5ICJ

Crystal structure of the Mycobacterium tuberculosis transcriptional repressor EthR2 in complex with BDM41420


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420.

Blondiaux, N.Moune, M.Desroses, M.Frita, R.Flipo, M.Mathys, V.Soetaert, K.Kiass, M.Delorme, V.Djaout, K.Trebosc, V.Kemmer, C.Wintjens, R.Wohlkonig, A.Antoine, R.Huot, L.Hot, D.Coscolla, M.Feldmann, J.Gagneux, S.Locht, C.Brodin, P.Gitzinger, M.Deprez, B.Willand, N.Baulard, A.R.

(2017) Science 355: 1206-1211

  • DOI: https://doi.org/10.1126/science.aag1006
  • Primary Citation of Related Structures:  
    5ICJ, 5N1C, 5N1I

  • PubMed Abstract: 

    Antibiotic resistance is one of the biggest threats to human health globally. Alarmingly, multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis have now spread worldwide. Some key antituberculosis antibiotics are prodrugs, for which resistance mechanisms are mainly driven by mutations in the bacterial enzymatic pathway required for their bioactivation. We have developed drug-like molecules that activate a cryptic alternative bioactivation pathway of ethionamide in M. tuberculosis , circumventing the classic activation pathway in which resistance mutations have now been observed. The first-of-its-kind molecule, named SMARt-420 (Small Molecule Aborting Resistance), not only fully reverses ethionamide-acquired resistance and clears ethionamide-resistant infection in mice, it also increases the basal sensitivity of bacteria to ethionamide.


  • Organizational Affiliation

    Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable transcriptional regulatory protein
A, B
221Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv0078LH57_00450
UniProt
Find proteins for O53623 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O53623 
Go to UniProtKB:  O53623
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO53623
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
69Y
Query on 69Y

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4,4,4-trifluoro-1-(3-phenyl-1-oxa-2,8-diazaspiro[4.5]dec-2-en-8-yl)butan-1-one
C17 H19 F3 N2 O2
IBVDSAFESRHIBV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.8α = 90
b = 74.21β = 90
c = 88.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
MOLREPphasing
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description