SMTL ID : 9hpv.1

Crystal structure of OXA-163 in complex with nacubactam (16 hour soak)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-dimer

Ligands

2 x OP0: (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide(Covalent)

OP0.1: 13 residues within 4Å: Chain A: A.49, S.50, K.53, S.98, V.100, L.138, K.188, T.189, G.190, Y.191, T.193, R.226 Ligands: 01.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.191 Hydrogen bonds: A:S.50, A:S.98, A:S.98, A:T.189, A:Y.191 Water bridges: A:K.188, A:R.226, A:R.226 Salt bridges: A:K.188, A:R.226 OP0.6: 13 residues within 4Å: Chain B: A.49, S.50, K.53, W.85, S.98, V.100, L.138, K.188, T.189, G.190, Y.191, R.226 Ligands: 01.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.50, B:S.98, B:S.98, B:T.189, B:Y.191 Water bridges: B:K.188, B:R.226, B:R.226, B:R.226 Salt bridges: B:K.188, B:R.226

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

EDO.2: 6 residues within 4Å: Chain A: E.178, A.179, N.180 Chain B: E.178, A.179, N.180 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.178, B:E.178, B:N.180, A:E.178, A:N.180

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.74, W.75, D.76, R.80, P.101, V.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.76, A:R.80, A:P.101 GOL.8: 7 residues within 4Å: Chain B: K.74, W.75, D.76, R.80, P.101, V.102, E.105 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.76, B:R.80 Water bridges: B:D.76, B:P.101, B:E.105, B:R.108

2 x 01: (2S,5R)-N-(2-azanylethoxy)-1-methanoyl-5-(oxidanylamino)piperidine-2-carboxamide

01.4: 10 residues within 4Å: Chain A: A.49, S.50, K.53, S.98, V.100, L.138, G.190, Y.191, T.193 Ligands: OP0.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.191 Hydrogen bonds: A:S.50, A:S.98, A:S.98, A:Y.191 Water bridges: A:T.189, A:R.226 01.7: 11 residues within 4Å: Chain B: A.49, S.50, K.53, I.82, W.85, S.98, V.100, L.138, G.190, Y.191 Ligands: OP0.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.82 Hydrogen bonds: B:S.50, B:S.98, B:S.98, B:Y.191 Water bridges: B:T.189, B:T.189, B:R.226

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

CL.5: 2 residues within 4Å: Chain A: R.186 Chain B: R.186 Ligand excluded by PLIP

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.9: 2 residues within 4Å: Chain B: G.64, R.166 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoff, J.F. et al., Electrostatic interactions influence diazabicyclooctane inhibitor potency against OXA-48-like beta-lactamases. Rsc Med Chem (2025)

Release Date

2025-09-03

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase

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