20YD

Crystal structure of Escherichia coli ThrRS complexing with obafluorin derived inhibitor OB-D4

This is a non-PDB format compatible entry.

Summary for 20YD

• Entry DOI: 10.2210/pdb20yd/pdb
• Descriptor: Threonine--tRNA ligase, ZINC ION, (2~{S},3~{R})-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-4-(4-methoxyphenyl)-3-oxidanyl-butanoic acid, ... (4 entities in total)
• Functional Keywords: inhibitor, complex, covalent-inhibitor, ligase
• Biological source: Escherichia coli (strain K12)
• Total number of polymer chains: 1
• Total formula weight: 48354.27

Authors

Wang, Z.,Xia, M.,Fang, P. (deposition date: 2025-12-03, release date: 2026-10-21, Last modification date: 2026-11-04)

Primary citation

Wang, Z.,Zhang, Z.,Xia, M.,Fang, M.,Xu, H.,Qiao, H.,Ding, W.,Huang, J.,Li, G.,Luo, K.,Liu, W.,Wang, J.,Yu, B.,Fang, P.
Leveraging Protein Dynamics for Selective Inhibition of Threonyl-tRNA Synthetase by Obafluorin Analogs.
Angew.Chem.Int.Ed.Engl., 65:-, 2026

PubMed Abstract: The widespread emergence of antibiotic resistance necessitates the development of novel agents with unique mechanisms of action. Obafluorin (OB), a natural β-lactone antibiotic, is a covalent inhibitor of threonyl-tRNA synthetase (ThrRS), but the high conservation of the active site between prokaryote and eukaryote ThrRSs results in minimal selectivity, hindering the therapeutic potential of OB. Here, we report a structure dynamics-based design strategy that transforms OB into a selective antibacterial agent. OB inhibits human and bacterial ThrRSs with nearly equal potency due to identical binding modes. The nitrophenyl moiety of OB is proposed as a 'kinetic sensor' that discriminates between sensitive and resistant ThrRS paralogs. Guided by this insight, we designed a series of OB analogs through rational modification of this moiety. Among them, OB-D4 bearing a para-methoxyphenyl group in place of the nitrophenyl group, exhibited a 241-fold selectivity for bacterial over human ThrRS, along with a markedly improved safety profile with minimal cytotoxicity. In a murine skin infection model, OB-D4 effectively eradicated pathogens, resolving inflammation, and promoting wound healing. Together, this work establishes a 'kinetic sensor' strategy for achieving species selectivity, turning a fundamental challenge in drug discovery-high active-site conservation-into an exploitable opportunity based on dynamic differences.

PubMed: 42677972
DOI: 10.1002/anie.5509036

Experimental method

X-RAY DIFFRACTION (1.9 Å)