6R1S

EthR ligand complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds.

Tatum, N.J.Duarte, F.Kamerlin, S.C.L.Pohl, E.

(2019) J Phys Chem Lett 10: 2244-2249

  • DOI: 10.1021/acs.jpclett.9b00741
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transcriptional repressor EthR from Mycobacterium tuberculosis is a valuable target for antibiotic booster drugs. We previously reported a virtual screening campaign to identify EthR inhibitors for development. Two ligand binding orientations were of ...

    Transcriptional repressor EthR from Mycobacterium tuberculosis is a valuable target for antibiotic booster drugs. We previously reported a virtual screening campaign to identify EthR inhibitors for development. Two ligand binding orientations were often proposed, though only the top scoring pose was utilized for filtering of the large data set. We obtained biophysically validated hits, some of which yielded complex crystal structures. In some cases, the crystallized binding mode and top scoring mode agree, while for others an alternate ligand binding orientation was found. In this contribution, we combine rigid docking, molecular dynamics simulations, and the linear interaction energy method to calculate binding free energies and derive relative binding energies for a number of EthR inhibitors in both modes. This strategy allowed us to correctly predict the most favorable orientation. Therefore, this widely applicable approach will be suitable to triage multiple binding modes within EthR and other potential drug targets with similar characteristics.


    Related Citations: 
    • New active leads for tuberculosis booster drugs by structure-based drug discovery.
      Tatum, N.J.,Liebeschuetz, J.W.,Cole, J.C.,Frita, R.,Herledan, A.,Baulard, A.R.,Willand, N.,Pohl, E.
      (2017) Org.Biomol.Chem. 15: 10245


    Organizational Affiliation

    Department of Chemistry , Durham University , South Road , Durham DH1 3LE , U.K.,Biophysical Sciences Institute , Durham University , Durham DH1 3LE , U.K.,Department of Biosciences , Durham University , Durham DH1 3LE , U.K.,Department of Chemistry - BMC , Uppsala University , BMC Box 576, S-751 23 Uppsala , Sweden.,Department of Chemistry, Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HTH-type transcriptional regulator EthR
A
216Mycobacterium 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
JPK
Query on JPK

Download SDF File 
Download CCD File 
A
2-(3-methylphenyl)-~{N}-[[2-(oxan-4-yl)-7-oxidanyl-pyrazolo[1,5-a]pyrimidin-5-yl]methyl]ethanamide
C21 H24 N4 O3
WQHBERINDYVLKU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.200 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 120.894α = 90.00
b = 120.894β = 90.00
c = 33.676γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-03-14 
  • Released Date: 2020-02-19 
  • Deposition Author(s): Pohl, E., Tatum, N.

Revision History 

  • Version 1.0: 2020-02-19
    Type: Initial release