3HJ0

Transthyretin in complex with a covalent small molecule kinetic stabilizer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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


This is version 1.2 of the entry. See complete history


Literature

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: 10.1038/nchembio.281
  • Structures With Same Primary Citation

  • 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 ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TransthyretinA, B127Homo sapiensMutation(s): 0 
Gene Names: PALBTransthyretinTTR
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
NIH Common Fund Data Resources
PHAROS  P02766
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A93
Query on A93

Download CCD File 
A, B
4-fluorophenyl 3-[(E)-2-(4-hydroxy-3,5-dimethylphenyl)ethenyl]benzoate
C23 H19 F O3
YDSMVVNYVJZDET-VOTSOKGWSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A,BL-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A93IC50:  1960   nM  BindingDB
A93IC50 :  1960   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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