SMTL ID : 8b20.1 (1 other biounit)

NDM-1 metallo-beta-lactamase in complex with triazole-based inhibitor CP57

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: OQK.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.161 ZN.2: 4 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: OQK.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.96, A:C.180, A:H.222

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: E.124, D.195 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.124, A:E.124, A:D.195 CA.4: 2 residues within 4Å: Chain A: D.67, D.102 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.67, A:D.102, H2O.3

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 2 residues within 4Å: Chain A: H.233, R.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.233, A:R.236

1 x OQK: 2-[(~{E})-[3-sulfanyl-5-[4-(trifluoromethyl)phenyl]-1,2,4-triazol-4-yl]iminomethyl]benzoic acid(Non-covalent)

OQK.6: 16 residues within 4Å: Chain A: L.37, M.39, V.45, W.65, H.92, H.94, Q.95, D.96, H.161, C.180, K.183, G.191, N.192, H.222 Ligands: ZN.1, ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.45 Hydrogen bonds: A:N.192 Salt bridges: A:K.183 pi-Stacking: A:W.65, A:H.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bersani, M. et al., Structure-Based Optimization of 1,2,4-Triazole-3-Thione Derivatives: Improving Inhibition of NDM-/VIM-Type Metallo-beta-Lactamases and Synergistic Activity on Resistant Bacteria. Pharmaceuticals (2023)

Release Date

2023-12-27

Peptides

Beta-lactamase NDM-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase NDM-1

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