SMTL ID : 5k48.2 (1 other biounit)

VIM-2 Metallo Beta Lactamase in complex with 3-(mercaptomethyl)-[1,1'-biphenyl]-4-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x S5Z: 4-phenyl-2-(sulfanylmethyl)benzoic acid(Non-covalent)

S5Z.1: 12 residues within 4Å: Chain A: F.38, Y.43, W.63, H.92, D.94, H.155, C.174, R.181, N.186, H.216 Ligands: ZN.4, ZN.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.43, A:W.63 Hydrogen bonds: A:D.93 Water bridges: A:N.186 Salt bridges: A:H.92 pi-Stacking: A:F.38, A:Y.43, A:H.216

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

FMT.2: 4 residues within 4Å: Chain A: A.108, H.129 Ligands: FMT.3, ZN.6 No protein-ligand interaction detected (PLIP) FMT.3: 7 residues within 4Å: Chain A: V.107, A.108, T.109, T.128, H.129 Ligands: FMT.2, ZN.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.109 Water bridges: A:T.128

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: H.90, H.92, H.155 Ligands: S5Z.1, ZN.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:H.92, A:H.155 ZN.5: 6 residues within 4Å: Chain A: D.94, R.95, C.174, H.216 Ligands: S5Z.1, ZN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:C.174, A:H.216 ZN.6: 3 residues within 4Å: Chain A: H.129 Ligands: FMT.2, FMT.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cain, R. et al., In Silico Fragment-Based Design Identifies Subfamily B1 Metallo-beta-lactamase Inhibitors. J. Med. Chem. (2018)

Release Date

2017-06-07

Peptides

Beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Beta-lactamase VIM-2

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