SMTL ID : 6sp7.1 (1 other biounit)

Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with Taniborbactam (VNRX-5133)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.83, H.85, H.148 Ligands: K9B.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.83, A:H.85, A:H.148 ZN.2: 5 residues within 4Å: Chain A: D.87, R.88, C.167, H.209 Ligands: K9B.6 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.122 Ligands: ACT.4, ACT.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.122, ACT.5

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

ACT.4: 6 residues within 4Å: Chain A: A.101, T.102, T.121, H.122 Ligands: ZN.3, ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.121 Hydrogen bonds: A:T.102 Salt bridges: A:H.122 ACT.5: 4 residues within 4Å: Chain A: A.101, H.122 Ligands: ZN.3, ACT.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.101 Salt bridges: A:H.122

1 x K9B: (4~{R})-4-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid(Non-covalent)

K9B.6: 15 residues within 4Å: Chain A: F.31, Y.36, W.56, H.83, H.85, D.87, E.115, H.148, C.167, G.178, N.179, D.182, H.209 Ligands: ZN.1, ZN.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.31, A:Y.36, A:W.56, A:W.56, A:N.179 Hydrogen bonds: A:E.115, A:N.179, A:N.179, A:D.182 Water bridges: A:D.86, A:R.174 Salt bridges: A:H.148, A:H.209 pi-Stacking: A:F.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, B. et al., Discovery of Taniborbactam (VNRX-5133): A Broad-Spectrum Serine- and Metallo-beta-lactamase Inhibitor for Carbapenem-Resistant Bacterial Infections. J.Med.Chem. (2020)

Release Date

2020-01-22

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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