SMTL ID : 6mdu.1

Crystal structure of NDM-1 with compound 7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.83, H.85, H.152 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.83, A:H.85, A:H.152, H2O.1, H2O.6 ZN.2: 4 residues within 4Å: Chain A: D.87, C.171, H.213 Ligands: N1G.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.87, A:C.171, A:H.213, H2O.1

1 x N1G: 1,5-diphenyl-N-(1H-tetrazol-5-yl)-1H-pyrazole-3-carboxamide(Non-covalent)

N1G.3: 15 residues within 4Å: Chain A: L.28, M.30, F.33, G.34, V.36, W.56, Q.86, D.87, H.152, C.171, K.174, G.182, N.183, H.213 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.28, A:M.30, A:F.33, A:V.36, A:W.56 Hydrogen bonds: A:K.174, A:N.183 pi-Stacking: A:W.56

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: D.29, M.30, P.31 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Torelli, N.J. et al., Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery. Acs Infect Dis. (2019)

Release Date

2019-04-17

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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