8WGS

Crystal structure of V30M-TTR in complex with compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Development of Benziodarone Analogues with Enhanced Potency for Selective Binding to Transthyretin in Human Plasma.

Mizuguchi, M.Nakagawa, Y.Yokoyama, T.Okada, T.Fujii, K.Takahashi, K.Luan, N.N.T.Nabeshima, Y.Kanamitsu, K.Nakagawa, S.Yamakawa, S.Ueda, M.Ando, Y.Toyooka, N.

(2024) J Med Chem 67: 6987-7005

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02286
  • Primary Citation of Related Structures:  
    8WGS, 8WGT, 8WGU

  • PubMed Abstract: 

    Transthyretin amyloidosis is a fatal disorder caused by transthyretin amyloid aggregation. Stabilizing the native structure of transthyretin is an effective approach to inhibit amyloid aggregation. To develop kinetic stabilizers of transthyretin, it is crucial to explore compounds that selectively bind to transthyretin in plasma. Our recent findings demonstrated that the uricosuric agent benziodarone selectively binds to transthyretin in plasma. Here, we report the development of benziodarone analogues with enhanced potency for selective binding to transthyretin in plasma compared to benziodarone. These analogues featured substituents of chlorine, bromine, iodine, a methyl group, or a trifluoromethyl group, at the 4-position of the benzofuran ring. X-ray crystal structure analysis revealed that CH···O hydrogen bonds and a halogen bond are important for the binding of the compounds to the thyroxine-binding sites. The bioavailability of benziodarone analogues with 4-Br, 4-Cl, or 4-CH 3 was comparable to that of tafamidis, a current therapeutic agent for transthyretin amyloidosis.


  • Organizational Affiliation

    Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transthyretin
A, B
159Homo sapiensMutation(s): 1 
Gene Names: TTRPALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
GTEx:  ENSG00000118271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02766
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WGH (Subject of Investigation/LOI)
Query on WGH

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
[3,5-bis(iodanyl)-4-oxidanyl-phenyl]-(2-ethyl-4-iodanyl-1-benzofuran-3-yl)methanone
C17 H11 I3 O3
CIPAOTDUDSOTHT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.329α = 90
b = 85.949β = 90
c = 63.863γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-05-15 
  • Deposition Author(s): Yokoyama, T.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references