Structure of PDB 6cfo Chain B Binding Site BS01

Receptor Information
>6cfo Chain B (length=330) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLQVTVRDAINQGMDEELERDEKVFLLGEEVAQYDGAYKVSRGLWKKYGD
KRIIDTPISEMGFAGIAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAK
TYYMSGGLQPVPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWN
SEDAKGLIKSAIRDNNPVVVLENELMYGVPFEFPPEAQSKDFLIPIGKAK
IERQGTHITVVSHSRPVGHCLEAAAVLSKEGVECEVINMRTIRPMDMETI
EASVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGAD
VPMPYAKILEDNSIPQVKDIIFAIKKTLNI
Ligand information
Ligand IDA5X
InChIInChI=1S/C14H23N4O10P3S/c1-8-11(4-5-27-31(25,26)28-30(22,23)24)32-13(14(3,19)29(20)21)18(8)7-10-6-16-9(2)17-12(10)15/h6,19,29H,4-5,7H2,1-3H3,(H5-,15,16,17,20,21,22,23,24,25,26)/p+1/t14-/m0/s1
InChIKeyCAOFPOCACDCAFN-AWEZNQCLSA-O
SMILES
SoftwareSMILES
ACDLabs 12.01OP(=O)(O)OP(OCCc1c([n+](c(s1)C(P(O)=O)(C)O)Cc2cnc(nc2N)C)C)(O)=O
CACTVS 3.385Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@@](C)(O)[PH](O)=O)c(N)n1
CACTVS 3.385Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C](C)(O)[PH](O)=O)c(N)n1
OpenEye OEToolkits 2.0.6Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)(O)P(=O)O)CCOP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 2.0.6Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)P(=O)O)CCOP(=O)(O)OP(=O)(O)O
FormulaC14 H24 N4 O10 P3 S
Name3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-hydroxy-1-[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]ethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
ChEMBL
DrugBank
ZINC
PDB chain6cfo Chain C Residue 401 [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]
PDB6cfo Pyruvate dehydrogenase complex deficiency is linked to regulatory loop disorder in the alpha V138M variant of human pyruvate dehydrogenase.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		E28 I57 E59 F85 Q88
Binding residue
(residue number reindexed from 1)		E29 I58 E60 F86 Q89
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E59 H128
Catalytic site (residue number reindexed from 1) E60 H129
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6cfo, PDBe:6cfo, PDBj:6cfo
PDBsum6cfo
PubMed29970614
UniProtP11177|ODPB_HUMAN Pyruvate dehydrogenase E1 component subunit beta, mitochondrial (Gene Name=PDHB)

[Back to BioLiP]