8CDN | pdb_00008cdn

Crystal structure of human Brachyury in complex with a single T box binding element DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.302 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.273 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.275 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into human brachyury DNA recognition and discovery of progressible binders for cancer therapy.

Newman, J.A.Gavard, A.E.Imprachim, N.Aitkenhead, H.Sheppard, H.E.Te Poele, R.Clarke, P.A.Hossain, M.A.Temme, L.Oh, H.J.Wells, C.I.Davis-Gilbert, Z.W.Workman, P.Gileadi, O.Drewry, D.H.

(2025) Nat Commun 16: 1596-1596

  • DOI: https://doi.org/10.1038/s41467-025-56213-1
  • Primary Citation of Related Structures:  
    6F58, 6F59, 7ZK2, 7ZKF, 7ZL2, 8A10, 8A7N, 8CDN

  • PubMed Abstract: 

    Brachyury is a transcription factor that plays an essential role in tumour growth of the rare bone cancer chordoma and is implicated in other solid tumours. Brachyury is minimally expressed in healthy tissues, making it a potential therapeutic target. Unfortunately, as a ligandless transcription factor, brachyury has historically been considered undruggable. To investigate direct targeting of brachyury by small molecules, we determine the structure of human brachyury both alone and in complex with DNA. The structures provide insights into DNA binding and the context of the chordoma associated G177D variant. We use crystallographic fragment screening to identify hotspots on numerous pockets on the brachyury surface. Finally, we perform follow-up chemistry on fragment hits and describe the progression of a thiazole chemical series into binders with low µM potency. Thus we show that brachyury is ligandable and provide an example of how crystallographic fragment screening may be used to target protein classes that are difficult to address using other approaches.


  • Organizational Affiliation

    Centre for Medicines Discovery, University of Oxford, Oxford, UK. Joseph.newman@cmd.ox.ac.uk.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-box transcription factor T192Homo sapiensMutation(s): 0 
Gene Names: TBXTT
UniProt & NIH Common Fund Data Resources
Find proteins for O15178 (Homo sapiens)
Explore O15178 
Go to UniProtKB:  O15178
PHAROS:  O15178
GTEx:  ENSG00000164458 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15178
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.302 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.273 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.275 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.018α = 90
b = 63.018β = 90
c = 218.579γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Mark FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection
  • Version 1.2: 2025-02-26
    Changes: Database references, Structure summary