SMTL ID : 5mxr.1

Crystal Structure of the Acquired VIM-2 Metallo-beta-Lactamase in Complex with ANT-330 Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 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, JTY.5 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.122 Ligands: ACT.4, JTY.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.122, ACT.4

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 8 residues within 4Å: Chain A: R.96, V.100, A.101, T.102, T.121, H.122 Ligands: ZN.3, JTY.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.96, A:T.121 Hydrogen bonds: A:T.102, A:T.121 Salt bridges: A:H.122

2 x JTY: 5-(phenylsulfonylamino)-1,3-thiazole-4-carboxylic acid(Non-covalent)

JTY.5: 11 residues within 4Å: Chain A: F.31, Y.36, W.56, D.87, H.148, C.167, R.174, G.178, N.179, H.209 Ligands: ZN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.31, A:N.179 Hydrogen bonds: A:R.174, A:N.179 Water bridges: A:R.174, A:R.174 Salt bridges: A:H.148, A:R.174, A:H.209 pi-Stacking: A:Y.36 JTY.6: 6 residues within 4Å: Chain A: T.77, G.99, A.101, H.122 Ligands: ZN.3, ACT.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leiris, S. et al., SAR Studies Leading to the Identification of a Novel Series of Metallo-beta-lactamase Inhibitors for the Treatment of Carbapenem-Resistant Enterobacteriaceae Infections That Display Efficacy in an Animal Infection Model. Acs Infect Dis. (2019)

Release Date

2018-03-14

Peptides

Beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase VIM-2

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