5EYR

Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound 5 at 1.57A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A fragment merging approach towards the development of small molecule inhibitors of Mycobacterium tuberculosis EthR for use as ethionamide boosters.

Nikiforov, P.O.Surade, S.Blaszczyk, M.Delorme, V.Brodin, P.Baulard, A.R.Blundell, T.L.Abell, C.

(2016) Org.Biomol.Chem. 14: 2318-2326

  • DOI: 10.1039/c5ob02630j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • With the ever-increasing instances of resistance to frontline TB drugs there is the need to develop novel strategies to fight the worldwide TB epidemic. Boosting the effect of the existing second-line antibiotic ethionamide by inhibiting the mycobact ...

    With the ever-increasing instances of resistance to frontline TB drugs there is the need to develop novel strategies to fight the worldwide TB epidemic. Boosting the effect of the existing second-line antibiotic ethionamide by inhibiting the mycobacterial transcriptional repressor protein EthR is an attractive therapeutic strategy. Herein we report the use of a fragment based drug discovery approach for the structure-guided systematic merging of two fragment molecules, each binding twice to the hydrophobic cavity of EthR from M. tuberculosis. These together fill the entire binding pocket of EthR. We elaborated these fragment hits and developed small molecule inhibitors which have a 100-fold improvement of potency in vitro over the initial fragments.


    Organizational Affiliation

    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. ca26@cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EthR
A
228Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ethR (etaR)
Find proteins for P9WMC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WMC1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5T0
Query on 5T0

Download SDF File 
Download CCD File 
A
3-[1-[4-(methylaminomethyl)phenyl]piperidin-4-yl]-1-pyrrolidin-1-yl-propan-1-one
C20 H31 N3 O
VOLHWJLFFDGPRY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.186 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 120.885α = 90.00
b = 120.885β = 90.00
c = 33.829γ = 90.00
Software Package:
Software NamePurpose
AutoPROCdata reduction
PHASERphasing
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--
Bill & Melinda Gates FoundationUnited States--
European Union--

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence