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 

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

  • 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: 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1FL
Query on 1FL

Download SDF File 
Download CCD File 
A, B
5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID
Diflunisal
C13 H8 F2 O3
HUPFGZXOMWLGNK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1FLEC50: 5600 nM (99) BINDINGDB
1FLKd: 580 nM (99) BINDINGDB
1FLIC50: 25000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.800α = 90.00
b = 86.220β = 90.00
c = 64.320γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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