8AWW

Transthyretin conjugated with a tafamidis derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Combining Solid-State NMR with Structural and Biophysical Techniques to Design Challenging Protein-Drug Conjugates.

Cerofolini, L.Vasa, K.Bianconi, E.Salobehaj, M.Cappelli, G.Bonciani, A.Licciardi, G.Perez-Rafols, A.Padilla-Cortes, L.Antonacci, S.Rizzo, D.Ravera, E.Viglianisi, C.Calderone, V.Parigi, G.Luchinat, C.Macchiarulo, A.Menichetti, S.Fragai, M.

(2023) Angew Chem Int Ed Engl 62: e202303202-e202303202

  • DOI: https://doi.org/10.1002/anie.202303202
  • Primary Citation of Related Structures:  
    8AWW

  • PubMed Abstract: 

    Several protein-drug conjugates are currently being used in cancer therapy. These conjugates rely on cytotoxic organic compounds that are covalently attached to the carrier proteins or that interact with them via non-covalent interactions. Human transthyretin (TTR), a physiological protein, has already been identified as a possible carrier protein for the delivery of cytotoxic drugs. Here we show the structure-guided development of a new stable cytotoxic molecule based on a known strong binder of TTR and a well-established anticancer drug. This example is used to demonstrate the importance of the integration of multiple biophysical and structural techniques, encompassing microscale thermophoresis, X-ray crystallography and NMR. In particular, we show that solid-state NMR has the ability to reveal effects caused by ligand binding which are more easily relatable to structural and dynamical alterations that impact the stability of macromolecular complexes.


  • Organizational Affiliation

    Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transthyretin
A, B
116Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OIT (Subject of Investigation/LOI)
Query on OIT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
~{N}-(6-azanylhexyl)-2-[3,5-bis(chloranyl)phenyl]-1,3-benzoxazole-6-carboxamide
C20 H21 Cl2 N3 O2
VYSGGLIOFYGQHG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.48α = 90
b = 85.34β = 90
c = 63.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union956758

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description