Structure of PDB 3qc4 Chain B Binding Site BS01

Receptor Information
>3qc4 Chain B (length=279) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPLGSMDGTAKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEK
RHIVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRK
IGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITD
FGTAKVLSANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLP
PFRAGNEYLIFQKIIKLEYDFPAAFFPKARDLVEKLLVLDATKRLGCEEM
EGYGPLKAHPFFESVTWENLHQQTPPKLT
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 chain3qc4 Chain B Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qc4 Discovery of a potent and highly selective PDK1 inhibitor via fragment-based drug discovery.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		A109 K111 L137 F142 V143 L159 Y161 L196 L212 D223 F224 G225 A227
Binding residue
(residue number reindexed from 1)		A44 K46 L64 F69 V70 L86 Y88 L123 L139 D150 F151 G152 A154
Annotation score1
Binding affinityMOAD: ic50=0.002uM
BindingDB: EC50=1nM
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 T165
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:3qc4, PDBe:3qc4, PDBj:3qc4
PDBsum3qc4
PubMed21459573
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

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