6RTM

Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 1-[(dimethylamino)methyl]-2-naphthol at 2 hour of soaking


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Ectopic suicide inhibition of thioredoxin glutathione reductase.

Silvestri, I.Lyu, H.Fata, F.Banta, P.R.Mattei, B.Ippoliti, R.Bellelli, A.Pitari, G.Ardini, M.Petukhova, V.Thatcher, G.R.J.Petukhov, P.A.Williams, D.L.Angelucci, F.

(2020) Free Radic Biol Med 147: 200-211

  • DOI: https://doi.org/10.1016/j.freeradbiomed.2019.12.019
  • Primary Citation of Related Structures:  
    6RTJ, 6RTM, 6RTO

  • PubMed Abstract: 

    Selective suicide inhibitors represent a seductively attractive approach for inactivation of therapeutically relevant enzymes since they are generally devoid of off-target toxicity in vivo. While most suicide inhibitors are converted to reactive species at enzyme active sites, theoretically bioactivation can also occur in ectopic (secondary) sites that have no known function. Here, we report an example of such an "ectopic suicide inhibition", an unprecedented bioactivation mechanism of a suicide inhibitor carried out by a non-catalytic site of thioredoxin glutathione reductase (TGR). TGR is a promising drug target to treat schistosomiasis, a devastating human parasitic disease. Utilizing hits selected from a high throughput screening campaign, time-resolved X-ray crystallography, molecular dynamics, mass spectrometry, molecular modeling, protein mutagenesis and functional studies, we find that 2-naphtholmethylamino derivatives bound to this novel ectopic site of Schistosoma mansoni (Sm)TGR are transformed to covalent modifiers and react with its mobile selenocysteine-containing C-terminal arm. In particular, one 2-naphtholmethylamino compound is able to specifically induce the pro-oxidant activity in the inhibited enzyme. Since some 2-naphtholmethylamino analogues show worm killing activity and the ectopic site is not conserved in human orthologues, a general approach to development of novel and selective anti-parasitic therapeutics against schistosoma is proposed.


  • Organizational Affiliation

    Dept. of Life, Health and Environmental Sciences, University of L'Aquila, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin glutathione reductase598Schistosoma mansoniMutation(s): 0 
Gene Names: Smp_048430
EC: 1.8.1.9
UniProt
Find proteins for A0A3Q0KFL1 (Schistosoma mansoni)
Explore A0A3Q0KFL1 
Go to UniProtKB:  A0A3Q0KFL1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3Q0KFL1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
KJH (Subject of Investigation/LOI)
Query on KJH

Download Ideal Coordinates CCD File 
F [auth A]1-methylidenenaphthalen-2-one
C11 H8 O
CPUOMPRQOCEZSL-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.042α = 90
b = 102.002β = 112.78
c = 58.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR33AI127635

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references
  • Version 1.2: 2020-07-29
    Changes: Database references, Derived calculations
  • Version 1.3: 2022-03-30
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2024-01-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary