4I89

Crystal structure of transthyretin in complex with diflunisal at acidic pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural evidence for native state stabilization of a conformationally labile amyloidogenic transthyretin variant by fibrillogenesis inhibitors.

Zanotti, G.Cendron, L.Folli, C.Florio, P.Imbimbo, B.P.Berni, R.

(2013) FEBS Lett 587: 2325-2331

  • DOI: 10.1016/j.febslet.2013.06.016
  • Primary Citation of Related Structures:  
    4I85, 4I87, 4I89

  • PubMed Abstract: 
  • Several classes of chemicals are able to bind to the thyroxine binding sites of transthyretin (TTR), stabilizing its native state and inhibiting in vitro the amyloidogenic process. The amyloidogenic I84S TTR variant undergoes a large conformational c ...

    Several classes of chemicals are able to bind to the thyroxine binding sites of transthyretin (TTR), stabilizing its native state and inhibiting in vitro the amyloidogenic process. The amyloidogenic I84S TTR variant undergoes a large conformational change at moderately acidic pH. Structural evidence has been obtained by X-ray analysis for the native state stabilization of I84S TTR by two chemically distinct fibrillogenesis inhibitors. In fact, they fully prevent the acidic pH-induced protein conformational change as a result of a long-range stabilizing effect. This study provides further support to the therapeutic strategy based on the use of TTR stabilizers as anti-amyloidogenic drugs.


    Related Citations: 
    • Acidic pH-induced conformational changes in amyloidogenic mutant transthyretin.
      Pasquato, N., Berni, R., Folli, C., Alfieri, B., Cendron, L., Zanotti, G.
      (2007) J Mol Biol 366: 711
    • Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses.
      Cendron, L., Trovato, A., Seno, F., Folli, C., Alfieri, B., Zanotti, G., Berni, R.
      (2009) J Biol Chem 284: 25832

    Organizational Affiliation

    Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy. giuseppe.zanotti@unipd.it



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TransthyretinAB127Homo sapiensMutation(s): 1 
Gene Names: PALBTTR
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
NIH Common Fund Data Resources
PHAROS  P02766
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1FL
Query on 1FL

Download CCD File 
A, B
5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID
C13 H8 F2 O3
HUPFGZXOMWLGNK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1FLIC50:  25000   nM  BindingDB
1FLEC50:  5600   nM  BindingDB
1FLKd:  580   nM  BindingDB
1FLKd:  407   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.8α = 90
b = 86.22β = 90
c = 64.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2013-08-07
    Changes: Non-polymer description