Structure of PDB 4cok Chain B Binding Site BS02

Receptor Information
>4cok Chain B (length=549) Species: 272568 (Gluconacetobacter diazotrophicus PA1 5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTYTVGRYLADRLAQIGLKHHFAVAGDYNLVLLDQLLLNTDMQQIYCSNE
LNCGFSAEGYARANGAAAAIVTFSVGALSAFNALGGAYAENLPVILISGA
PNANDHGTGHILHHTLGTTDYGYQLEMARHITCAAESIVAAEDAPAKIDH
VIRTALREKKPAYLEIACNVAGAPCVRPGGIDADEASLKAAVDAALAFIE
QRGSVTMLVGSRIRAAGAQAQAVALADALGCAVTTMAAAKSFFPEDHPGY
RGHYWGEVSSPGAQQAVEGADGVICLAPVFNDYATVGWSAWPKGDNVMLV
ERHAVTVGGVAYAGIDMRDFLTRLAAHTVRRDATARGGAYVTPQTPAAAP
TAPLNNAEMARQIGALLTPRTTLTAETGDSWFNAVRMKLPHGARVELEMQ
WGHIGWSVPAAFGNALAAPERQHVLMVGDGSFQLTAQEVAQMIRHDLPVI
IFLINNHGYTIEVMIHDGPYNNVKNWDYAGLMEVFNAGEGNGLGLRARTG
GELAAAIEQARANRNGPTLIECTLDRDDCTQELVTWGKRVAAANARPPR
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 chain4cok Chain B Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4cok Structure and Functional Characterization of Pyruvate Decarboxylase from Gluconacetobacter Diazotrophicus.
Resolution1.69 Å
Binding residue
(original residue number in PDB)		D386 G409 H410 I411 G435 G437 S438 N463 G465 Y466 T467 I468 E469
Binding residue
(residue number reindexed from 1)		D379 G402 H403 I404 G428 G430 S431 N456 G458 Y459 T460 I461 E462
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G26 D27 Y28 N29 E50 T72 H113 H114 L116 G117 C168 A291 E383 T384 G409 I411 D436 N463 G465 I468 E469 R533
Catalytic site (residue number reindexed from 1) G26 D27 Y28 N29 E50 T72 H113 H114 L116 G117 C168 A284 E376 T377 G402 I404 D429 N456 G458 I461 E462 R526
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:4cok, PDBe:4cok, PDBj:4cok
PDBsum4cok
PubMed25369873
UniProtA9H275

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