Transthyretin in complex with a covalent small molecule kinetic stabilizer

Experimental Data Snapshot

  • Resolution: 1.34 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Chemoselective small molecules that covalently modify one lysine in a non-enzyme protein in plasma.

Choi, S.Connelly, S.Reixach, N.Wilson, I.A.Kelly, J.W.

(2010) Nat Chem Biol 6: 133-139

  • DOI: https://doi.org/10.1038/nchembio.281
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A small molecule that could bind selectively to and then react chemoselectively with a non-enzyme protein in a complex biological fluid, such as blood, could have numerous practical applications. Herein, we report a family of designed stilbenes that selectively and covalently modify the prominent plasma protein transthyretin in preference to more than 4,000 other human plasma proteins. They react chemoselectively with only one of eight lysine e-amino groups within transthyretin. The crystal structure confirms the expected binding orientation of the stilbene substructure and the anticipated conjugating amide bond. These covalent transthyretin kinetic stabilizers exhibit superior amyloid inhibition potency compared to their noncovalent counterparts, and they prevent cytotoxicity associated with amyloidogenesis. Though there are a few prodrugs that, upon metabolic activation, react with a cysteine residue inactivating a specific non-enzyme, we are unaware of designed small molecules that react with one lysine e-amine within a specific non-enzyme protein in a complex biological fluid.

  • Organizational Affiliation

    Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
127Homo sapiensMutation(s): 0 
Gene Names: PALBTransthyretinTTR
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on A93

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-fluorophenyl 3-[(E)-2-(4-hydroxy-3,5-dimethylphenyl)ethenyl]benzoate
C23 H19 F O3
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CSD
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
A93 PDBBind:  3HJ0 IC50: 1960 (nM) from 1 assay(s)
BindingDB:  3HJ0 IC50: 1960 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.34 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.654α = 90
b = 85.459β = 90
c = 63.971γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-11-19
    Changes: Non-polymer description