5BOJ

Crystal Structure of Human Transthyretin in Complex with Gemfibrozil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Enthalpic Forces Correlate with the Selectivity of Transthyretin-Stabilizing Ligands in Human Plasma.

Iakovleva, I.Brannstrom, K.Nilsson, L.Gharibyan, A.L.Begum, A.Anan, I.Walfridsson, M.Sauer-Eriksson, A.E.Olofsson, A.

(2015) J.Med.Chem. 58: 6507-6515

  • DOI: 10.1021/acs.jmedchem.5b00544

  • PubMed Abstract: 
  • The plasma protein transthyretin (TTR) is linked to human amyloidosis. Dissociation of its native tetrameric assembly is a rate-limiting step in the conversion from a native structure into a pathological amyloidogenic fold. Binding of small molecule ...

    The plasma protein transthyretin (TTR) is linked to human amyloidosis. Dissociation of its native tetrameric assembly is a rate-limiting step in the conversion from a native structure into a pathological amyloidogenic fold. Binding of small molecule ligands within the thyroxine binding site of TTR can stabilize the tetrameric integrity and is a potential therapeutic approach. However, through the characterization of nine different tetramer-stabilizing ligands we found that unspecific binding to plasma components might significantly compromise ligand efficacy. Surprisingly the binding strength between a particular ligand and TTR does not correlate well with its selectivity in plasma. However, through analysis of the thermodynamic signature using isothermal titration calorimetry we discovered a better correlation between selectivity and the enthalpic component of the interaction. This is of specific interest in the quest for more efficient TTR stabilizers, but a high selectivity is an almost universally desired feature within drug design and the finding might have wide-ranging implications for drug design.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Umeå University , 901 87 Umeå, Sweden.




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
4TX
Query on 4TX

Download SDF File 
Download CCD File 
A, B
5-(2,5-dimethylphenoxy)-2,2-dimethylpentanoic acid
C15 H22 O3
HEMJJKBWTPKOJG-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4TXKd: 100 nM (100) BINDINGDB
4TXIC50: 180000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.685α = 90.00
b = 85.409β = 90.00
c = 63.624γ = 90.00
Software Package:
Software NamePurpose
SADABSdata scaling
PHENIXphasing
SAINTdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Database references
  • Version 1.2: 2015-09-09
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence