SMTL ID : 8r5u.1 (1 other biounit)

VIM-2 metallo-beta-lactamase in complex with benzebisheterocycle compound 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

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

FMT.1: 7 residues within 4Å: Chain A: R.103, A.108, T.109, T.128, H.129 Ligands: FMT.2, ZN.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.107, A:T.109, A:T.128 Water bridges: A:T.109 FMT.2: 4 residues within 4Å: Chain A: A.108, H.129 Ligands: FMT.1, ZN.5 No protein-ligand interaction detected (PLIP) FMT.7: 9 residues within 4Å: Chain A: H.155, C.174, Y.177, R.181, G.185, N.186, H.216 Ligands: ZN.4, Y4E.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.155, A:N.186 Water bridges: A:Y.177, A:Y.177

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: H.90, H.92, H.155, C.174 Ligands: ZN.4, Y4E.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:H.92, A:H.155 ZN.4: 8 residues within 4Å: Chain A: H.90, D.94, R.95, C.174, H.216 Ligands: ZN.3, Y4E.6, FMT.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:C.174, A:H.216 ZN.5: 4 residues within 4Å: Chain A: A.108, H.129 Ligands: FMT.1, FMT.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.129

1 x Y4E: [(1~{R},3~{a}~{R})-1,3,3~{a},4-tetrahydro-[1,3]thiazolo[3,4-a]benzimidazol-1-yl]methanethiol(Non-covalent)

Y4E.6: 15 residues within 4Å: Chain A: F.38, Y.43, W.63, H.90, H.92, D.93, D.94, R.95, H.155, C.174, N.186, H.216 Ligands: ZN.3, ZN.4, FMT.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.63 pi-Stacking: A:F.38, A:Y.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Villamil, V. et al., Rational Design of Benzobisheterocycle Metallo-beta-Lactamase Inhibitors: A Tricyclic Scaffold Enhances Potency against Target Enzymes. J.Med.Chem. (2024)

Release Date

2024-04-10

Peptides

Beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase VIM-2

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