SMTL ID : 9r0y.1

Crystal structure of NDM-1 with thiol compound 22b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.96, D.100, C.184, S.225, H.226 Ligands: ZN.2, 01.4 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, 01.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:H.98, A:H.165 ZN.5: 6 residues within 4Å: Chain B: H.96, H.98, H.165, C.184 Ligands: 01.6, ZN.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.96, B:H.98, B:H.165 ZN.7: 8 residues within 4Å: Chain B: H.96, D.100, K.101, C.184, S.225, H.226 Ligands: ZN.5, 01.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.100, B:C.184, B:H.226

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

SO4.3: 3 residues within 4Å: Chain A: R.210, T.236, R.240 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.236, A:T.236 Salt bridges: A:R.210, A:R.240

2 x 01: ~{N}-naphthalen-2-yl-2-sulfanyl-ethanamide

01.4: 12 residues within 4Å: Chain A: M.43, V.49, W.69, H.96, H.98, Q.99, D.100, H.165, C.184, H.226 Ligands: ZN.1, ZN.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.43, A:V.49, A:V.49 01.6: 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.5, ZN.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.46, B:V.49, B:V.49

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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