Structure of PDB 2wva Chain Z Binding Site BS01

Receptor Information
>2wva Chain Z (length=565) Species: 542 (Zymomonas mobilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNEL
NCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAP
NNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHV
IKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEE
TLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFP
EENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDP
KKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAG
ELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLP
NGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVA
QMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAGLMEVFNGNGG
YDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKW
GKRVAAANSRKPVNK
Ligand information
Ligand IDTPU
InChIInChI=1S/C11H18N6O7P2/c1-7-10(3-4-23-26(21,22)24-25(18,19)20)15-16-17(7)6-9-5-13-8(2)14-11(9)12/h5H,3-4,6H2,1-2H3,(H,21,22)(H2,12,13,14)(H2,18,19,20)
InChIKeyWHMXQEYVWLIXHH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(OCCc1nnn(c1C)Cc2cnc(nc2N)C)O
OpenEye OEToolkits 1.6.1Cc1c(nnn1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.6.1Cc1c(nnn1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.352Cc1ncc(Cn2nnc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
FormulaC11 H18 N6 O7 P2
Name2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000035299603
PDB chain2wva Chain V Residue 600 [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]
PDB2wva Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase from Zymomonas Mobilis
Resolution2.2 Å
Binding residue
(original residue number in PDB)		A25 E50 V75 H114
Binding residue
(residue number reindexed from 1)		A24 E49 V74 H113
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.70,Kd=20pM
Enzymatic activity
Catalytic site (original residue number in PDB) L116 G117 T388 G413 D440 N467 G469 I472 E473
Catalytic site (residue number reindexed from 1) L115 G116 T387 G412 D439 N466 G468 I471 E472
Enzyme Commision number 4.1.1.1: pyruvate decarboxylase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004737 pyruvate decarboxylase activity
GO:0016831 carboxy-lyase activity
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
Biological Process
GO:0000949 aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
GO:0019752 carboxylic acid metabolic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2wva, PDBe:2wva, PDBj:2wva
PDBsum2wva
PubMed20099870
UniProtP06672|PDC_ZYMMO Pyruvate decarboxylase (Gene Name=pdc)

[Back to BioLiP]