Structure of PDB 1zpd Chain B Binding Site BS01

Receptor Information
>1zpd Chain B (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
IKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVDE
TLKFIANRDKVAVLVGSKLRAAGAEEAAVKFTDALGGAVATMAAAKSFFP
EENALYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDP
KKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGSLDFFKSLNAG
ELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLP
NGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVA
QMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAGLMEVFNGNGG
YDSGAAKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKW
GKRVAAANSRKPVNK
Ligand information
Ligand IDDPX
InChIInChI=1S/C11H20N4O8P2S/c1-6(13-3-8-4-14-7(2)15-11(8)12)10(26)9(16)5-22-25(20,21)23-24(17,18)19/h4,9,13,16,26H,3,5H2,1-2H3,(H,20,21)(H2,12,14,15)(H2,17,18,19)/b10-6-/t9-/m1/s1
InChIKeyXHCFSNVIKLFNIT-WPVMNKCKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C\C(NCc1cnc(C)nc1N)=C(S)/[C@H](O)CO[P@@](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.5.0Cc1ncc(c(n1)N)CN/C(=C(/[C@@H](CO[P@](=O)(O)OP(=O)(O)O)O)\S)/C
CACTVS 3.341CC(NCc1cnc(C)nc1N)=C(S)[CH](O)CO[P](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC(O)C(/S)=C(/NCc1cnc(nc1N)C)C
OpenEye OEToolkits 1.5.0Cc1ncc(c(n1)N)CNC(=C(C(COP(=O)(O)OP(=O)(O)O)O)S)C
FormulaC11 H20 N4 O8 P2 S
NameMONO-{4-[(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-AMINO]-2-HYDROXY-3-MERCAPTO-PENT-3-ENYL-PHOSPHONO} ESTER
ChEMBL
DrugBank
ZINCZINC000103539480
PDB chain1zpd Chain A Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1zpd High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis. Implications for substrate activation in pyruvate decarboxylases.
Resolution1.86 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) D27 Y28 E50 Y73 H113 H114 L116 G117 C168 Y290 T388 G413 I415 D440 N467 G469 I472 E473
Catalytic site (residue number reindexed from 1) D26 Y27 E49 Y72 H112 H113 L115 G116 C167 Y289 T387 G412 I414 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1zpd, PDBe:1zpd, PDBj:1zpd
PDBsum1zpd
PubMed9685367
UniProtP06672|PDC_ZYMMO Pyruvate decarboxylase (Gene Name=pdc)

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