6HS2

EthR2 in complex with compound 31 (BDM76150)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A fragment-based approach towards the discovery of N-substituted tropinones as inhibitors of Mycobacterium tuberculosis transcriptional regulator EthR2.

Prevet, H.Moune, M.Tanina, A.Kemmer, C.Herledan, A.Frita, R.Wohlkonig, A.Bourotte, M.Villemagne, B.Leroux, F.Gitzinger, M.Baulard, A.R.Deprez, B.Wintjens, R.Willand, N.Flipo, M.

(2019) Eur J Med Chem 167: 426-438

  • DOI: 10.1016/j.ejmech.2019.02.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tuberculosis (TB) caused by the pathogen Mycobacterium tuberculosis, represents one of the most challenging threat to public health worldwide, and with the increasing resistance to approved TB drugs, it is needed to develop new strategies to address ...

    Tuberculosis (TB) caused by the pathogen Mycobacterium tuberculosis, represents one of the most challenging threat to public health worldwide, and with the increasing resistance to approved TB drugs, it is needed to develop new strategies to address this issue. Ethionamide is one of the most widely used drugs for the treatment of multidrug-resistant TB. It is a prodrug that requires activation by mycobacterial monooxygenases to inhibit the enoyl-ACP reductase InhA, which is involved in mycolic acid biosynthesis. Very recently, we identified that inhibition of a transcriptional repressor, termed EthR2, derepresses a new bioactivation pathway that results in the boosting of ethionamide activation. Herein, we describe the identification of potent EthR2 inhibitors using fragment-based screening and structure-based optimization. A target-based screening of a fragment library using thermal shift assay followed by X-ray crystallography identified 5 hits. Rapid optimization of the tropinone chemical series led to compounds with improved in vitro potency.


    Organizational Affiliation

    Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable transcriptional regulatory protein
A, B
221Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Find proteins for O53623 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  O53623
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNZ
Query on GNZ

Download SDF File 
Download CCD File 
B
(1~{S},5~{R})-8-[2-[4-(trifluoromethyl)phenyl]ethyl]-8-azabicyclo[3.2.1]octan-3-one
C16 H18 F3 N O
AOEXBMYHDDUFNM-OKILXGFUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.480α = 90.00
b = 73.570β = 90.00
c = 91.100γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
AutoPROCdata collection
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release