4FI6

Kinetic Stabilization of transthyretin through covalent modification of K15 by 3-(5-(3,5-dichlorophenyl)-1,3,4-oxadiazol-2-yl)-benzenesulfonamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Aromatic Sulfonyl Fluorides Covalently Kinetically Stabilize Transthyretin to Prevent Amyloidogenesis while Affording a Fluorescent Conjugate.

Grimster, N.P., Connelly, S., Baranczak, A., Dong, J., Krasnova, L.B., Sharpless, K.B., Powers, E.T., Wilson, I.A., Kelly, J.W.

(2013) J.Am.Chem.Soc. 135: 5656-5668

  • DOI: 10.1021/ja311729d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Molecules that bind selectively to a given protein and then undergo a rapid chemoselective reaction to form a covalent conjugate have utility in drug development. Herein a library of 1,3,4-oxadiazoles substituted at the 2 position with an aryl sulfon ...

    Molecules that bind selectively to a given protein and then undergo a rapid chemoselective reaction to form a covalent conjugate have utility in drug development. Herein a library of 1,3,4-oxadiazoles substituted at the 2 position with an aryl sulfonyl fluoride and at the 5 position with a substituted aryl known to have high affinity for the inner thyroxine binding subsite of transthyretin (TTR) was conceived of by structure-based design principles and was chemically synthesized. When bound in the thyroxine binding site, most of the aryl sulfonyl fluorides react rapidly and chemoselectively with the pKa-perturbed K15 residue, kinetically stabilizing TTR and thus preventing amyloid fibril formation, known to cause polyneuropathy. Conjugation t50s range from 1 to 4 min, ~1400 times faster than the hydrolysis reaction outside the thyroxine binding site. X-ray crystallography confirms the anticipated binding orientation and sheds light on the sulfonyl fluoride activation leading to the sulfonamide linkage to TTR. A few of the aryl sulfonyl fluorides efficiently form conjugates with TTR in plasma. Eleven of the TTR covalent kinetic stabilizers synthesized exhibit fluorescence upon conjugation and therefore could have imaging applications as a consequence of the environment sensitive fluorescence of the chromophore.

    Organizational Affiliation: 

    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, 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
0U7
Query on 0U7
Download SDF File 
Download CCD File 
A, B
3-[5-(3,5-dichlorophenyl)-1,3,4-oxadiazol-2-yl]benzenesulfonyl fluoride
C14 H7 Cl2 F N2 O3 S
XFQASTJKVRWJHI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.903α = 90.00
b = 85.294β = 90.00
c = 63.758γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references
  • Version 1.2: 2013-05-01
    Type: Database references
  • Version 1.3: 2014-01-29
    Type: Other