5E23

Human transthyretin (TTR) complexed with (2,7-Dibromo-fluoren-9-ylideneaminooxy)-acetic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis and structural analysis of halogen substituted fibril formation inhibitors of Human Transthyretin (TTR).

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

(2016) J Enzyme Inhib Med Chem 31: 40-51

  • DOI: 10.3109/14756366.2016.1167048
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transthyretin (TTR), a β-sheet-rich tetrameric protein, in equilibrium with an unstable amyloidogenic monomeric form is responsible for extracellular deposition of amyloid fibrils, is associated with the onset of neurodegenerative diseases, such as s ...

    Transthyretin (TTR), a β-sheet-rich tetrameric protein, in equilibrium with an unstable amyloidogenic monomeric form is responsible for extracellular deposition of amyloid fibrils, is associated with the onset of neurodegenerative diseases, such as senile systemic amyloidosis, familial amyloid polyneuropathy and familial amyloid cardiomyopathy. One of the therapeutic strategies is to use small molecules to stabilize the TTR tetramer and thus curb amyloid fibril formation. Here, we report the synthesis, the in vitro evaluation of several halogen substituted 9-fluorenyl- and di-benzophenon-based ligands and their three-dimensional crystallographic analysis in complex with TTR. The synthesized compounds bind TTR and stabilize the tetramer with different potency. Of these compounds, 2c is the best inhibitor. The dual binding mode prevalent in the absence of substitutions on the fluorenyl ring, is disfavored by (2,7-dichloro-fluoren-9-ylideneaminooxy)-acetic acid (1b), (2,7-dibromo-fluoren-9-ylideneaminooxy)-acetic acid (1c) and (E/Z)-((3,4-dichloro-phenyl)-methyleneaminooxy)-acetic acid (2c), all with halogen substitutions.


    Organizational Affiliation

    a Dipartimento di Farmacia , Università di Pisa , Pisa , Italy 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
L32
Query on L32

Download SDF File 
Download CCD File 
A
{[(2,7-dibromo-9H-fluoren-9-ylidene)amino]oxy}acetic acid
C15 H9 Br2 N O3
SSUCUHRDWSCTFP-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 43.222α = 90.00
b = 85.961β = 90.00
c = 63.348γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACphasing
XSCALEdata scaling
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Ministero dell' IstruzioneItalyPRIN 20109MXHMR_007

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references
  • Version 1.2: 2016-12-07
    Type: Database references