Structure of PDB 1vgn Chain B Binding Site BS03

Receptor Information
>1vgn Chain B (length=218) Species: 615 (Serratia marcescens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTA
KDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTN
ELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKI
LFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDA
SLLKLTLEQAVKGLNESK
Ligand information
Ligand IDOPS
InChIInChI=1S/C6H10O2S2/c7-3-1-5-10-6(8)2-4-9/h3,9H,1-2,4-5H2/p-1
InChIKeyLHLHVBHXBHTTIV-UHFFFAOYSA-M
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(SCCC=O)CC[S-]
OpenEye OEToolkits 1.5.0C(CSC(=O)CC[S-])C=O
CACTVS 3.341[S-]CCC(=O)SCCC=O
FormulaC6 H9 O2 S2
Name3-OXO-3-[(3-OXOPROPYL)SULFANYL]PROPANE-1-THIOLATE;
2-(3-OXO-PROPYLSULFANYLCARBONYL)-ETHANETHIOLATE
ChEMBL
DrugBankDB04749
ZINC
PDB chain1vgn Chain B Residue 1161 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1vgn Irreversible Inhibition of Metallo-beta-lactamase (IMP-1) by 3-(3-Mercaptopropionylsulfanyl)propionic Acid Pentafluorophenyl Ester
Resolution2.63 Å
Binding residue
(original residue number in PDB)		D81 H139 K161 N167 H197
Binding residue
(residue number reindexed from 1)		D78 H136 K158 N164 H194
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H77 H79 D81 H139 C158 K161 N167 H197
Catalytic site (residue number reindexed from 1) H74 H76 D78 H136 C155 K158 N164 H194
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0017001 antibiotic catabolic process
GO:0046677 response to antibiotic
Cellular Component
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1vgn, PDBe:1vgn, PDBj:1vgn
PDBsum1vgn
PubMed15892033
UniProtP52699|BLAB_SERMA Metallo-beta-lactamase type 2

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