9JIR

Crystal structure of V30M-TTR in complex with ioxynil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Repurposing of Agrochemicals as ATTRv Amyloidosis Inhibitors.

Yokoyama, T.Fujiwara, S.Nishikubo, K.Mizuguchi, M.Nabeshima, Y.Toyooka, N.Okada, T.Nakagawa, Y.

(2025) J Med Chem 68: 1572-1586

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02221
  • Primary Citation of Related Structures:  
    9JIQ, 9JIR, 9JIS

  • PubMed Abstract: 

    Transthyretin (TTR), a plasma protein, undergoes transformation into amyloid fibers, leading to ATTRv amyloidosis, a disease characterized by organ deposition of TTR amyloid fibrils and subsequent organ failure. Developing compounds that bind and kinetically stabilize TTR is a crucial strategy in the treatment of ATTRv amyloidosis. In this study, we narrowed 651 pesticide-related compounds down to 14 possible TTR binders through in silico screening; subsequent in vitro analysis revealed that 7 of them exhibited amyloid fibril formation inhibition activity. The herbicide components bromoxynil ( 6 ) and ioxynil ( 21 ) showed especially high ligand efficiency and efficiently inhibited amyloid fibril formation of amyloidogenic V30M-TTR. Additionally, aclonifen ( 9 ) exhibited moderate fibril formation inhibition activity, but showed selective binding to TTR comparable to that of tafamidis. While improvement is needed to the selective TTR-binding or fibril formation inhibition activity, the compounds identified herein are promising lead candidates for the development of ATTRv amyloidosis therapeutics.


  • Organizational Affiliation

    Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transthyretin
A, B
159Homo sapiensMutation(s): 1 
Gene Names: TTRPALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
PHAROS:  P02766
GTEx:  ENSG00000118271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02766
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.252α = 90
b = 84.398β = 90
c = 63.368γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-01-22 
  • Deposition Author(s): Yokoyama, T.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Database references