SMTL ID : 6lj5.1

Crystal structure of NDM-1 in complex with D-captopril derivative wss04145

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

monomer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: A.137, N.138, G.139, F.155, Y.156, P.157, G.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.138 Water bridges: A:G.139

1 x EF0: 1-[(2S)-2-methyl-3-sulfanyl-propanoyl]piperidine-4-carboxylic acid(Non-covalent)

EF0.2: 13 residues within 4Å: Chain A: M.39, F.42, V.45, W.65, H.94, D.96, H.161, C.180, G.191, N.192, H.222 Ligands: ZN.3, ZN.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.42, A:V.45, A:W.65, A:N.192 Hydrogen bonds: A:N.192, A:N.192 Water bridges: A:K.183 Salt bridges: A:K.183, A:H.222

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: EF0.2, ZN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.161 ZN.4: 5 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: EF0.2, ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.96, A:C.180, A:H.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, G. et al., Structure-guided optimization of D-captopril for discovery of potent NDM-1 inhibitors. Bioorg.Med.Chem. (2020)

Release Date

2020-12-16

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase type 2

Related Entries With Identical Sequence