SMTL ID : 6j8r.1

Metallo-Beta-Lactamase VIM-2 in complex with Dual MBL/SBL Inhibitor MS01

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.83, H.85, D.87, H.148 Ligands: ZN.2, BHU.3 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, BHU.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.87, A:C.167, A:H.209

1 x BHU: [[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methylboronic acid(Non-covalent)

BHU.3: 14 residues within 4Å: Chain A: F.31, Y.36, W.56, H.83, H.85, D.87, H.148, C.167, R.174, N.179, H.209 Ligands: ZN.1, ZN.2, FMT.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.56 Hydrogen bonds: A:R.174, A:R.174, A:N.179, A:N.179

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

FMT.4: 6 residues within 4Å: Chain A: H.148, Y.170, G.178, N.179, H.209 Ligands: BHU.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179 Water bridges: A:Y.36, A:R.174 FMT.5: 4 residues within 4Å: Chain A: D.20, G.21, R.44 Ligands: FMT.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.44 FMT.6: 7 residues within 4Å: Chain A: D.20, G.21, V.43, R.44, P.138, S.159 Ligands: FMT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.44, A:S.159 FMT.7: 3 residues within 4Å: Chain A: S.107, R.110, L.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.110 FMT.8: 2 residues within 4Å: Chain A: P.106, R.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.110, A:R.110 Water bridges: A:S.107 FMT.9: 4 residues within 4Å: Chain A: H.85, D.86, E.115, N.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.86, A:E.115, A:N.117 FMT.10: 4 residues within 4Å: Chain A: F.84, S.149, T.150, D.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.150, A:D.182 Water bridges: A:D.182

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: S.105, S.107, T.108, L.127, S.128, Y.143, D.151, L.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.105, A:S.105, A:S.128, A:D.151 GOL.12: 4 residues within 4Å: Chain A: L.65, P.75, V.76, A.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.76 GOL.13: 3 residues within 4Å: Chain A: E.171, S.173, L.211 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.173, A:S.173, A:L.211 Water bridges: A:V.5, A:E.171

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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