3P3T

Human transthyretin (TTR) complexed with 4-(3-(2-flourophenoxy)propyl)-3,5-dimethyl-1H-pyrazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Potent kinetic stabilizers that prevent transthyretin-mediated cardiomyocyte proteotoxicity.

Alhamadsheh, M.M.Connelly, S.Cho, A.Reixach, N.Powers, E.T.Pan, D.W.Wilson, I.A.Kelly, J.W.Graef, I.A.

(2011) Sci Transl Med 3: 97ra81-97ra81

  • DOI: 10.1126/scitranslmed.3002473
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A valine-to-isoleucine mutation at position 122 of the serum protein transthyretin (TTR), found in 3 to 4% of African Americans, alters its stability, leading to amyloidogenesis and cardiomyopathy. In addition, 10 to 15% of individuals older than 65 ...

    A valine-to-isoleucine mutation at position 122 of the serum protein transthyretin (TTR), found in 3 to 4% of African Americans, alters its stability, leading to amyloidogenesis and cardiomyopathy. In addition, 10 to 15% of individuals older than 65 years develop senile systemic amyloidosis and cardiac TTR deposits because of wild-type TTR amyloidogenesis. Although several drugs are in development, no approved therapies for TTR amyloid cardiomyopathy are yet available, so the identification of additional compounds that prevent amyloid-mediated cardiotoxicity is needed. To this aim, we developed a fluorescence polarization-based high-throughput screen and used it to identify several new chemical scaffolds that target TTR. These compounds were potent kinetic stabilizers of TTR and prevented TTR tetramer dissociation, partial unfolding, and aggregation of both wild type and the most common cardiomyopathy-associated TTR mutant, V122I-TTR. High-resolution co-crystal structures and characterization of the binding energetics revealed how these diverse structures bound to tetrameric TTR. These compounds effectively inhibited the proteotoxicity of V122I-TTR toward human cardiomyocytes. Several of these ligands stabilized TTR in human serum more effectively than diflunisal, which is a well-studied inhibitor of TTR aggregation, and may be promising leads for the treatment or prevention of TTR-mediated cardiomyopathy.


    Organizational Affiliation

    Department of Pathology, Stanford University Medical School, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
127Homo sapiensMutation(s): 0 
Gene 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
3M3
Query on 3M3

Download SDF File 
Download CCD File 
A, B
4-[3-(2-fluorophenoxy)propyl]-3,5-dimethyl-1H-pyrazole
C14 H17 F N2 O
SIXWAFDHGGAHMK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3M3IC50: 296 nM (100) BINDINGDB
3M3Kd: 57.91 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 43.009α = 90.00
b = 85.371β = 90.00
c = 64.006γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data collection
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2013-01-09
    Type: Database references