5AGR

Crystal structure of the LeuRS editing domain of Mycobacterium tuberculosis in complex with the adduct (S)-3-(Aminomethyl)-7-ethoxybenzo[c][1,2]oxaborol-1(3H)-ol-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery of Novel Oral Protein Synthesis Inhibitors of Mycobacterium Tuberculosis that Target Leucyl-tRNA Synthetase.

Palencia, A.Li, X.Bu, W.Choi, W.Ding, C.Z.Easom, E.E.Feng, L.Hernandez, V.Houston, P.Liu, L.Meewan, M.Mohan, M.Rock, F.L.Sexton, H.Zhang, S.Zhou, Y.Wan, B.Wang, Y.Franzblau, S.G.Woolhiser, L.Gruppo, V.Lenaerts, A.J.O'Malley, T.Parish, T.Cooper, C.B.Waters, M.G.Ma, Z.Ioerger, T.R.Sacchettini, J.C.Rullas, J.Angulo-Barturen, I.Perez-Herran, E.Mendoza, A.Barros, D.Cusack, S.Plattner, J.J.Alley, M.R.K.

(2016) Antimicrob.Agents Chemother. 60: 6271

  • DOI: 10.1128/AAC.01339-16
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The recent development and spread of extensively drug-resistant and totally drug-resistant resistant (TDR) strains of Mycobacterium tuberculosis highlight the need for new antitubercular drugs. Protein synthesis inhibitors have played an important ro ...

    The recent development and spread of extensively drug-resistant and totally drug-resistant resistant (TDR) strains of Mycobacterium tuberculosis highlight the need for new antitubercular drugs. Protein synthesis inhibitors have played an important role in the treatment of tuberculosis (TB) starting with the inclusion of streptomycin in the first combination therapies. Although parenteral aminoglycosides are a key component of therapy for multidrug-resistant TB, the oxazolidinone linezolid is the only orally available protein synthesis inhibitor that is effective against TB. Here, we show that small-molecule inhibitors of aminoacyl-tRNA synthetases (AARSs), which are known to be excellent antibacterial protein synthesis targets, are orally bioavailable and effective against M. tuberculosis in TB mouse infection models. We applied the oxaborole tRNA-trapping (OBORT) mechanism, which was first developed to target fungal cytoplasmic leucyl-tRNA synthetase (LeuRS), to M. tuberculosis LeuRS. X-ray crystallography was used to guide the design of LeuRS inhibitors that have good biochemical potency and excellent whole-cell activity against M. tuberculosis Importantly, their good oral bioavailability translates into in vivo efficacy in both the acute and chronic mouse models of TB with potency comparable to that of the frontline drug isoniazid.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEUCINE--TRNA LIGASE
A
232Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: leuS
EC: 6.1.1.4
Find proteins for P9WFV1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WFV1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A52
Query on A52

Download SDF File 
Download CCD File 
A
3-AMINOMETHYL-7-(ETHOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine
C20 H23 B N6 O9 P
WLOBNXOMDQETEC-IMBSHPNCSA-L
 Ligand Interaction
LEU
Query on LEU

Download SDF File 
Download CCD File 
A
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MET
Query on MET

Download SDF File 
Download CCD File 
A
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.330α = 90.00
b = 61.850β = 90.00
c = 77.080γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-08-24
    Type: Database references
  • Version 1.2: 2016-10-05
    Type: Database references
  • Version 1.3: 2018-06-20
    Type: Advisory, Data collection, Derived calculations