SMTL ID : 9h15.1

Crystal structure of OXA-163 in complex with nacubactam

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 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, W.85, S.98, V.100, K.188, T.189, G.190, Y.191, D.192, T.193, R.226 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.191 Hydrogen bonds: A:S.50, A:S.98, A:S.98, A:T.189, A:T.189, A:Y.191 Salt bridges: A:K.188, A:R.226 OP0.8: 13 residues within 4Å: Chain B: A.49, S.50, I.82, W.85, S.98, V.100, L.138, K.188, T.189, G.190, Y.191, T.193, R.226 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:T.189, B:Y.191 Salt bridges: B:K.188, B:R.226

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

EDO.2: 5 residues within 4Å: Chain A: K.74, W.75, D.76, P.101, E.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.76 Water bridges: A:F.73, A:K.74 EDO.10: 5 residues within 4Å: Chain B: K.74, W.75, D.76, R.80, P.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.76, B:R.80, B:P.101 Water bridges: B:K.74

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Y.157, K.172, E.203 Chain B: E.69, H.70, Q.173 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.157, A:E.203, B:E.69, B:Q.173 Water bridges: A:K.172, A:R.186 GOL.5: 9 residues within 4Å: Chain A: N.180, G.181, D.182, Y.183, I.184, E.203, L.204, D.205 Chain B: K.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.180, A:E.203, A:D.205 GOL.11: 7 residues within 4Å: Chain A: E.69, H.70, Q.173 Chain B: Y.157, K.172, R.186, E.203 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.172, B:E.203, A:E.69, A:E.69, A:Q.173 Water bridges: B:R.169

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: R.154, H.158, K.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.160 PEG.9: 4 residues within 4Å: Chain B: R.154, K.155, H.158, K.160 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.154, B:K.160 PEG.12: 9 residues within 4Å: Chain A: K.96, L.176, T.177 Chain B: N.180, G.181, Y.183, I.184, L.204, D.205 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:L.176, A:T.177 Hydrogen bonds: B:L.204

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

CL.6: 2 residues within 4Å: Chain A: R.186 Chain B: R.186 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: K.53, V.100, W.137 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: K.53, V.100, W.137 Ligand excluded by PLIP

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.13: 4 residues within 4Å: Chain B: K.96, L.176, T.177, A.187 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.188

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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