Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.30 kDa 
• Atom Count: 2152 
• Residue Count: 229 
• Unique protein chains: 1

4FI6

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

• DOI: 10.2210/pdb4FI6/pdb

• Classification: HORMONE/HORMONE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-06-08 Released: 2013-02-20 
• Deposition Author(s): Connelly, S., Grimster, N., Wilson, I.A., Kelly, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.182 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

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

• PubMed: 23350654 
• DOI: 10.1021/ja311729d
• Primary Citation of Related Structures:  
  4FI6, 4FI7, 4FI8


• 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 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.

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Organizational Affiliation: 

Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transthyretin	A, B	127	Homo sapiens	Mutation(s): 0  Gene Names: TTR, PALB
Find proteins for P02766 (Homo sapiens) Explore P02766  Go to UniProtKB:  P02766
NIH Common Fund Data Resources
PHAROS  P02766 GTEx  ENSG00000118271

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0U7	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.182 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.903	α = 90
b = 85.294	β = 90
c = 63.758	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-08 
• Released Date: 2013-02-20 
Deposition Author(s): Connelly, S., Grimster, N., Wilson, I.A., Kelly, J.W.

Revision History 

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