SMTL ID : 9h12.1

Crystal structure of OXA-48 in complex with nacubactam

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: S.50, K.53, V.100, W.137 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: R.186 Chain B: R.186 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: S.50, K.53, V.100, W.137 Ligand excluded by PLIP

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 13 residues within 4Å: Chain A: I.92, K.96, L.176, T.177 Chain B: N.180, G.181, Y.183, I.184, E.207, L.208, D.209 Ligands: PGE.5, EDO.26 No protein-ligand interaction detected (PLIP) PGE.5: 11 residues within 4Å: Chain A: K.96, A.174, L.176, T.177, A.187, K.188, T.189, Q.231 Ligands: PGE.3, EDO.14, OP0.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.231 Water bridges: A:K.188, A:K.188 PGE.19: 2 residues within 4Å: Chain A: L.39, K.40 No protein-ligand interaction detected (PLIP) PGE.20: 12 residues within 4Å: Chain A: N.180, G.181, Y.183, I.184, E.207, L.208, D.209 Chain B: I.92, K.96, L.176, T.177 Ligands: PGE.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.208, A:D.209 PGE.32: 11 residues within 4Å: Chain B: M.95, K.96, A.174, L.176, T.177, A.187, K.188, T.189, Q.231 Ligands: PGE.20, OP0.29 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.231 Water bridges: B:S.98, B:K.188, B:K.188, B:R.230, B:Q.231

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

PEG.4: 1 residues within 4Å: Chain A: R.108 No protein-ligand interaction detected (PLIP) PEG.6: 3 residues within 4Å: Chain A: L.63, R.114, K.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.117 Water bridges: A:R.114 PEG.7: 6 residues within 4Å: Chain A: R.87, D.88, H.89, Y.97 Chain B: D.209 Ligands: DMS.18 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.87, B:D.209 Water bridges: A:D.88 PEG.8: 4 residues within 4Å: Chain A: R.154, K.155, H.158, K.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.154, A:R.154 PEG.27: 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

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

EDO.9: 5 residues within 4Å: Chain A: L.61, D.62, S.164, R.166, S.167 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.62, A:D.62, A:S.164, A:R.166, A:S.167 EDO.10: 4 residues within 4Å: Chain A: W.5, L.39, N.43 Ligands: GOL.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.43 Water bridges: A:T.147, A:T.147 EDO.11: 6 residues within 4Å: Chain A: K.19, S.20, D.220, P.222, T.223, L.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.19 EDO.12: 4 residues within 4Å: Chain A: T.177, E.178, Q.231, K.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.178, A:K.235 EDO.13: 3 residues within 4Å: Chain A: H.158, N.159, K.160 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.158, A:K.160 Water bridges: A:N.159 EDO.14: 3 residues within 4Å: Chain A: Y.97 Ligands: PGE.5, OP0.15 No protein-ligand interaction detected (PLIP) EDO.17: 6 residues within 4Å: Chain A: N.12, F.15, Q.21, G.22, N.37, N.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.22, A:N.37, A:N.38 EDO.26: 4 residues within 4Å: Chain A: K.96, Y.97 Chain B: G.181 Ligands: PGE.3 No protein-ligand interaction detected (PLIP) EDO.28: 4 residues within 4Å: Chain B: G.64, V.65, K.67, Q.71 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.71, B:Q.71 Water bridges: B:K.67, B:Q.109 EDO.31: 6 residues within 4Å: Chain B: N.12, F.15, Q.21, G.22, N.37, N.38 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.22, B:N.38 EDO.33: 3 residues within 4Å: Chain B: I.82, Y.97 Ligands: OP0.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.97

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

OP0.15: 13 residues within 4Å: Chain A: A.49, S.50, W.85, S.98, V.100, K.188, T.189, G.190, Y.191, R.194, R.230 Ligands: PGE.5, EDO.14 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:Y.191 Water bridges: A:K.188 Salt bridges: A:K.188, A:R.230 OP0.29: 15 residues within 4Å: Chain B: A.49, S.50, W.85, S.98, V.100, L.138, K.188, T.189, G.190, Y.191, T.193, R.194, R.230 Ligands: PGE.32, EDO.33 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.191 Hydrogen bonds: B:S.50, B:S.98, B:S.98, B:T.189, B:Y.191, B:T.193, B:T.193, B:R.194 Water bridges: B:K.188, B:R.194 Salt bridges: B:K.188, B:R.230

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

DMS.16: 6 residues within 4Å: Chain A: W.27, T.147, I.150, S.151, R.154 Ligands: GOL.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.154 pi-Cation interactions: A:W.27 DMS.18: 8 residues within 4Å: Chain A: V.72, D.88, H.89, N.90, T.93 Chain B: D.209, D.210 Ligands: PEG.7 No protein-ligand interaction detected (PLIP) DMS.30: 7 residues within 4Å: Chain B: E.4, W.5, W.27, T.147, I.150, S.151, R.154 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:W.27

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 4 residues within 4Å: Chain A: E.4, W.5 Ligands: EDO.10, DMS.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.147 GOL.23: 6 residues within 4Å: Chain B: F.73, K.74, W.75, D.76, R.80, P.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.76, B:R.80 Water bridges: B:E.105 GOL.25: 7 residues within 4Å: Chain A: D.209, D.210 Chain B: V.72, R.87, D.88, N.90, T.93 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.209, A:D.210, B:R.87, B:D.88, B:N.90 Water bridges: B:N.90

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.24: 2 residues within 4Å: Chain B: R.114, K.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.117

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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