RCSB PDB - 8PLC: Thioredoxin glutathione reductase of Schistosoma mansoni fragment screen hit 13.

 8PLC

Thioredoxin glutathione reductase of Schistosoma mansoni fragment screen hit 13.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni.

de Souza Neto, L.R.Montoya, B.O.Brandao-Neto, J.Verma, A.Bowyer, S.Moreira-Filho, J.T.Dantas, R.F.Neves, B.J.Andrade, C.H.von Delft, F.Owens, R.J.Furnham, N.Silva-Jr, F.P.

(2024) Sci Rep 14: 1582-1582

  • DOI: https://doi.org/10.1038/s41598-024-52018-2
  • Primary Citation of Related Structures:  
    8PDD, 8PL0, 8PL1, 8PL2, 8PL3, 8PL4, 8PL5, 8PL6, 8PL7, 8PL8, 8PL9, 8PLA, 8PLB, 8PLC, 8PLD, 8PLE, 8PLF, 8PLG, 8PLH, 8PLI, 8PLJ, 8PLK, 8PLL, 8PLM, 8PLN, 8PLO, 8PLP, 8PLQ, 8PLR, 8PLS, 8PLT, 8PLU, 8PLV, 8PLW, 8PLX, 8PLY

  • PubMed Abstract: 

    Schistosomiasis is caused by parasites of the genus Schistosoma, which infect more than 200 million people. Praziquantel (PZQ) has been the main drug for controlling schistosomiasis for over four decades, but despite that it is ineffective against juvenile worms and size and taste issues with its pharmaceutical forms impose challenges for treating school-aged children. It is also important to note that PZQ resistant strains can be generated in laboratory conditions and observed in the field, hence its extensive use in mass drug administration programs raises concerns about resistance, highlighting the need to search for new schistosomicidal drugs. Schistosomes survival relies on the redox enzyme thioredoxin glutathione reductase (TGR), a validated target for the development of new anti-schistosomal drugs. Here we report a high-throughput fragment screening campaign of 768 compounds against S. mansoni TGR (SmTGR) using X-ray crystallography. We observed 49 binding events involving 35 distinct molecular fragments which were found to be distributed across 16 binding sites. Most sites are described for the first time within SmTGR, a noteworthy exception being the "doorstop pocket" near the NADPH binding site. We have compared results from hotspots and pocket druggability analysis of SmTGR with the experimental binding sites found in this work, with our results indicating only limited coincidence between experimental and computational results. Finally, we discuss that binding sites at the doorstop/NADPH binding site and in the SmTGR dimer interface, should be prioritized for developing SmTGR inhibitors as new antischistosomal drugs.


  • Organizational Affiliation

    LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin glutathione reductase
A, B
597Schistosoma mansoniMutation(s): 0 
Gene Names: TGR
EC: 1.6.4.5 (PDB Primary Data), 1.8.1.9 (UniProt)
UniProt
Find proteins for Q962Y6 (Schistosoma mansoni)
Explore Q962Y6 
Go to UniProtKB:  Q962Y6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ962Y6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.12α = 90
b = 103.29β = 92.03
c = 133.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
xia2data reduction
xia2data scaling
DIMPLEphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A7NClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/M026221/1
Other government--
Medical Research Council (MRC, United Kingdom)United KingdomMR/K018779/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary