8PMO

Crystal structure of human V122I transthyretin in complex with PITB (Pharmacokinetically Improved TTR Binder)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

PITB: A high affinity transthyretin aggregation inhibitor with optimal pharmacokinetic properties.

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

(2023) Eur J Med Chem 261: 115837-115837

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115837
  • Primary Citation of Related Structures:  
    8PM8, 8PM9, 8PMA, 8PMO

  • PubMed Abstract: 

    The aggregation of wild-type transthyretin (TTR) and over 130 genetic TTR variants underlies a group of lethal disorders named TTR amyloidosis (ATTR). TTR chemical chaperones are molecules that hold great promise to modify the course of ATTR progression. In previous studies, we combined rational design and molecular dynamics simulations to generate a series of TTR selective kinetic stabilizers displaying exceptionally high affinities. In an effort to endorse the previously developed molecules with optimal pharmacokinetic properties, we conducted structural design optimization, leading to the development of PITB. PITB binds with high affinity to TTR, effectively inhibiting tetramer dissociation and aggregation of both the wild-type protein and the two most prevalent disease-associated TTR variants. Importantly, PITB selectively binds and stabilizes TTR in plasma, outperforming tolcapone, a drug currently undergoing clinical trials for ATTR. Pharmacokinetic studies conducted on mice confirmed that PITB exhibits encouraging pharmacokinetic properties, as originally intended. Furthermore, PITB demonstrates excellent oral bioavailability and lack of toxicity. These combined attributes position PITB as a lead compound for future clinical trials as a disease-modifying therapy for 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): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZP2 (Subject of Investigation/LOI)
Query on ZP2

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3-fluoranyl-5-oxidanyl-phenyl)-(3-methoxy-5-nitro-4-oxidanyl-phenyl)methanone
C14 H10 F N O6
LHCGDAFIWWCKGM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.406α = 90
b = 43.782β = 90
c = 66.045γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPGC2018-098423-B-I00

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release