SMTL ID : 8hy2.1

Crystal structure of B1 VIM-2 MBL in complex with 2-amino-5-phenethylthiazole-4-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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.5 ZN.2: 5 residues within 4Å: Chain A: D.87, C.167, H.209 Ligands: ZN.1, 5ZX.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.5

1 x 5ZX: 2-azanyl-5-(2-phenylethyl)-1,3-thiazole-4-carboxylic acid(Non-covalent)

5ZX.3: 9 residues within 4Å: Chain A: Y.36, W.56, D.87, H.148, C.167, R.174, H.209 Ligands: ZN.2, FMT.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.36, A:Y.36, A:H.209 Hydrogen bonds: A:D.87 Water bridges: A:Y.170, A:Y.170, A:R.174, A:R.174, A:R.174 Salt bridges: A:H.148, A:R.174, A:H.209 pi-Cation interactions: A:H.209

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

FMT.4: 4 residues within 4Å: Chain A: H.85, D.86, D.87 Ligands: 5ZX.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.86, A:D.87 Water bridges: A:D.86 FMT.5: 5 residues within 4Å: Chain A: D.20, G.21, V.22, R.44, S.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.44, A:S.159 Water bridges: A:R.44 FMT.6: 3 residues within 4Å: Chain A: K.70, Q.71, I.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Y.H. et al., Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-beta-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding. J.Med.Chem. (2023)

Release Date

2023-11-01

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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