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

Crystal structure of VIM-2 in complex with triazole-based inhibitor OP24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.94, H.96, H.159 Ligands: N8Z.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.94, A:H.96, A:H.159 ZN.2: 5 residues within 4Å: Chain A: D.98, R.99, C.178, H.220 Ligands: N8Z.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.98, A:C.178, A:H.220 ZN.7: 3 residues within 4Å: Chain A: H.133 Ligands: FMT.3, FMT.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.133

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

FMT.3: 7 residues within 4Å: Chain A: V.111, A.112, T.113, T.132, H.133 Ligands: FMT.4, ZN.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.113, A:T.132 FMT.4: 4 residues within 4Å: Chain A: A.112, H.133 Ligands: FMT.3, ZN.7 No protein-ligand interaction detected (PLIP) FMT.5: 5 residues within 4Å: Chain A: Y.181, R.185, G.189, N.190 Ligands: N8Z.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.190 Water bridges: A:Y.181, A:Y.181, A:R.185 FMT.6: 1 residues within 4Å: Chain A: E.151 No protein-ligand interaction detected (PLIP)

1 x N8Z: 5-(4-chloranyl-1,5-dimethyl-pyrazol-3-yl)-4-ethyl-1,2,4-triazole-3-thiol(Non-covalent)

N8Z.8: 13 residues within 4Å: Chain A: F.42, W.67, H.94, H.96, D.97, D.98, H.159, C.178, N.190, H.220 Ligands: ZN.1, ZN.2, FMT.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.67, A:W.67 Hydrogen bonds: A:N.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spyrakis, F. et al., Virtual screening identifies broad-spectrum beta-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases. Sci Rep (2020)

Release Date

2020-10-14

Peptides

Vim-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vim-1

Related Entries With Identical Sequence