SMTL ID : 7chv.1

Metallo-Beta-Lactamase VIM-2 in complex with 1-benzyl-1H-imidazole-2-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

3 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, FZX.4 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 ZN.3: 3 residues within 4Å: Chain A: H.220 Ligands: FMT.5, FMT.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.220

1 x FZX: 1-(phenylmethyl)imidazole-2-carboxylic acid(Non-covalent)

FZX.4: 8 residues within 4Å: Chain A: Y.36, W.56, D.87, H.148, C.167, R.174, H.209 Ligands: ZN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.36 Water bridges: A:Y.170 Salt bridges: A:H.148, A:R.174, A:H.209 pi-Stacking: A:Y.36 pi-Cation interactions: A:H.209

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 4 residues within 4Å: Chain A: T.175, H.220 Ligands: ZN.3, FMT.6 No protein-ligand interaction detected (PLIP) FMT.6: 4 residues within 4Å: Chain A: H.220, N.223 Ligands: ZN.3, FMT.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, Q. et al., AncPhore: A versatile tool for anchor pharmacophore steered drug discovery with applications in discovery of new inhibitors targeting metallo-beta-lactamases and indoleamine/tryptophan 2,3-dioxygenases. Acta Pharm Sin B (2021)

Release Date

2021-07-14

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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