6FP4

Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 1,8-Naphthyridine-2-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Fragment-Based Discovery of a Regulatory Site in Thioredoxin Glutathione Reductase Acting as "Doorstop" for NADPH Entry.

Silvestri, I.Lyu, H.Fata, F.Boumis, G.Miele, A.E.Ardini, M.Ippoliti, R.Bellelli, A.Jadhav, A.Lea, W.A.Simeonov, A.Cheng, Q.Arner, E.S.J.Thatcher, G.R.J.Petukhov, P.A.Williams, D.L.Angelucci, F.

(2018) ACS Chem Biol 13: 2190-2202

  • DOI: 10.1021/acschembio.8b00349
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Members of the FAD/NAD-linked reductase family are recognized as crucial targets in drug development for cancers, inflammatory disorders, and infectious diseases. However, individual FAD/NAD reductases are difficult to inhibit in a selective manner w ...

    Members of the FAD/NAD-linked reductase family are recognized as crucial targets in drug development for cancers, inflammatory disorders, and infectious diseases. However, individual FAD/NAD reductases are difficult to inhibit in a selective manner with off-target inhibition reducing usefulness of identified compounds. Thioredoxin glutathione reductase (TGR), a high molecular weight thioredoxin reductase-like enzyme, has emerged as a promising drug target for the treatment of schistosomiasis, a parasitosis afflicting more than 200 million people. Taking advantage of small molecules selected from a high-throughput screen and using X-ray crystallography, functional assays, and docking studies, we identify a critical secondary site of the enzyme. Compounds binding at this site interfere with well-known and conserved conformational changes associated with NADPH reduction, acting as a doorstop for cofactor entry. They selectively inhibit TGR from Schistosoma mansoni and are active against parasites in culture. Since many members of the FAD/NAD-linked reductase family have similar catalytic mechanisms, the unique mechanism of inhibition identified in this study for TGR broadly opens new routes to selectively inhibit homologous enzymes of central importance in numerous diseases.


    Organizational Affiliation

    Department of Life, Health and Environmental Sciences , University of L'Aquila , 67100 L'Aquila , Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thioredoxin glutathione reductaseA598Schistosoma mansoniMutation(s): 0 
Gene Names: Smp_048430
EC: 1.8.1.9
Find proteins for G4V8J4 (Schistosoma mansoni)
Explore G4V8J4 
Go to UniProtKB:  G4V8J4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
250
Query on 250

Download CCD File 
A
(2R)-2-hydroxy-3-[4-(2-hydroxyethyl)piperazin-1-yl]propane-1-sulfonic acid
C9 H20 N2 O5 S
GIZQLVPDAOBAFN-SECBINFHSA-N
 Ligand Interaction
E1T
Query on E1T

Download CCD File 
A
1,8-naphthyridine-2-carboxylic acid
C9 H6 N2 O2
SNLMOXFUCILIPL-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
E1TIC50:  1100000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.316α = 90
b = 101.584β = 112.78
c = 58.783γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NIH-NIAIDUnited States1R21AI27635-01

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references