8CDN

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

Summary for 8CDN

• Entry DOI: 10.2210/pdb8cdn/pdb
• Descriptor: T-box transcription factor T, DNA (5'-D(*AP*GP*GP*TP*GP*TP*GP*AP*GP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*CP*TP*CP*AP*CP*AP*CP*CP*T)-3'), ... (4 entities in total)
• Functional Keywords: brachyury, tbxt, transcription
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 29348.15

Authors

Newman, J.A.,Gavard, A.E.,von Delft, F.,Gileadi, O.,Bountra, C. (deposition date: 2023-01-31, release date: 2023-03-22, Last modification date: 2025-02-26)

Primary citation

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.
Structural insights into human brachyury DNA recognition and discovery of progressible binders for cancer therapy.
Nat Commun, 16:1596-1596, 2025

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.

PubMed: 39952925
DOI: 10.1038/s41467-025-56213-1

Experimental method

X-RAY DIFFRACTION (2.55 Å)