3ZJT

Ternary complex of E.coli leucyl-tRNA synthetase, tRNA(Leu)574 and the benzoxaborole AN3017 in the editing conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1128/AAC.02058-12
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEUCYL-TRNA SYNTHETASE
A
880Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: leuS
EC: 6.1.1.4
Find proteins for P07813 (Escherichia coli (strain K12))
Go to UniProtKB:  P07813
Entity ID: 2
MoleculeChainsLengthOrganism
TRNALEU5 UAA ISOACCEPTORB88Escherichia coli K-12
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
574
Query on 574
B
RNA LINKINGC18 H22 B N6 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.900α = 90.00
b = 118.800β = 90.00
c = 140.400γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History