SMTL ID : 7pp0.1

Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in complex with compound 28 (JMV-7038)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.88, H.90, H.153 Ligands: 7ZN.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: 7ZN.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 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.127

1 x 7ZN: 2-[2-[3-[3-(2-morpholin-4-ylethoxy)phenyl]-5-sulfanylidene-1H-1,2,4-triazol-4-yl]ethyl]benzoic acid(Non-covalent)

7ZN.6: 15 residues within 4Å: Chain A: Y.41, W.61, H.88, H.90, D.91, D.92, H.153, C.172, Y.175, R.179, G.183, N.184, H.214 Ligands: ZN.1, ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.41, A:W.61, A:H.214 Hydrogen bonds: A:N.184 Water bridges: A:D.91, A:G.183, A:G.183, A:N.184, A:N.184 Salt bridges: A:H.153 pi-Stacking: A:W.61, A:H.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Verdirosa, F. et al., 1,2,4-Triazole-3-Thione Analogues with a 2-Ethylbenzoic Acid at Position 4 as VIM-type Metallo-beta-Lactamase Inhibitors. Chemmedchem (2022)

Release Date

2022-03-16

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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