SMTL ID : 6rtn.1

Crystal structure of OXA-10 with VNRX-5133

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 1 residues within 4Å: Chain A: L.25 Ligand excluded by PLIP CL.2: 1 residues within 4Å: Ligands: KJK.6 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: L.46, R.142 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: A.80, P.100 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: R.232, K.233 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.91 Chain B: E.209 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain B: E.226 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: K.31, E.153 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: L.46 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: K.43, E.44 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: R.79, A.80, P.100 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: P.230, R.232 Ligand excluded by PLIP

2 x KJK: (3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid(Covalent)

KJK.6: 14 residues within 4Å: Chain A: A.48, S.49, K.52, W.84, S.97, V.99, K.187, T.188, G.189, F.190, S.191, G.192, R.232 Ligands: CL.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.84, A:V.99, A:F.190, A:F.190, A:F.190 Hydrogen bonds: A:S.49, A:S.97, A:T.188, A:F.190, A:F.190, A:F.190 Salt bridges: A:K.187, A:R.232 KJK.14: 16 residues within 4Å: Chain B: A.48, S.49, K.52, M.81, W.84, S.97, V.99, L.137, K.187, T.188, G.189, F.190, S.191, G.192, E.226, R.232 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.84, B:V.99, B:F.190 Hydrogen bonds: B:S.49, B:S.97, B:S.97, B:F.190, B:F.190, B:F.190 Water bridges: B:T.188 Salt bridges: B:K.187, B:R.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krajnc, A. et al., Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-beta-Lactamases. J.Med.Chem. (2019)

Release Date

2019-09-11

Peptides

Beta-lactamase OXA-10: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase OXA-10

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