SMTL ID : 9dew.1

Crystal structure of NDM-1 complexed with compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

2 x 01: [(7-cyclopropyl-1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)methyl]phosphonic acid

01.1: 14 residues within 4Å: Chain A: M.30, F.33, V.36, W.56, H.83, H.85, D.87, H.152, C.171, N.183, H.213 Ligands: 01.2, ZN.3, ZN.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.33, A:F.33, A:V.36, A:V.36 Hydrogen bonds: A:N.183 pi-Stacking: A:H.213 01.2: 10 residues within 4Å: Chain A: F.33, H.152, C.171, K.174, L.181, G.182, N.183, H.213 Ligands: 01.1, ZN.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.33, A:N.183 Hydrogen bonds: A:K.174, A:L.181, A:N.183

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.83, H.85, H.152, C.171 Ligands: 01.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.83, A:H.85, A:H.152 ZN.4: 7 residues within 4Å: Chain A: D.87, H.152, C.171, S.212, H.213 Ligands: 01.1, 01.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.171, A:H.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacobs, L.M.C. et al., Hit to Lead Optimization of Heteroaryl Phosphonates Reversible, Broad-Spectrum Inhibitors of Serine and Metallo Carbapenemases. To Be Published

Release Date

2025-09-03

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase type 2

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