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 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1016/j.ejmech.2019.02.023
  • Primary Citation of Related Structures:  
    6HRW, 6HRX, 6HRY, 6HRZ, 6HS0, 6HS1, 6HS2

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable transcriptional regulatory protein
A, B
221Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv0078
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
GNZ
Query on GNZ

Download Ideal Coordinates CCD File 
C [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
GNZ Binding MOAD:  6HS2 IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.48α = 90
b = 73.57β = 90
c = 91.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
MOLREPphasing
autoPROCdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description