SMTL ID : 5dtk.1 (2 other biounits)

Fragments bound to the OXA-48 beta-lactamase: Compound 17

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: Q.193, L.196, R.206 Chain B: Q.193, L.196, R.206 Ligand excluded by PLIP

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

EDO.2: 8 residues within 4Å: Chain A: V.92, R.107, D.108, H.109, N.110, T.113 Chain B: D.229, D.230 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.107, B:D.229 EDO.3: 9 residues within 4Å: Chain A: H.38, K.39, S.40, M.239, D.240, M.241, P.242, G.246, L.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.39 Water bridges: A:G.246 EDO.4: 6 residues within 4Å: Chain A: L.81, D.82, S.184, R.186, S.187, I.190 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.184, A:R.186, A:S.187, A:S.187 Water bridges: A:S.184 EDO.5: 8 residues within 4Å: Chain A: F.93, K.94, W.95, D.96, R.100, P.121, V.122, E.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.96, A:D.96, A:R.100 EDO.8: 7 residues within 4Å: Chain B: N.32, F.35, T.36, S.40, Q.41, G.42, N.57 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.42, B:G.42 Water bridges: B:N.32, B:N.32, B:N.57, B:N.58

2 x 5F3: 3,5-di(pyridin-4-yl)benzoic acid(Non-covalent)

5F3.6: 14 residues within 4Å: Chain A: A.69, S.70, K.73, I.102, T.104, W.105, Y.117, S.118, V.120, L.158, T.209, G.210, Y.211, R.250 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.102, A:I.102, A:W.105, A:W.105, A:V.120, A:Y.211 Hydrogen bonds: A:T.209 Water bridges: A:T.104, A:S.118, A:S.118, A:T.209, A:Y.211, A:T.213 Salt bridges: A:K.208, A:R.250 5F3.7: 12 residues within 4Å: Chain B: S.70, K.73, I.102, W.105, S.118, V.120, L.158, T.209, Y.211, S.244, L.247, R.250 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.102, B:Y.211 Hydrogen bonds: B:T.209 Water bridges: B:T.213, B:T.213, B:R.214, B:R.250 Salt bridges: B:R.250 pi-Stacking: B:W.105, B:Y.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lund, B.A. et al., Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening. J.Med.Chem. (2016)

Release Date

2016-05-25

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Beta-lactamase

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