SMTL ID : 6sp6.1

Ultra-high Resolution Crystal Structure of the CTX-M-15 Extended-Spectrum beta-Lactamase in Complex with Taniborbactam (VNRX-5133)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 1 residues within 4Å: Chain A: K.171 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.169, A:K.171 Salt bridges: A:K.171 SO4.2: 1 residues within 4Å: Chain A: R.127 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.127 SO4.3: 3 residues within 4Å: Chain A: R.138, T.142, R.152 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.142 Water bridges: A:R.152, A:R.152, A:R.152 Salt bridges: A:R.138, A:R.152 SO4.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.5: 4 residues within 4Å: Chain A: S.211, S.246, R.248 Ligands: KJK.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.211, A:S.246 Water bridges: A:S.246, A:S.246 Salt bridges: A:R.248

1 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: 12 residues within 4Å: Chain A: C.43, S.44, N.78, Y.79, S.104, N.106, N.144, K.208, T.209, G.210, S.211 Ligands: SO4.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.79, A:N.144 Hydrogen bonds: A:S.44, A:N.78, A:S.104, A:N.106, A:T.209, A:S.211, A:S.211, A:S.211, A:S.211 Water bridges: A:N.144 Salt bridges: A:K.208

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

EDO.7: 2 residues within 4Å: Chain A: P.240, P.242 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: R.18, R.39, P.148, G.149, D.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.149 Water bridges: A:R.18, A:R.18, A:R.18, A:R.39

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

PGE.9: 5 residues within 4Å: Chain A: V.182, T.183, K.186, V.204, W.224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, B. et al., Discovery of Taniborbactam (VNRX-5133): A Broad-Spectrum Serine- and Metallo-beta-lactamase Inhibitor for Carbapenem-Resistant Bacterial Infections. J.Med.Chem. (2020)

Release Date

2020-01-22

Peptides

Beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase

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