SMTL ID : 6tmc.1

VIM-2_1dh-Triazole inhibitors with promising inhibitor effects against antibiotic resistance metallo-beta-lactamases

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x NL5: 4-[2-(phenylsulfonyl)ethyl]-5-(propan-2-yloxymethyl)-1~{H}-1,2,3-triazole(Non-covalent)

NL5.1: 17 residues within 4Å: Chain A: F.62, Y.67, P.68, W.87, H.116, D.117, D.118, H.179, C.198, R.205, A.208, G.209, N.210, H.240 Ligands: ZN.3, OH.4, IOD.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.62, A:Y.67, A:W.87, A:N.210, A:H.240 Water bridges: A:H.179, A:H.179, A:R.205, A:R.205 pi-Stacking: A:Y.67, A:H.240 pi-Cation interactions: A:H.179

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.114, H.116, H.179 Ligands: OH.4 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.114, A:H.116, A:H.179, OH.4, H2O.5 ZN.3: 7 residues within 4Å: Chain A: H.114, D.118, R.119, C.198, H.240 Ligands: NL5.1, OH.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.118, A:C.198, A:H.240

1 x OH: HYDROXIDE ION(Non-covalent)

OH.4: 8 residues within 4Å: Chain A: H.114, H.116, D.118, H.179, C.198 Ligands: NL5.1, ZN.2, ZN.3 No protein-ligand interaction detected (PLIP)

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 3 residues within 4Å: Chain A: Y.67, R.205 Ligands: NL5.1 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muhammad, Z. et al., Structural studies of triazole inhibitors with promising inhibitor effects against antibiotic resistance metallo-beta-lactamases. Bioorg.Med.Chem. (2020)

Release Date

2020-07-22

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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