SMTL ID : 6lj2.1

Crystal structure of NDM-1 in complex with heterodimer of D-captopril derivative wss02127 stereoisomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: OH.3, EEX.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.92, A:H.94, A:H.161, OH.3 ZN.2: 5 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: OH.3, EEX.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.96, A:C.180, A:H.222, OH.3

1 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 8 residues within 4Å: Chain A: H.92, H.94, D.96, H.161, C.180 Ligands: ZN.1, ZN.2, EEX.4 No protein-ligand interaction detected (PLIP)

1 x EEX: (1R)-2-[(2S)-2-methyl-3-sulfanyl-propanoyl]-3,4-dihydro-1H-isoquinoline-1-carboxylic acid(Non-covalent)

EEX.4: 12 residues within 4Å: Chain A: V.45, H.94, D.96, H.161, C.180, K.183, L.193, H.222 Ligands: ZN.1, ZN.2, OH.3, EKX.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.45, A:L.193 Salt bridges: A:H.161, A:K.183, A:H.222 pi-Stacking: A:H.222

1 x EKX: (1S)-2-[(2S)-2-methyl-3-sulfanyl-propanoyl]-3,4-dihydro-1H-isoquinoline-1-carboxylic acid(Non-covalent)

EKX.5: 6 residues within 4Å: Chain A: M.39, F.42, W.65, Q.95, L.193 Ligands: EEX.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.39, A:F.42, A:F.42, A:L.193 pi-Stacking: A:F.42

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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