3G1M

EthR from Mycobacterium tuberculosis in complex with compound BDM31381


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Synthetic EthR inhibitors boost antituberculous activity of ethionamide.

Willand, N.Dirie, B.Carette, X.Bifani, P.Singhal, A.Desroses, M.Leroux, F.Willery, E.Mathys, V.Deprez-Poulain, R.Delcroix, G.Frenois, F.Aumercier, M.Locht, C.Villeret, V.Deprez, B.Baulard, A.R.

(2009) Nat Med 15: 537-544

  • DOI: 10.1038/nm.1950
  • Primary Citation of Related Structures:  
    3G1O, 3G1L, 3G1M

  • PubMed Abstract: 
  • The side effects associated with tuberculosis therapy bring with them the risk of noncompliance and subsequent drug resistance. Increasing the therapeutic index of antituberculosis drugs should thus improve treatment effectiveness. Several antituberculosis compounds require in situ metabolic activation to become inhibitory ...

    The side effects associated with tuberculosis therapy bring with them the risk of noncompliance and subsequent drug resistance. Increasing the therapeutic index of antituberculosis drugs should thus improve treatment effectiveness. Several antituberculosis compounds require in situ metabolic activation to become inhibitory. Various thiocarbamide-containing drugs, including ethionamide, are activated by the mycobacterial monooxygenase EthA, the production of which is controlled by the transcriptional repressor EthR. Here we identify drug-like inhibitors of EthR that boost the bioactivation of ethionamide. Compounds designed and screened for their capacity to inhibit EthR-DNA interaction were co-crystallized with EthR. We exploited the three-dimensional structures of the complexes for the synthesis of improved analogs that boosted the ethionamide potency in culture more than tenfold. In Mycobacterium tuberculosis-infected mice, one of these analogs, BDM31343, enabled a substantially reduced dose of ethionamide to lessen the mycobacterial load as efficiently as the conventional higher-dose treatment. This provides proof of concept that inhibiting EthR improves the therapeutic index of thiocarbamide derivatives, which should prompt reconsideration of their use as first-line drugs.


    Related Citations: 
    • Insights into mechanisms of induction and ligands recognition in the transcriptional repressor EthR from Mycobacterium tuberculosis.
      Frenois, F., Baulard, A.R., Villeret, V.
      (2006) Tuberculosis (Edinb) 86: 110
    • Structure of EthR in a ligand bound conformation reveals therapeutic perspectives against tuberculosis.
      Frenois, F., Engohang-Ndong, J., Locht, C., Baulard, A.R., Villeret, V.
      (2004) Mol Cell 16: 301
    • EthR, a repressor of the TetR/CamR family implicated in ethionamide resistance in mycobacteria, octamerizes cooperatively on its operator.
      Engohang-Ndong, J., Baillat, D., Aumercier, M., Bellefontaine, F., Besra, G.S., Locht, C., Baulard, A.R.
      (2004) Mol Microbiol 51: 175

    Organizational Affiliation

    Institut National de la Santé et de la Recherche Médicale, Lille, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHRA236Mycobacterium tuberculosisMutation(s): 0 
Gene Names: ethRMT3970Rv3855
UniProt
Find proteins for P9WMC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMC1 
Go to UniProtKB:  P9WMC1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RF3
Query on RF3

Download Ideal Coordinates CCD File 
B [auth A]1-(thiophen-2-ylacetyl)-4-(3-thiophen-2-yl-1,2,4-oxadiazol-5-yl)piperidine
C17 H17 N3 O2 S2
SJEVDMFUHCVNPM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RF3IC50:  500   nM  BindingDB
RF3IC50 :  500   nM  PDBBind
RF3IC50:  522   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.87α = 90
b = 121.87β = 90
c = 33.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-03-12
    Changes: Database references