFEPE-VWLOTQADSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C5Nc4ccc(OCC(c1ccccc1)NC(=O)C2=CC=CN(C2=O)Cc3cc(F)c(F)cc3)cc4N5
CACTVS 3.370Fc1ccc(CN2C=CC=C(C(=O)N[C@@H](COc3ccc4NC(=O)Nc4c3)c5ccccc5)C2=O)cc1F
OpenEye OEToolkits 1.7.0c1ccc(cc1)C(COc2ccc3c(c2)NC(=O)N3)NC(=O)C4=CC=CN(C4=O)Cc5ccc(c(c5)F)F
OpenEye OEToolkits 1.7.0c1ccc(cc1)[C@H](COc2ccc3c(c2)NC(=O)N3)NC(=O)C4=CC=CN(C4=O)Cc5ccc(c(c5)F)F
CACTVS 3.370Fc1ccc(CN2C=CC=C(C(=O)N[CH](COc3ccc4NC(=O)Nc4c3)c5ccccc5)C2=O)cc1F
FormulaC28 H22 F2 N4 O4
Name1-(3,4-difluorobenzyl)-2-oxo-N-{(1R)-2-[(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)oxy]-1-phenylethyl}-1,2-dihydropyridine-3-carboxamide
ChEMBLCHEMBL1234429
DrugBank
ZINCZINC000058660574
PDB chain3nax Chain A Residue 363 [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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PDB3nax Genetic and pharmacological inhibition of PDK1 in cancer cells: characterization of a selective allosteric kinase inhibitor.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		G91 A109 K111 P125 Y126 M134 F142 V143 L159 Y161 A162 L196 L212 I221 T222 D223 F224 A227
Binding residue
(residue number reindexed from 1)		G16 A34 K36 P50 Y51 M59 F67 V68 L84 Y86 A87 L121 L137 I146 T147 D148 F149 A152
Annotation score1
Binding affinityBindingDB: EC50=1nM
Enzymatic activity
Catalytic site (original residue number in PDB) D205 K207 E209 N210 D223
Catalytic site (residue number reindexed from 1) D130 K132 E134 N135 D148
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
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Biological Process
External links
PDB RCSB:3nax, PDBe:3nax, PDBj:3nax
PDBsum3nax
PubMed21118801
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

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