SMTL ID : 6yrp.1

Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with JMV-4690 (Cpd 31)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 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: PJB.4 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: PJB.4 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.225 Ligands: ACT.8, ACT.9 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.225, ACT.8, ACT.9

1 x PJB: 2-[[[3-(5-methoxy-2-oxidanyl-phenyl)-5-sulfanylidene-1~{H}-1,2,4-triazol-4-yl]amino]methyl]benzoic acid(Non-covalent)

PJB.4: 17 residues within 4Å: Chain A: F.36, 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, DMS.10 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.41, A:W.61, A:H.214 Hydrogen bonds: A:D.91, A:N.184, A:N.184 Water bridges: A:Y.175, A:Y.175 Salt bridges: A:H.153, A:R.179 pi-Stacking: A:F.36, A:W.61, A:H.214

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: S.112, S.133, Y.148, T.155, D.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.112 EDO.6: 2 residues within 4Å: Chain A: E.120, G.121 No protein-ligand interaction detected (PLIP) EDO.7: 1 residues within 4Å: Chain A: G.121 No protein-ligand interaction detected (PLIP)

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

ACT.8: 5 residues within 4Å: Chain A: D.221, H.225, N.228 Ligands: ZN.3, ACT.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.225 ACT.9: 5 residues within 4Å: Chain A: T.180, H.225, N.228 Ligands: ZN.3, ACT.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.228 Hydrogen bonds: A:T.180 Salt bridges: A:H.225

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.10: 3 residues within 4Å: Chain A: Y.41, N.184 Ligands: PJB.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gavara, L. et al., 4-Amino-1,2,4-triazole-3-thione-derived Schiff bases as metallo-beta-lactamase inhibitors. Eur.J.Med.Chem. (2020)

Release Date

2020-09-30

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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