SMTL ID : 7due.1 (1 other biounit)

Crystal structure of VIM-2 MBL in complex with (R)-1-(sec-butyl)-1H-imidazole-2-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: 5 residues within 4Å: Chain A: D.87, C.167, H.209 Ligands: ZN.1, HL3.4 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 HL3: 1-[(2~{R})-butan-2-yl]imidazole-2-carboxylic acid(Non-covalent)

HL3.4: 10 residues within 4Å: Chain A: Y.36, W.56, D.87, H.148, C.167, R.174, G.178, N.179, H.209 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.36 Hydrogen bonds: A:N.179 Water bridges: A:G.178 Salt bridges: A:H.148, A:H.209 pi-Stacking: A:H.209

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

FMT.5: 5 residues within 4Å: Chain A: T.175, H.220, N.223 Ligands: ZN.3, FMT.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.223 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

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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