Structure of PDB 2vbi Chain B Binding Site BS01

Receptor Information
>2vbi Chain B (length=554) Species: 438 (Acetobacter pasteurianus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TYTVGMYLAERLVQIGLKHHFAVAGDYNLVLLDQLLLNKDMKQIYCCNEL
NCGFSAEGYARSNGAAAAVVTFSVGAISAMNALGGAYAENLPVILISGAP
NSNDQGTGHILHHTIGKTDYSYQLEMARQVTCAAESITDAHSAPAKIDHV
IRTALRERKPAYLDIACNIASEPCVRPGPVSSLLSEPEIDHTSLKAAVDA
TVALLEKSASPVMLLGSKLRAANALAATETLADKLQCAVTIMAAAKGFFP
EDHAGFRGLYWGEVSNPGVQELVETSDALLCIAPVFNDYSTVGWSAWPKG
PNVILAEPDRVTVDGRAYDGFTLRAFLQALAEKAPARPASAQKSSVPTCS
LTATSDEAGLTNDEIVRHINALLTSNTTLVAETGDSWFNAMRMTLPRGAR
VELEMQWGHIGWSVPSAFGNAMGSQDRQHVVMVGDGSFQLTAQEVAQMVR
YELPVIIFLINNRGYVIEIAIHDGPYNYIKNWDYAGLMEVFNAGEGHGLG
LKATTPKELTEAIARAKANTRGPTLIECQIDRTDCTDMLVQWGRKVASTN
ARKT
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 chain2vbi Chain A Residue 2000 [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]
PDB2vbi ?
Resolution2.75 Å
Binding residue
(original residue number in PDB)		A25 E50 V75
Binding residue
(residue number reindexed from 1)		A24 E49 V74
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G26 D27 Y28 N29 E50 T72 H113 H114 I116 G117 C168 S291 T384 G409 I411 D436 N463 G465 Y466 I468 E469 R533
Catalytic site (residue number reindexed from 1) G25 D26 Y27 N28 E49 T71 H112 H113 I115 G116 C167 S290 T383 G408 I410 D435 N462 G464 Y465 I467 E468 R532
Enzyme Commision number 4.1.1.1: pyruvate decarboxylase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0016831 carboxy-lyase activity
GO:0030976 thiamine pyrophosphate binding

View graph for
Molecular Function
External links
PDB RCSB:2vbi, PDBe:2vbi, PDBj:2vbi
PDBsum2vbi
PubMed
UniProtQ8L388

[Back to BioLiP]