7QC5

Crystal structure of human wild type transthyretin in complex with (3,4-dihydroxy-5-nitrophenyl)-(3-fluoro-5-hydroxyphenyl)methanone compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development of a Highly Potent Transthyretin Amyloidogenesis Inhibitor: Design, Synthesis, and Evaluation.

Pinheiro, F.Pallares, I.Peccati, F.Sanchez-Morales, A.Varejao, N.Bezerra, F.Ortega-Alarcon, D.Gonzalez, D.Osorio, M.Navarro, S.Velazquez-Campoy, A.Almeida, M.R.Reverter, D.Busque, F.Alibes, R.Sodupe, M.Ventura, S.

(2022) J Med Chem 65: 14673-14691

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01195
  • Primary Citation of Related Structures:  
    7QC5

  • PubMed Abstract: 

    Transthyretin amyloidosis (ATTR) is a group of fatal diseases described by the misfolding and amyloid deposition of transthyretin (TTR). Discovering small molecules that bind and stabilize the TTR tetramer, preventing its dissociation and subsequent aggregation, is a therapeutic strategy for these pathologies. Departing from the crystal structure of TTR in complex with tolcapone, a potent binder in clinical trials for ATTR, we combined rational design and molecular dynamics (MD) simulations to generate a series of novel halogenated kinetic stabilizers. Among them, M-23 displays one of the highest affinities for TTR described so far. The TTR/ M-23 crystal structure confirmed the formation of unprecedented protein-ligand contacts, as predicted by MD simulations, leading to an enhanced tetramer stability both in vitro and in whole serum. We demonstrate that MD-assisted design of TTR ligands constitutes a new avenue for discovering molecules that, like M-23 , hold the potential to become highly potent drugs to treat ATTR.


  • Organizational Affiliation

    Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transthyretin
A, B
127Homo sapiensMutation(s): 0 
Gene Names: TTRPALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
PHAROS:  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
AQI (Subject of Investigation/LOI)
Query on AQI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3-fluoranyl-5-oxidanyl-phenyl)-[3-nitro-4,5-bis(oxidanyl)phenyl]methanone
C13 H8 F N O6
UHVIBVZISWKHAF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.374α = 90
b = 43.818β = 90
c = 65.467γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPGC2018-098423-B-I00

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description