SMTL ID : 4xuz.1

Structure of CTX-M-15 bound to RPX-7009 at 1.5 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: P.203, A.204 Ligand excluded by PLIP

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 2 residues within 4Å: Chain A: K.75, S.77 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.77 Water bridges: A:S.77, A:D.78 Salt bridges: A:K.75, A:K.75

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

EDO.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: A.56, K.60, V.119, F.128 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.119, A:S.124, A:Q.131 EDO.5: 4 residues within 4Å: Chain A: L.68, S.179, Q.180, Q.183 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.179 Water bridges: A:Q.180, A:Q.183, A:Q.183 EDO.6: 4 residues within 4Å: Chain A: E.15, G.20, R.21, R.38 No protein-ligand interaction detected (PLIP) EDO.7: 5 residues within 4Å: Chain A: I.27, N.32, Q.34, Q.165, R.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.165, A:R.168, A:R.168 Water bridges: A:N.32 EDO.8: 6 residues within 4Å: Chain A: L.36, Y.37, R.38, A.39, D.40, R.161 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.36, A:A.39 Water bridges: A:R.38, A:D.40, A:D.40, A:D.40 EDO.9: 5 residues within 4Å: Chain A: K.60, E.64, L.67, Q.70, H.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.60, A:E.64 Water bridges: A:H.118 EDO.10: 5 residues within 4Å: Chain A: R.21, R.42, P.151, G.152, D.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.152 Water bridges: A:R.21, A:R.21 EDO.11: 1 residues within 4Å: Chain A: Q.131 No protein-ligand interaction detected (PLIP)

1 x 4D6: Vaborbactam(Covalent)

4D6.12: 15 residues within 4Å: Chain A: C.46, S.47, K.50, N.81, Y.82, S.107, N.109, P.144, N.147, K.211, T.212, G.213, S.214, G.215, G.216 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.82, A:N.147 Hydrogen bonds: A:S.47, A:N.81, A:S.107, A:S.107, A:N.109, A:S.214, A:S.214, A:S.214 Water bridges: A:N.147 Salt bridges: A:K.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hecker, S.J. et al., Discovery of a Cyclic Boronic Acid beta-Lactamase Inhibitor (RPX7009) with Utility vs Class A Serine Carbapenemases. J.Med.Chem. (2015)

Release Date

2015-04-01

Peptides

Beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase