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 
  • R-Value Observed: 0.173 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.3109/14756366.2016.1167048
  • Primary Citation of Related Structures:  
    5E23, 5E4A, 5E4O

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transthyretin
A, B
127Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L32
Query on L32

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

Download Ideal Coordinates CCD File 
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.222α = 90
b = 85.961β = 90
c = 63.348γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell' IstruzioneItalyPRIN 20109MXHMR_007

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2016-12-07
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description