SMTL ID : 7up1.2 (1 other biounit)

NDM1-inhibitor co-structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.11 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.98, H.100, D.102, H.167 Ligands: ZN.2, NZR.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.98, A:H.100, A:H.167 ZN.2: 5 residues within 4Å: Chain A: D.102, C.186, H.228 Ligands: ZN.1, NZR.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.102, A:C.186, A:H.228

2 x CD: CADMIUM ION(Non-covalent)

CD.3: 2 residues within 4Å: Chain A: E.130, D.201 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.130, A:E.130, A:D.201, A:D.201 CD.4: 2 residues within 4Å: Chain A: D.73, D.108 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.73, A:D.108, H2O.4, H2O.7

1 x NZR: (2M)-4'-methyl-2-(2H-tetrazol-5-yl)[1,1'-biphenyl]-3-sulfonamide(Non-covalent)

NZR.5: 15 residues within 4Å: Chain A: I.13, V.51, W.71, H.98, H.100, D.102, H.167, C.186, K.189, L.196, G.197, N.198, H.228 Ligands: ZN.1, ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.13, A:I.13, A:V.51, A:W.71 Hydrogen bonds: A:N.198, A:N.198 Water bridges: A:K.189, A:K.189, A:K.189 pi-Stacking: A:H.228 pi-Cation interactions: A:H.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mandal, M. et al., Rapid Evolution of a Fragment-like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads toward Clinical Candidates. J.Med.Chem. (2022)

Release Date

2023-03-08

Peptides

Metallo beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Metallo beta-lactamase

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