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 
  • R-Value Observed: 0.172 

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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
  • Primary Citation of Related Structures:  
    5BOJ

  • 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 ligands within the thyroxine binding site of TTR can stabilize the tetrameric integrity and is a potential therapeutic approach ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TransthyretinA, B127Homo sapiensMutation(s): 0 
Gene Names: TTRPALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
PHAROS:  P02766
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02766
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4TX
Query on 4TX

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
5-(2,5-dimethylphenoxy)-2,2-dimethylpentanoic acid
C15 H22 O3
HEMJJKBWTPKOJG-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4TX BindingDB:  5BOJ Kd: 100 (nM) from 1 assay(s)
IC50: 1.80e+5 (nM) from 1 assay(s)
Binding MOAD:  5BOJ Kd: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.685α = 90
b = 85.409β = 90
c = 63.624γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SAINTdata reduction
SADABSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

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