6FP4 | pdb_00006fp4

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 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6FP4

Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/acschembio.8b00349
  • Primary Citation Related Structures: 
    6FMU, 6FMZ, 6FP4, 6FTC

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 66.66 kDa 
  • Atom Count: 4,694 
  • Modeled Residue Count: 587 
  • Deposited Residue Count: 598 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thioredoxin glutathione reductase598Schistosoma mansoniMutation(s): 0 
Gene Names: Smp_048430
EC: 1.8.1.9

Small Molecules

Ligands 5 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
250

Query on 250



Download:Ideal Coordinates CCD File
G [auth A](2R)-2-hydroxy-3-[4-(2-hydroxyethyl)piperazin-1-yl]propane-1-sulfonic acid
C9 H20 N2 O5 S
GIZQLVPDAOBAFN-SECBINFHSA-N
E1T
(Subject of Investigation/LOI)

Query on E1T



Download:Ideal Coordinates CCD File
E [auth A]1,8-naphthyridine-2-carboxylic acid
C9 H6 N2 O2
SNLMOXFUCILIPL-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
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.229 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
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



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 States1R21AI27635-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary