SMTL ID : 7dv0.1

Crystal structure of VIM-2 MBL in complex with 1-(4-(trifluoromethyl)benzyl)-1H-imidazole-2-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.83, H.85, D.87, H.148 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.83, A:H.85, A:H.148, H2O.1 ZN.2: 6 residues within 4Å: Chain A: D.87, R.88, C.167, H.209 Ligands: ZN.1, HML.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.87, A:C.167, A:H.209, H2O.1

1 x HML: 1-[[4-(trifluoromethyl)phenyl]methyl]imidazole-2-carboxylic acid(Non-covalent)

HML.3: 11 residues within 4Å: Chain A: F.31, Y.36, P.37, W.56, D.87, H.148, C.167, E.171, R.174, H.209 Ligands: ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.36, A:Y.36, A:H.209 Water bridges: A:R.174, A:R.174, A:R.174 Salt bridges: A:H.148, A:R.174, A:H.209 pi-Stacking: A:F.31, A:H.209

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: D.20, G.21, V.22, V.43, R.44, P.138, S.159 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.20, A:R.44, A:R.44, A:S.159 Water bridges: A:P.138, A:S.159 GOL.5: 3 residues within 4Å: Chain A: P.75, V.76, A.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.76 Water bridges: A:L.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Y.H. et al., Structure-guided optimization of 1H-imidazole-2-carboxylic acid derivatives affording potent VIM-Type metallo-beta-lactamase inhibitors. Eur.J.Med.Chem. (2022)

Release Date

2022-01-19

Peptides

Beta-lactamase class B VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase class B VIM-2

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