PDBsum entry 7cbh

Ligase/inhibitor

PDB id: 7cbh

Contents

Protein chains

401 a.a.

Ligands

FQR

Metals

_ZN ×2

Waters ×474

PDB id:

7cbh

Name:

Ligase/inhibitor

Title:

Crystal structure of threonyl-tRNA synthetase (thrrs) from salmonella enterica in complex with an inhibitor

Structure:

Threonine--tRNA ligase. Chain: a, b. Synonym: threonyl-tRNA synthetase,thrrs. Engineered: yes

Source:

Salmonella enterica subsp. Enterica serovar cubana str. 76814. Organism_taxid: 1192560. Gene: thrs, a628_05061. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

1.95Å R-factor: 0.178 R-free: 0.215

Authors:

J.Guo,B.Chen,H.Zhou

Key ref:

J.Guo et al. (2020). Structure-guided optimization and mechanistic study of a class of quinazolinone-threonine hybrids as antibacterial ThrRS inhibitors. Eur J Med Chem, 207, 112848. PubMed id: 32980741 DOI: 10.1016/j.ejmech.2020.112848

Date:

12-Jun-20 Release date: 07-Oct-20

Protein chains

V7II86  (V7II86_SALET) -  Threonine--tRNA ligase from Salmonella enterica subsp. enterica serovar Cubana str. 76814

Seq: 622 a.a.

Struc: 401 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.6.1.1.3 - threonine--tRNA ligase.
• Reaction: tRNA(Thr) + L-threonine + ATP = L-threonyl-tRNA(Thr) + AMP + diphosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.ejmech.2020.112848

Eur J Med Chem 207:112848 (2020)

PubMed id: 32980741

Structure-guided optimization and mechanistic study of a class of quinazolinone-threonine hybrids as antibacterial ThrRS inhibitors.

J.Guo, B.Chen, Y.Yu, B.Cheng, Y.Ju, J.Tang, Z.Cai, Q.Gu, J.Xu, H.Zhou.

ABSTRACT

Aminoacyl-tRNA synthetases (aaRSs) are an attractive class of antibacterial drug targets due to their essential roles in protein translation. While most traditional aaRS inhibitors target the binding pockets of substrate amino acids and/or ATP, we recently developed a class of novel tRNA-amino acid dual-site inhibitors including inhibitor 3 ((2S,3R)-2-amino-N-((E)-4-(6,7-dichloro-4-oxoquinazolin-3(4H)-yl)but-2-en-1-yl)-3-hydroxybutanamide) against threonyl-tRNA synthetase (ThrRS). Here, the binding modes and structure-activity relationships (SARs) of these inhibitors were analyzed by the crystal structures of Salmonella enterica ThrRS (SeThrRS) in complex with three of them. Based on the cocrystal structures, twelve quinazolinone-threonine hybrids were designed and synthesized, and their affinities, enzymatic inhibitory activities, and cellular potencies were evaluated. The best derivative 8g achieved a K_d value of 0.40 μM, an IC₅₀ value of 0.50 μM against SeThrRS and MIC values of 16-32 μg/mL against the tested bacterial strains. The cocrystal structure of the SeThrRS-8g complex revealed that 8g induced a bended conformation for Met332 by forming hydrophobic interactions, which better mimicked the binding of tRNA^Thr to ThrRS. Moreover, the inhibitory potency of 8g was less impaired than a reported ATP competitive inhibitor at high concentrations of ATP, supporting our hypothesis that tRNA site inhibitors are likely superior to ATP site inhibitors in vivo, where ATP typically reaches millimolar concentrations.