Structure of PDB 5j6a Chain A Binding Site BS01

Receptor Information
>5j6a Chain A (length=337) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASLAGAPKYIEHFSKFSPSPLSMKQFLDFGSCEKTSFTFLRQELPVRLAN
IMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFT
DALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRI
SIRMLINQHTLIFDHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDL
EIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPP
IKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTGFGYGLPISRLY
AKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPV
Ligand information
Ligand IDP46
InChIInChI=1S/C23H27N5O6S/c24-19(11-22(25)31)23(32)27-7-5-16(6-8-27)26-17-2-1-14-12-28(13-15(14)9-17)35(33,34)21-4-3-18(29)10-20(21)30/h1-4,9-10,12-13,16,19,26,29-30H,5-8,11,24H2,(H2,25,31)/t19-/m0/s1
InChIKeyHAMJZOUVHDEUSM-IBGZPJMESA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1(cc(c(cc1)S(=O)(=O)n3cc2cc(ccc2c3)NC4CCN(C(C(CC(=O)N)N)=O)CC4)O)O
OpenEye OEToolkits 2.0.4c1cc2cn(cc2cc1NC3CCN(CC3)C(=O)C(CC(=O)N)N)S(=O)(=O)c4ccc(cc4O)O
OpenEye OEToolkits 2.0.4c1cc2cn(cc2cc1NC3CCN(CC3)C(=O)[C@H](CC(=O)N)N)S(=O)(=O)c4ccc(cc4O)O
CACTVS 3.385N[CH](CC(N)=O)C(=O)N1CCC(CC1)Nc2ccc3cn(cc3c2)[S](=O)(=O)c4ccc(O)cc4O
CACTVS 3.385N[C@@H](CC(N)=O)C(=O)N1CCC(CC1)Nc2ccc3cn(cc3c2)[S](=O)(=O)c4ccc(O)cc4O
FormulaC23 H27 N5 O6 S
Name(3S)-3-amino-4-[4-({2-[(2,4-dihydroxyphenyl)sulfonyl]-2H-isoindol-5-yl}amino)piperidin-1-yl]-4-oxobutanamide
ChEMBL
DrugBank
ZINCZINC000584905678
PDB chain5j6a Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5j6a Development of Dihydroxyphenyl Sulfonylisoindoline Derivatives as Liver-Targeting Pyruvate Dehydrogenase Kinase Inhibitors.
Resolution2.045 Å
Binding residue
(original residue number in PDB)		N255 R258 A259 E262 S263 D290 G294 V295 T354
Binding residue
(residue number reindexed from 1)		N233 R236 A237 E240 S241 D268 G272 V273 T318
Annotation score1
Binding affinityMOAD: Kd=22nM
PDBbind-CN: -logKd/Ki=7.77,Kd=17nM
Enzymatic activity
Catalytic site (original residue number in PDB) H247 E251 K254 N255
Catalytic site (residue number reindexed from 1) H225 E229 K232 N233
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5j6a, PDBe:5j6a, PDBj:5j6a
PDBsum5j6a
PubMed28085286
UniProtQ15119|PDK2_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (Gene Name=PDK2)

[Back to BioLiP]