SMTL ID : 5y6d.1 (3 other biounits)

VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-fluorophenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 11)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.87, R.88, C.167, H.209 Ligands: ZN.2, 8PL.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.87, A:C.167, A:H.209 ZN.2: 6 residues within 4Å: Chain A: H.83, H.85, D.87, H.148 Ligands: ZN.1, 8PL.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.83, A:H.85, A:H.148 ZN.3: 1 residues within 4Å: Chain A: D.47 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.47, H2O.1, H2O.2, H2O.4

1 x 8PL: (2R)-2-(4-fluorophenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic acid(Non-covalent)

8PL.4: 15 residues within 4Å: Chain A: F.31, Y.36, W.56, H.83, H.85, D.87, H.148, C.167, Y.170, R.174, G.178, N.179, H.209 Ligands: ZN.1, ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.31, A:Y.36, A:Y.36, A:W.56 Hydrogen bonds: A:N.179, 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:H.209

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

FMT.5: 2 residues within 4Å: Chain A: R.96, T.121 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., ((S)-3-Mercapto-2-methylpropanamido)acetic acid derivatives as metallo-beta-lactamase inhibitors: Synthesis, kinetic and crystallographic studies. Eur J Med Chem (2018)

Release Date

2018-01-24

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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