SMTL ID : 5mxq.1

Crystal Structure of the Acquired VIM-2 Metallo-beta-Lactamase in Complex with ANT-90 Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.220 Ligands: ACT.6, ACT.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.220, ACT.6, ACT.7 ZN.2: 5 residues within 4Å: Chain A: H.83, H.85, D.87, H.148 Ligands: ZN.3 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.3: 6 residues within 4Å: Chain A: D.87, R.88, C.167, H.209 Ligands: ZN.2, U8K.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

1 x U8K: 3-(phenylsulfonylamino)pyridine-2-carboxylic acid(Covalent)

U8K.4: 12 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.3, CL.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.31, A:W.56 Hydrogen bonds: A:N.179 Water bridges: A:R.174, A:R.174, A:R.174, A:R.174, A:N.179 Salt bridges: A:H.148, A:R.174, A:H.209 pi-Stacking: A:Y.36

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: Y.36, W.56 Ligands: U8K.4 Ligand excluded by PLIP

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

ACT.6: 5 residues within 4Å: Chain A: T.175, H.220, N.223 Ligands: ZN.1, ACT.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.223 Hydrogen bonds: A:N.223 Salt bridges: A:H.220 ACT.7: 6 residues within 4Å: Chain A: D.216, K.219, H.220, N.223 Ligands: ZN.1, ACT.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.219 Hydrogen bonds: A:N.223 Salt bridges: A:H.220

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

2018-02-28

Peptides

Beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase VIM-2

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