5AGS

Crystal structure of the LeuRS editing domain of Mycobacterium tuberculosis in complex with the adduct 3-(Aminomethyl)-4-bromo-7-ethoxybenzo[c][1,2]oxaborol-1(3H)-ol-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    5AGR, 5AGS, 5AGT

  • 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 role in the treatment of tuberculosis (TB) starting with the inclusion of streptomycin in the first combination therapies ...

    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

    Anacor Pharmaceuticals, Palo Alto, California, USA dickon_alley@mac.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LEUCYL-TRNA SYNTHETASEA232Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: leuSRv0041MTCY21D4.04
EC: 6.1.1.4
UniProt
Find proteins for P9WFV1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFV1 
Go to UniProtKB:  P9WFV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFV1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
38Y
Query on 38Y

Download Ideal Coordinates CCD File 
C [auth A]3-(AMINOMETHYL)-4-BROMO-7-ETHOXYBENZO[C][1,2]OXABOROL-1(3H)-OL-MODIFIED ADENOSINE
C20 H25 B Br N6 O9 P
SFZDVNHRQSVZOB-CDUMDVBJSA-N
 Ligand Interaction
MET
Query on MET

Download Ideal Coordinates CCD File 
B [auth A]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.75α = 90
b = 62.16β = 90
c = 76.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2016-10-05
    Changes: Database references
  • Version 1.3: 2017-08-09
    Changes: Data collection