Structure of PDB 3dva Chain F Binding Site BS01

Receptor Information
>3dva Chain F (length=324) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGED
RVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARI
RYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTP
YDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKRE
GKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSV
EKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPF
AQAESVWLPNFKDVIETAKKVMNF
Ligand information
Ligand IDTPW
InChIInChI=1S/C13H19N3O7P2S/c1-8-11(5-10-6-15-9(2)16-13(10)14)7-26-12(8)3-4-22-25(20,21)23-24(17,18)19/h6-7H,3-5H2,1-2H3,(H,20,21)(H2,14,15,16)(H2,17,18,19)
InChIKeyIOGGWTLVIZLGGZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1scc(c1C)Cc2c(nc(nc2)C)N
CACTVS 3.341Cc1ncc(Cc2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
CACTVS 3.341Cc1ncc(Cc2csc(CCO[P@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(csc1CCOP(=O)(O)OP(=O)(O)O)Cc2cnc(nc2N)C
OpenEye OEToolkits 1.5.0Cc1c(csc1CCO[P@@](=O)(O)OP(=O)(O)O)Cc2cnc(nc2N)C
FormulaC13 H19 N3 O7 P2 S
Name2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE;
3-DEAZA-THDP
ChEMBLCHEMBL1236381
DrugBank
ZINCZINC000038653211
PDB chain3dva Chain G Residue 1370 [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]
PDB3dva Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex
Resolution2.35 Å
Binding residue
(original residue number in PDB)		L57 E59 F85
Binding residue
(residue number reindexed from 1)		L57 E59 F85
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E59 E88 H128
Catalytic site (residue number reindexed from 1) E59 E88 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

View graph for
Molecular Function
External links
PDB RCSB:3dva, PDBe:3dva, PDBj:3dva
PDBsum3dva
PubMed19081062
UniProtP21874|ODPB_GEOSE Pyruvate dehydrogenase E1 component subunit beta (Gene Name=pdhB)

[Back to BioLiP]