SMTL ID : 6jn6.1 (1 other biounit)

Metallo-Beta-Lactamase VIM-2 in complex with Dual MBL/SBL Inhibitor MS19

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.83, H.85, H.148 Ligands: ZN.2, BY0.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.83, A:H.85, A:H.148 ZN.2: 6 residues within 4Å: Chain A: D.87, R.88, C.167, H.209 Ligands: ZN.1, BY0.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.87, A:C.167, A:H.209 ZN.3: 3 residues within 4Å: Chain A: H.220 Ligands: FMT.6, FMT.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.220

1 x BY0: [(1S)-2-(1-benzofuran-3-yl)-1-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethyl]boronic acid(Non-covalent)

BY0.4: 12 residues within 4Å: Chain A: F.31, W.56, H.83, H.85, D.87, H.148, R.174, N.179, H.209 Ligands: ZN.1, ZN.2, FMT.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.31, A:W.56 Hydrogen bonds: A:R.174, A:R.174, A:N.179 pi-Stacking: A:F.31, A:F.31

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

FMT.5: 7 residues within 4Å: Chain A: H.148, Y.170, R.174, G.178, N.179, H.209 Ligands: BY0.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.179 FMT.6: 4 residues within 4Å: Chain A: H.220, N.223 Ligands: ZN.3, FMT.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.223 FMT.7: 4 residues within 4Å: Chain A: H.220, N.223 Ligands: ZN.3, FMT.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y.L. et al., Structure-Based Development of (1-(3'-Mercaptopropanamido)methyl)boronic Acid Derived Broad-Spectrum, Dual-Action Inhibitors of Metallo- and Serine-beta-lactamases. J.Med.Chem. (2019)

Release Date

2019-07-17

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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