4TQI

Human transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid in a dual binding mode


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystal structure and activity of fluorenyl-based compounds as transthyretin fibrillogenesis inhibitors.

Ciccone, L.Nencetti, S.Rossello, A.Tepshi, L.Stura, E.A.Orlandini, E.

(2015) J Enzyme Inhib Med Chem --: 1-10

  • DOI: 10.3109/14756366.2015.1070265
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transthyretin (TTR) is a 54 kDa homotetrameric protein that transports thyroxine (T4) and retinol (vitamin A), through its association with retinol binding protein (RBP). Under unknown conditions, it aggregates to form fibrils associated with TTR amy ...

    Transthyretin (TTR) is a 54 kDa homotetrameric protein that transports thyroxine (T4) and retinol (vitamin A), through its association with retinol binding protein (RBP). Under unknown conditions, it aggregates to form fibrils associated with TTR amyloidosis. Ligands able to inhibit fibril formation have been studied by X-ray crystallography. The use of polyethylene glycol (PEG) instead of ammonium sulphate or citrate has been evaluated as an alternative to obtain new TTR complexes with (R)-3-(9-fluoren-9-ylideneaminooxy)-2-methyl-N-(methylsulfonyl) propionamide (48R(1)) and 2-(9H-fluoren-9-ylideneaminooxy) acetic acid (ES8(2)). The previously described fluorenyl based inhibitors (S)-3-((9H-fluoren-9-ylideneamino)oxy)-2-methylpropanoic acid (6BD) and 3-((9H-fluoren-9-ylideneamino)oxy)propanoic acid (7BD) have been re-evaluated with the changed crystallization method. The new TTR complexes with compounds of the same family show that the 9-fluorenyl motif can occupy alternative hydrophobic binding sites. This augments the potential use of this scaffold to yield a large variety of differently substituted mono-aryl compounds able to inhibit TTR fibril formation.


    Organizational Affiliation

    a CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
127Homo sapiensGene Names: TTR (PALB)
Find proteins for P02766 (Homo sapiens)
Go to Gene View: TTR
Go to UniProtKB:  P02766
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6BD
Query on 6BD

Download SDF File 
Download CCD File 
A, B
(2S)-3-[(9H-fluoren-9-ylideneamino)oxy]-2-methylpropanoic acid
(S)-3-(9H-fluoren-9-ylideneaminooxy)-2-methylpropanoic acid
C17 H15 N O3
ZHFDVDMCVXUGGF-NSHDSACASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 43.250α = 90.00
b = 86.370β = 90.00
c = 63.340γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata scaling
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Derived calculations, Refinement description