SMTL ID : 9d9n.2 (1 other biounit)

Crystal structure of NDM-1 complexed with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

2 x 01: {[1-methyl-2-oxo-7-(pyrrolidin-1-yl)-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.4, ZN.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.33, 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.183 Hydrogen bonds: A:K.174, A:L.181, A:N.183

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: G.200, R.219, I.222, T.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.219

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: D.87, H.152, C.171, H.213 Ligands: 01.1, 01.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.171, A:H.213 ZN.5: 6 residues within 4Å: Chain A: H.83, H.85, D.87, 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

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
B

Metallo-beta-lactamase type 2

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