SMTL ID : 8a4m.1

Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in complex with compound 8 (JMV-7061)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.88, H.90, D.92, H.153 Ligands: L2R.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.88, A:H.90, A:H.153 ZN.2: 5 residues within 4Å: Chain A: D.92, R.93, C.172, H.214 Ligands: L2R.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.92, A:C.172, A:H.214 ZN.3: 3 residues within 4Å: Chain A: H.127 Ligands: ACT.4, ACT.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.127, ACT.5

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 8 residues within 4Å: Chain A: R.101, V.105, A.106, T.107, T.126, H.127 Ligands: ZN.3, ACT.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.101, A:T.126 Hydrogen bonds: A:T.107 Water bridges: A:T.126 Salt bridges: A:H.127 ACT.5: 4 residues within 4Å: Chain A: A.106, H.127 Ligands: ZN.3, ACT.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.106 Salt bridges: A:H.127

1 x L2R: (2~{S})-2-[bis(1~{H}-imidazol-4-ylmethyl)amino]-5-(3-phenyl-5-sulfanylidene-1~{H}-1,2,4-triazol-4-yl)pentanoic acid(Non-covalent)

L2R.6: 14 residues within 4Å: Chain A: Y.41, W.61, H.88, H.90, D.91, D.92, H.153, C.172, R.179, G.183, N.184, H.214 Ligands: ZN.1, ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.91 Hydrogen bonds: A:N.184 Salt bridges: A:R.179 pi-Stacking: A:W.61, A:W.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Legru, A. et al., Optimization of 1,2,4-Triazole-3-thiones toward Broad-Spectrum Metallo-beta-lactamase Inhibitors Showing Potent Synergistic Activity on VIM- and NDM-1-Producing Clinical Isolates. J.Med.Chem. (2022)

Release Date

2023-04-26

Peptides

Metallo-beta-lactamase VIM-2-like protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase VIM-2-like protein

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