SMTL ID : 6lj8.1

Crystal structure of NDM-1 in complex with D-captopril derivative wss04134

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x EG0: 2-[1-[(2S)-2-methyl-3-sulfanyl-propanoyl]piperidin-4-yl]ethanoic acid(Non-covalent)

EG0.1: 12 residues within 4Å: Chain A: M.39, F.42, V.45, W.65, H.94, D.96, H.161, C.180, N.192, H.222 Ligands: ZN.5, ZN.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.42, A:F.42, A:V.45, A:W.65, A:N.192 Hydrogen bonds: A:N.192 Salt bridges: A:H.222

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

EDO.2: 3 residues within 4Å: Chain A: P.122, Q.123, G.125 No protein-ligand interaction detected (PLIP) EDO.3: 3 residues within 4Å: Chain A: L.37, T.66, Q.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.95, A:Q.95 EDO.4: 4 residues within 4Å: Chain A: G.209, R.228, I.231, T.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.228

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: H.92, H.94, H.161, C.180 Ligands: EG0.1, ZN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.161 ZN.6: 5 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: EG0.1, ZN.5 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

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