SMTL ID : 8b20.2 (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, D.96, H.161 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.161 ZN.2: 3 residues within 4Å: Chain A: D.96, C.180, H.222 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.96, A:C.180, A:H.222

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: E.124, D.195 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.124, A:E.124, A:D.195, A:D.195, H2O.3

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 3 residues within 4Å: Chain A: R.206, T.232, R.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.236 Salt bridges: A:R.206, A:R.236

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

EDO.5: 4 residues within 4Å: Chain A: A.27, P.28, G.172, T.173 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.172 EDO.6: 4 residues within 4Å: Chain A: A.44, V.45, A.46, H.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.46

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
B

Beta-lactamase NDM-1

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