Structure of PDB 5euj Chain D Binding Site BS01

Receptor Information
>5euj Chain D (length=555) Species: 33074 (Zymobacter palmae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MYTVGMYLAERLAQIGLKHHFAVAGDYNLVLLDQLLLNKDMEQVYCCNEL
NCGFSAEGYARARGAAAAIVTFSVGAISAMNAIGGAYAENLPVILISGSP
NTNDYGTGHILHHTIGTTDYNYQLEMVKHVTCAAESIVSAEEAPAKIDHV
IRTALRERKPAYLEIACNVAGAECVRPGPINSLLRELEVDQTSVTAAVDA
AVEWLQDRQNVVMLVGSKLRAAAAEKQAVALADRLGCAVTIMAAAKGFFP
EDHPNFRGLYWGEVSSEGAQELVENADAILCLAPVFNDYATVGWNSWPKG
DNVMVMDTDRVTFAGQSFEGLSLSTFAAALAEKAPSRPATTQGTQAPVLG
IEAAEPNAPLTNDEMTRQIQSLITSDTTLTAETGDSWFNASRMPIPGGAR
VELEMQWGHIGWSVPSAFGNAVGSPERRHIMMVGDGSFQLTAQEVAQMIR
YEIPVIIFLINNRGYVIEIAIHDGPYNYIKNWNYAGLIDVFNDEDGHGLG
LKASTGAELEGAIKKALDNRRGPTLIECNIAQDDCTETLIAWGKRVAATN
SRKPQ
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 chain5euj Chain C Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5euj Crystal structure of pyruvate decarboxylase from Zymobacter palmae.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		A24 E49 V74
Binding residue
(residue number reindexed from 1)		A24 E49 V74
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G25 D26 Y27 N28 E49 T71 H112 H113 I115 G116 C167 E263 A290 E382 T383 G408 D435 N462 G464 I467 E468
Catalytic site (residue number reindexed from 1) G25 D26 Y27 N28 E49 T71 H112 H113 I115 G116 C167 E263 A290 E382 T383 G408 D435 N462 G464 I467 E468
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5euj, PDBe:5euj, PDBj:5euj
PDBsum5euj
PubMed27599861
UniProtQ8KTX6

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