Structure of PDB 3duf Chain E Binding Site BS02

Receptor Information
>3duf Chain E (length=365) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRM
VYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYR
DVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAG
VALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNR
FAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAI
NGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFL
EAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPF
NLKEQYEIYKEKESK
Ligand information
Ligand IDR1T
InChIInChI=1S/C15H23N3O8P2S/c1-8-12(6-11-7-17-10(3)18-15(11)16)14(9(2)19)29-13(8)4-5-25-28(23,24)26-27(20,21)22/h7,9,19H,4-6H2,1-3H3,(H,23,24)(H2,16,17,18)(H2,20,21,22)/t9-/m1/s1
InChIKeyORVRYSKZCUVOLA-SECBINFHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(sc(c1Cc2cnc(nc2N)C)C(C)O)CCOP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc(c1Cc2cnc(nc2N)C)[C@@H](C)O)CCO[P@](=O)(O)OP(=O)(O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc(c(c1C)Cc2cnc(nc2N)C)C(O)C
CACTVS 3.341C[CH](O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)c1Cc2cnc(C)nc2N
CACTVS 3.341C[C@@H](O)c1sc(CCO[P@@](O)(=O)O[P](O)(O)=O)c(C)c1Cc2cnc(C)nc2N
FormulaC15 H23 N3 O8 P2 S
Name2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE;
2-[(1R)-1-HYDROXYETHYL]-3-DEAZA-THDP
ChEMBL
DrugBank
ZINCZINC000016052593
PDB chain3duf Chain E Residue 1370 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3duf Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y102 R103 I142 I144 G172 D173 G174 F204 I206 H271
Binding residue
(residue number reindexed from 1)		Y99 R100 I139 I141 G169 D170 G171 F201 I203 H268
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S65 I143
Catalytic site (residue number reindexed from 1) S62 I140
Enzyme Commision number 1.2.4.1: pyruvate dehydrogenase (acetyl-transferring).
Gene Ontology
Molecular Function
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
Biological Process
GO:0009083 branched-chain amino acid catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3duf, PDBe:3duf, PDBj:3duf
PDBsum3duf
PubMed19081062
UniProtP21873|ODPA_GEOSE Pyruvate dehydrogenase E1 component subunit alpha (Gene Name=pdhA)

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