6HO0

TRANSCRIPTIONAL REPRESSOR ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH BDM41325


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR.

Tanina, A.Wohlkonig, A.Soror, S.H.Flipo, M.Villemagne, B.Prevet, H.Deprez, B.Moune, M.Peree, H.Meyer, F.Baulard, A.R.Willand, N.Wintjens, R.

(2018) Biochim Biophys Acta Proteins Proteom 1867: 248-258

  • DOI: 10.1016/j.bbapap.2018.12.003
  • Primary Citation of Related Structures:  
    6HO6, 6HO5, 6HO8, 6HO7, 6HNX, 6HO9, 6HNZ, 6HO0, 6HO2, 6HO1, 6HO4, 6HO3, 6HOF, 6HOE, 6HOB, 6HOA, 6HOD, 6HOC

  • PubMed Abstract: 
  • The Mycobacterium tuberculosis EthR is a member of the TetR family of repressors, controlling the expression of EthA, a mono-oxygenase responsible for the bioactivation of the prodrug ethionamide. This protein was established as a promising therapeutic target against tuberculosis, allowing, when inhibited by a drug-like molecule, to boost the action of ethionamide ...

    The Mycobacterium tuberculosis EthR is a member of the TetR family of repressors, controlling the expression of EthA, a mono-oxygenase responsible for the bioactivation of the prodrug ethionamide. This protein was established as a promising therapeutic target against tuberculosis, allowing, when inhibited by a drug-like molecule, to boost the action of ethionamide. Dozens of EthR crystal structures have been solved in complex with ligands. Herein, we disclose EthR structures in complex with 18 different small molecules and then performed in-depth analysis on the complete set of EthR structures that provides insights on EthR-ligand interactions. The 81 molecules solved in complex with EthR show a large diversity of chemical structures that were split up into several chemical clusters. Two of the most striking common points of EthR-ligand interactions are the quasi-omnipresence of a hydrogen bond bridging compounds with Asn 179 and the high occurrence of π-π interactions involving Phe 110 . A systematic analysis of the protein-ligand contacts identified eight hot spot residues that defined the basic structural features governing the binding mode of small molecules to EthR. Implications for the design of new potent inhibitors are discussed.


    Organizational Affiliation

    Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium. Electronic address: Wintjens@ulb.ac.be.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HTH-type transcriptional regulator EthRA228Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: ethRetaRRv3855
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
GFK (Subject of Investigation/LOI)
Query on GFK

Download Ideal Coordinates CCD File 
B [auth A]4,4,4-tris(fluoranyl)-1-[4-[3-(6-methoxy-1,3-benzothiazol-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl]butan-1-one
C19 H19 F3 N4 O3 S
MDFQKZXRTVTODM-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GFK BindingDB:  6HO0 IC50: 1000 (nM) from 1 assay(s)
EC50: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.385α = 90
b = 121.385β = 90
c = 33.715γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references