Structure of PDB 6lio Chain B Binding Site BS01

Receptor Information
>6lio Chain B (length=371) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKALLKNASLAGAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFL
RQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDP
EDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQY
FLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNCNVSEVVKD
AYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELF
KNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERL
FSYMYSTTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKAL
STDSVERLPVYNKSAWRHYQT
Ligand information
Ligand IDEH3
InChIInChI=1S/C30H34ClN3O9S/c1-44(40,41)34-12-10-21(11-13-34)42-20-8-6-18(7-9-20)26-27(29(37)32-16-17-2-4-19(5-3-17)30(38)39)33-43-28(26)22-14-23(31)25(36)15-24(22)35/h6-9,14-15,17,19,21,35-36H,2-5,10-13,16H2,1H3,(H,32,37)(H,38,39)/t17-,19+
InChIKeyAKZGGZLLGOJKMH-IZAXUBKRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[S](=O)(=O)N1CCC(CC1)Oc2ccc(cc2)c3c(onc3C(=O)NC[C@H]4CC[C@H](CC4)C(O)=O)c5cc(Cl)c(O)cc5O
CACTVS 3.385C[S](=O)(=O)N1CCC(CC1)Oc2ccc(cc2)c3c(onc3C(=O)NC[CH]4CC[CH](CC4)C(O)=O)c5cc(Cl)c(O)cc5O
OpenEye OEToolkits 2.0.7CS(=O)(=O)N1CCC(CC1)Oc2ccc(cc2)c3c(onc3C(=O)NCC4CCC(CC4)C(=O)O)c5cc(c(cc5O)O)Cl
FormulaC30 H34 Cl N3 O9 S
Name4-[[[5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-4-[4-(1-methylsulfonylpiperidin-4-yl)oxyphenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]cyclohexane-1-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6lio Chain B Residue 404 [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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PDB6lio Structural basis for the inhibition of PDK2 by novel ATP- and lipoyl-binding site targeting compounds.
Resolution1.76 Å
Binding residue
(original residue number in PDB)		N255 R258 A259 D290 G294 V295 K299 L303 Y308 G327 L330 T354
Binding residue
(residue number reindexed from 1)		N252 R255 A256 D287 G291 V292 K296 L300 Y305 G314 L317 T341
Annotation score1
Binding affinityMOAD: Kd=64.4nM
Enzymatic activity
Enzyme Commision number 2.7.11.2: [pyruvate dehydrogenase (acetyl-transferring)] kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004740 pyruvate dehydrogenase (acetyl-transferring) kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0006006 glucose metabolic process
GO:0006111 regulation of gluconeogenesis
GO:0006885 regulation of pH
GO:0008286 insulin receptor signaling pathway
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate
GO:0010565 regulation of cellular ketone metabolic process
GO:0010906 regulation of glucose metabolic process
GO:0016310 phosphorylation
GO:0031670 cellular response to nutrient
GO:0034614 cellular response to reactive oxygen species
GO:0042593 glucose homeostasis
GO:0050848 regulation of calcium-mediated signaling
GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:0045254 pyruvate dehydrogenase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6lio, PDBe:6lio, PDBj:6lio
PDBsum6lio
PubMed32444142
UniProtQ15119|PDK2_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (Gene Name=PDK2)

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