SMTL ID : 6v1p.1 (1 other biounit)

Structure of VIM-2 bound to QPX7728 at 1.20 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x QNA: (1~{a}~{R},7~{b}~{S})-5-fluoranyl-2,2-bis(oxidanyl)-1~{a},7~{b}-dihydro-1~{H}-cyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid(Non-covalent)

QNA.1: 15 residues within 4Å: Chain A: F.38, Y.43, W.63, H.90, H.92, D.94, H.155, C.174, R.181, G.185, N.186, H.216 Ligands: ZN.2, ZN.3, GOL.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.43, A:W.63, A:D.94, A:N.186 Hydrogen bonds: A:N.186 Salt bridges: A:H.155, A:H.216 pi-Stacking: A:F.38 Halogen bonds: A:R.181

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.90, H.92, H.155 Ligands: QNA.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:H.92, A:H.155 ZN.3: 5 residues within 4Å: Chain A: D.94, R.95, C.174, H.216 Ligands: QNA.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:C.174, A:H.216 ZN.4: 3 residues within 4Å: Chain A: H.227 Ligands: ACT.5, ACT.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.227, ACT.6

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

ACT.5: 6 residues within 4Å: Chain A: D.223, K.226, H.227, N.230 Ligands: ZN.4, ACT.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.226 Hydrogen bonds: A:N.230 Salt bridges: A:H.227 ACT.6: 4 residues within 4Å: Chain A: H.227, N.230 Ligands: ZN.4, ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.230 Hydrogen bonds: A:N.230 Salt bridges: A:H.227

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: F.38, Y.43, R.181, G.185, N.186 Ligands: QNA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.181, A:R.181 Water bridges: A:D.39, A:G.185, A:V.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hecker, S.J. et al., Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-beta-lactamases. J.Med.Chem. (2020)

Release Date

2020-03-25

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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