Structure of PDB 3exf Chain D Binding Site BS01

Receptor Information
>3exf Chain D (length=329) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LQVTVRDAINQGMDEELERDEKVFLLGEEVAQYDGAYKVSRGLWKKYGDK
RIIDTPISEMGFAGIAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAKT
YYMSGGLQPVPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNS
EDAKGLIKSAIRDNNPVVVLENELMYGVPFEFPPEAQSKDFLIPIGKAKI
ERQGTHITVVSHSRPVGHCLEAAAVLSKEGVECEVINMRTIRPMDMETIE
ASVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGADV
PMPYAKILEDNSIPQVKDIIFAIKKTLNI
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 chain3exf Chain A Residue 1003 [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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PDB3exf Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.
Resolution2.998 Å
Binding residue
(original residue number in PDB)		E28 I57 E59 F85 Q88
Binding residue
(residue number reindexed from 1)		E28 I57 E59 F85 Q88
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.54,Kd=0.29uM
Enzymatic activity
Catalytic site (original residue number in PDB) E59 H128
Catalytic site (residue number reindexed from 1) E59 H128
Enzyme Commision number 1.2.4.1: pyruvate dehydrogenase (acetyl-transferring).
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004739 pyruvate dehydrogenase (acetyl-transferring) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
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:0006099 tricarboxylic acid cycle
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
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:3exf, PDBe:3exf, PDBj:3exf
PDBsum3exf
PubMed19081061
UniProtP11177|ODPB_HUMAN Pyruvate dehydrogenase E1 component subunit beta, mitochondrial (Gene Name=PDHB)

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