SMTL ID : 9r0x.1

Crystal structure of NDM-1 with thiol compound 14a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: H.96, D.100, K.101, C.184, S.225, H.226 Ligands: ZN.2, 01.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.100, A:C.184, A:H.226 ZN.2: 6 residues within 4Å: Chain A: H.96, H.98, H.165, C.184 Ligands: ZN.1, 01.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:H.98, A:H.165 ZN.7: 6 residues within 4Å: Chain B: H.96, H.98, H.165, C.184 Ligands: ZN.8, 01.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.96, B:H.98, B:H.165 ZN.8: 8 residues within 4Å: Chain B: H.96, D.100, K.101, C.184, S.225, H.226 Ligands: ZN.7, 01.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.100, B:C.184, B:H.226

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

SO4.3: 3 residues within 4Å: Chain A: R.210, T.236, R.240 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.210 Salt bridges: A:R.210, A:R.240 SO4.4: 5 residues within 4Å: Chain A: K.187, K.190, A.191, K.192, S.193 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.192, A:S.193, A:S.193 Salt bridges: A:K.187

2 x 01: ~{N}-(3-chlorophenyl)-2-sulfanyl-ethanamide

01.5: 10 residues within 4Å: Chain A: M.43, V.49, W.69, H.98, D.100, H.165, C.184, H.226 Ligands: ZN.1, ZN.2 No protein-ligand interaction detected (PLIP) 01.9: 11 residues within 4Å: Chain B: M.43, F.46, V.49, W.69, H.98, D.100, H.165, C.184, H.226 Ligands: ZN.7, ZN.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.49 pi-Stacking: B:F.46

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: A.31, P.32, N.33, V.34, T.177 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kavas, V. et al., Repurposing of compound libraries yields new inhibitors of NDM-1 metallo-beta-lactamase with diverse zinc-binding moieties. Eur J Med Chem Rep (2025)

Release Date

2025-07-09

Peptides

Metallo-beta-lactamase type 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metallo-beta-lactamase type 2

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