Ternary complex of E .coli leucyl-tRNA synthetase, tRNA(Leu) and the benzoxaborole AN3213 in the editing conformation

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report

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Discovery of a Novel Class of Boron-Based Antibacterials with Activity Against Gram-Negative Bacteria.

Hernandez, V.Crepin, T.Palencia, A.Cusack, S.Akama, T.Baker, S.J.Bu, W.Feng, L.Freund, Y.R.Liu, L.Meewan, M.Mohan, M.Mao, W.Rock, F.L.Sexton, H.Sheoran, A.Zhang, Y.Zhang, Y.Zhou, Y.Nieman, J.A.Anugula, M.R.Keramane, E.M.Savariraj, K.Reddy, D.S.Sharma, R.Subedi, R.Singh, R.O'Leary, A.Simon, N.L.De Marsh, P.L.Mushtaq, S.Warner, M.Livermore, D.M.Alley, M.R.K.Plattner, J.J.

(2013) Antimicrob Agents Chemother 57: 1394

  • DOI: https://doi.org/10.1128/AAC.02058-12
  • Primary Citation of Related Structures:  
    3ZJT, 3ZJU, 3ZJV

  • PubMed Abstract: 

    Gram-negative bacteria cause approximately 70% of the infections in intensive care units. A growing number of bacterial isolates responsible for these infections are resistant to currently available antibiotics and to many in development. Most agents under development are modifications of existing drug classes, which only partially overcome existing resistance mechanisms. Therefore, new classes of Gram-negative antibacterials with truly novel modes of action are needed to circumvent these existing resistance mechanisms. We have previously identified a new a way to inhibit an aminoacyl-tRNA synthetase, leucyl-tRNA synthetase (LeuRS), in fungi via the oxaborole tRNA trapping (OBORT) mechanism. Herein, we show how we have modified the OBORT mechanism using a structure-guided approach to develop a new boron-based antibiotic class, the aminomethylbenzoxaboroles, which inhibit bacterial leucyl-tRNA synthetase and have activity against Gram-negative bacteria by largely evading the main efflux mechanisms in Escherichia coli and Pseudomonas aeruginosa. The lead analogue, AN3365, is active against Gram-negative bacteria, including Enterobacteriaceae bearing NDM-1 and KPC carbapenemases, as well as P. aeruginosa. This novel boron-based antibacterial, AN3365, has good mouse pharmacokinetics and was efficacious against E. coli and P. aeruginosa in murine thigh infection models, which suggest that this novel class of antibacterials has the potential to address this unmet medical need.

  • Organizational Affiliation

    Anacor Pharmaceuticals Inc., Palo Alto, CA, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LEUCINE--TRNA LIGASE880Escherichia coliMutation(s): 0 
Find proteins for P07813 (Escherichia coli (strain K12))
Explore P07813 
Go to UniProtKB:  P07813
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07813
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
TRNALEU5 UAA ISOACCEPTOR87Escherichia coli K-12
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.37α = 90
b = 76.94β = 102.37
c = 90.71γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description