3GS4

Human transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid (inhibitor 15)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Novel transthyretin amyloid fibril formation inhibitors: synthesis, biological evaluation, and X-ray structural analysis.

Palaninathan, S.K.Mohamedmohaideen, N.N.Orlandini, E.Ortore, G.Nencetti, S.Lapucci, A.Rossello, A.Freundlich, J.S.Sacchettini, J.C.

(2009) Plos One 4: e6290-e6290

  • DOI: 10.1371/journal.pone.0006290
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transthyretin (TTR) is one of thirty non-homologous proteins whose misfolding, dissociation, aggregation, and deposition is linked to human amyloid diseases. Previous studies have identified that TTR amyloidogenesis can be inhibited through stabiliza ...

    Transthyretin (TTR) is one of thirty non-homologous proteins whose misfolding, dissociation, aggregation, and deposition is linked to human amyloid diseases. Previous studies have identified that TTR amyloidogenesis can be inhibited through stabilization of the native tetramer state by small molecule binding to the thyroid hormone sites of TTR. We have evaluated a new series of beta-aminoxypropionic acids (compounds 5-21), with a single aromatic moiety (aryl or fluorenyl) linked through a flexible oxime tether to a carboxylic acid. These compounds are structurally distinct from the native ligand thyroxine and typical halogenated biaryl NSAID-like inhibitors to avoid off-target hormonal or anti-inflammatory activity. Based on an in vitro fibril formation assay, five of these compounds showed significant inhibition of TTR amyloidogenesis, with two fluorenyl compounds displaying inhibitor efficacy comparable to the well-known TTR inhibitor diflunisal. Fluorenyl 15 is the most potent compound in this series and importantly does not show off-target anti-inflammatory activity. Crystal structures of the TTR:inhibitor complexes, in agreement with molecular docking studies, revealed that the aromatic moiety, linked to the sp(2)-hybridized oxime carbon, specifically directed the ligand in either a forward or reverse binding mode. Compared to the aryl family members, the bulkier fluorenyl analogs achieved more extensive interactions with the binding pockets of TTR and demonstrated better inhibitory activity in the fibril formation assay. Preliminary optimization efforts are described that focused on replacement of the C-terminal acid in both the aryl and fluorenyl series (compounds 22-32). The compounds presented here constitute a new class of TTR inhibitors that may hold promise in treating amyloid diseases associated with TTR misfolding.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
127Homo sapiensMutation(s): 0 
Gene Names: TTR (PALB)
Find proteins for P02766 (Homo sapiens)
Go to Gene View: TTR
Go to UniProtKB:  P02766
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7BD
Query on 7BD

Download SDF File 
Download CCD File 
A, B
3-[(9H-fluoren-9-ylideneamino)oxy]propanoic acid
3-(9H-fluoren-9-ylideneaminooxy)propanoic acid
C16 H13 N O3
LASWLEUVWJDDBA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 43.185α = 90.00
b = 85.726β = 90.00
c = 64.775γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata scaling
AMoREphasing
CrystalCleardata reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance