SMTL ID : 7ovh.1

Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in Complex with compound 14 (JMV-6931)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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: UNL.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: UNL.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 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.127, ACT.4, 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, 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 UNL: UNKNOWN LIGAND

UNL.6: 13 residues within 4Å: Chain A: F.36, Y.41, W.61, H.88, H.90, D.91, D.92, H.153, C.172, 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 pi-Stacking: A:F.36, A:W.61, A:W.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Legru, A. et al., 1,2,4-Triazole-3-thione compounds with a 4-ethyl alkyl/aryl sulfide substituent are broad-spectrum metallo-beta-lactamase inhibitors with re-sensitization activity. Eur.J.Med.Chem. (2021)

Release Date

2021-10-20

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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