Structure of PDB 1jm6 Chain A Binding Site BS01

Receptor Information
>1jm6 Chain A (length=339) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASLAGAPKYIEHFSKFSPSPLSMKQFLDFGACEKTSFTFLRQELPVRLAN
IMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFT
DALVTIRNRHNDVVPTMAQGVLEYDPVSNQNIQYFLDRFYLSRISIRMLI
NQHTLIFDPKHIGSIDPNCSVSDVVKDAYDMAKLLCDKYYMASPDLEIQE
VNATNATQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLTLPPIKIM
VALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPAGFGYGLPISRL
YAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVY
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain1jm6 Chain A Residue 3500 [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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PDB1jm6 Structure of pyruvate dehydrogenase kinase. Novel folding pattern for a serine protein kinase.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		N1247 V1287 L1295 S1301 T1302 G1317 F1318 G1319 G1321 L1322
Binding residue
(residue number reindexed from 1)		N229 V269 L277 S283 T284 G290 F291 G292 G294 L295
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H1239 E1243 K1246 N1247
Catalytic site (residue number reindexed from 1) H221 E225 K228 N229
Enzyme Commision number 2.7.11.2: [pyruvate dehydrogenase (acetyl-transferring)] kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004740 pyruvate dehydrogenase (acetyl-transferring) kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0044877 protein-containing complex binding
Biological 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:0018105 peptidyl-serine 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:0005739 mitochondrion
GO:0005759 mitochondrial matrix
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:1jm6, PDBe:1jm6, PDBj:1jm6
PDBsum1jm6
PubMed11483605
UniProtQ64536|PDK2_RAT [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (Gene Name=Pdk2)

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