8PMA | pdb_00008pma

Crystal structure of human V30M transthyretin in complex with PITB (Pharmacokinetically Improved TTR Binder)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.201 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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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 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.

Macromolecule Content 

  • Total Structure Weight: 28.23 kDa 
  • Atom Count: 2,122 
  • Modeled Residue Count: 232 
  • Deposited Residue Count: 254 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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: 1.20 Å
  • R-Value Free:  0.201 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.058α = 90
b = 65.344β = 90
c = 85.214γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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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