SMTL ID : 5le1.1

VIM-2 metallo-beta-lactamase in complex with 2-(2-chloro-6-fluorobenzyl)-3-oxoisoindoline-4-carboxylic acid (compound 16)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.118, R.119, C.198, H.240 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.118, A:C.198, A:H.240, H2O.1, H2O.5 ZN.2: 6 residues within 4Å: Chain A: H.114, H.116, D.118, H.179 Ligands: ZN.1, 6UW.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.114, A:H.116, A:H.179, H2O.5

1 x 6UW: 2-[(2-chloranyl-6-fluoranyl-phenyl)methyl]-3-oxidanylidene-1~{H}-isoindole-4-carboxylic acid(Non-covalent)

6UW.3: 12 residues within 4Å: Chain A: F.62, Y.67, W.87, H.116, D.117, D.118, H.179, G.209, N.210, H.240 Ligands: ZN.2, GOL.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.62, A:F.62, A:Y.67, A:W.87 Hydrogen bonds: A:N.210, A:N.210 Water bridges: A:H.179 Salt bridges: A:H.179 pi-Stacking: A:F.62, A:H.240 Halogen bonds: A:N.210

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

FMT.4: 3 residues within 4Å: Chain A: S.138, R.141, L.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.141

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: Y.67, P.68, E.202, R.205, H.240 Ligands: 6UW.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.202, A:R.205 GOL.6: 7 residues within 4Å: Chain A: D.51, G.52, V.53, V.74, R.75, P.169, S.190 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.51, A:R.75, A:R.75, A:S.190 Water bridges: A:P.169, A:S.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, G.B. et al., NMR-filtered virtual screening leads to non-metal chelating metallo-beta-lactamase inhibitors. Chem Sci (2017)

Release Date

2017-02-15

Peptides

Metallo-beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase VIM-2

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