8CDN | pdb_00008cdn

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

• PDB DOI: https://doi.org/10.2210/pdb8CDN/pdb
• NAKB: 8CDN

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-31 Released: 2023-03-22 
• Deposition Author(s): Newman, J.A., Gavard, A.E., von Delft, F., Gileadi, O., Bountra, C.
• Funding Organization(s): The Mark Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.302 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.273 (Depositor), 0.279 (DCC) 
• R-Value Observed: 
  0.275 (Depositor) 

Starting Model: experimental

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

• PubMed: 39952925 
• DOI: https://doi.org/10.1038/s41467-025-56213-1
• Primary Citation 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.

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Organizational Affiliation: 
• Centre for Medicines Discovery, University of Oxford, Oxford, UK. [e-mail].
Centre for Medicines Discovery, University of Oxford, Oxford, UK.
Exscientia, Oxford, UK.
Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Diamond Light Source Ltd, Didcot, UK.
Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, UK.
Sano Genetics Ltd, Cambridge, UK.
SGC-UNC, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Institute of Pharmacy, University of Hamburg, Hamburg, Germany.
GlaxoSmithKline, Collegeville, PA, USA.
Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, UK. [e-mail].
SGC Karolinska, Centre for Molecular Medicine, Stockholm, Sweden.
SGC-UNC, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. [e-mail].
UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.35 kDa 
• Atom Count: 1,937 
• Modeled Residue Count: 205 
• Deposited Residue Count: 216 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-box transcription factor T	A	192	Homo sapiens	Mutation(s): 0  Gene Names: TBXT, T
UniProt & NIH Common Fund Data Resources
Find proteins for O15178 (Homo sapiens) Explore O15178  Go to UniProtKB:  O15178
PHAROS:  O15178 GTEx:  ENSG00000164458

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*TP*GP*TP*GP*AP*GP*CP*CP*T)-3')	B [auth C]	12	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*CP*TP*CP*AP*CP*AP*CP*CP*T)-3')	C [auth D]	12	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.302 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.273 (Depositor), 0.279 (DCC) 
• R-Value Observed: 0.275 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.018	α = 90
b = 63.018	β = 90
c = 218.579	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Newman, J.A., Gavard, A.E., von Delft, F., Gileadi, O., Bountra, C.

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Funding Organization	Location	Grant Number
The Mark Foundation	United States	--

Revision History  

• 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