SMTL ID : 8r5t.1 (1 other biounit)

Crystal structure of NDM-1 in complex with benzobisheterocycle compound 14.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

1 x Y4E: [(1~{R},3~{a}~{R})-1,3,3~{a},4-tetrahydro-[1,3]thiazolo[3,4-a]benzimidazol-1-yl]methanethiol(Non-covalent)

Y4E.1: 12 residues within 4Å: Chain A: M.41, F.44, V.47, W.67, H.96, Q.97, D.98, H.163, C.182, H.224 Ligands: ZN.2, ZN.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.47 pi-Stacking: A:H.224

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 8 residues within 4Å: Chain A: H.94, D.98, K.99, C.182, S.223, H.224 Ligands: Y4E.1, ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.98, A:C.182, A:H.224 ZN.3: 6 residues within 4Å: Chain A: H.94, H.96, H.163, C.182 Ligands: Y4E.1, ZN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.94, A:H.96, A:H.163

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: Q.132, H.133, S.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.134, A:S.134 Water bridges: A:H.133, A:S.134 Salt bridges: A:H.133 SO4.5: 3 residues within 4Å: Chain A: R.208, T.234, R.238 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.234 Salt bridges: A:R.208, A:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Villamil, V. et al., Rational Design of Benzobisheterocycle Metallo-beta-Lactamase Inhibitors: A Tricyclic Scaffold Enhances Potency against Target Enzymes. J.Med.Chem. (2024)

Release Date

2024-04-10

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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