Structure of PDB 3exe Chain A Binding Site BS02

Receptor Information
>3exe Chain A (length=363) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQTVRRMELK
ADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTR
GLSVREILAELTGRKGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGI
ALACKYNGKDEVCLTLYGDGAANQGQIFEAYNMAALWKLPCIFICENNRY
GMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGK
GPILMELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNS
NLASVEELKEIDVEVRKEIEDAAQFATADPEPPLEELGYHIYSSDPPFEV
RGANQWIKFKSVS
Ligand information
Ligand IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain3exe Chain A Residue 1005 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3exe Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.
Resolution1.979 Å
Binding residue
(original residue number in PDB)		Y89 R90 V138 G166 D167 G168 A169 N196 Y198 G199 H263
Binding residue
(residue number reindexed from 1)		Y91 R92 V140 G168 D169 G170 A171 N198 Y200 G201 H265
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q51 G136 R259 H263 S264 Y272
Catalytic site (residue number reindexed from 1) Q53 G138 R261 H265 S266 Y274
Enzyme Commision number 1.2.4.1: pyruvate dehydrogenase (acetyl-transferring).
Gene Ontology
Molecular Function
GO:0004738 pyruvate dehydrogenase activity
GO:0004739 pyruvate dehydrogenase (acetyl-transferring) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
GO:0034604 pyruvate dehydrogenase (NAD+) activity
GO:0046872 metal ion binding
Biological Process
GO:0006006 glucose metabolic process
GO:0006086 acetyl-CoA biosynthetic process from pyruvate
GO:0006090 pyruvate metabolic process
GO:0006099 tricarboxylic acid cycle
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0043231 intracellular membrane-bounded organelle
GO:0045254 pyruvate dehydrogenase complex
GO:1902494 catalytic complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3exe, PDBe:3exe, PDBj:3exe
PDBsum3exe
PubMed19081061
UniProtP08559|ODPA_HUMAN Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (Gene Name=PDHA1)

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