9I0T image
Deposition Date 2025-01-15
Release Date 2025-05-21
Last Version Date 2025-06-25
Entry Detail
PDB ID:
9I0T
Keywords:
Title:
Crystal structure of TRIM25 PRYSPRY covalently bound to 2-chloro-1-[4-(3-methyl-4-phenyl-phenyl)carbonyl-1,4-diazepan-1-yl]ethanone
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Free:
0.24
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin/ISG15 ligase TRIM25
Gene (Uniprot):TRIM25
Chain IDs:A
Chain Length:199
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Discovery and optimisation of a covalent ligand for TRIM25 and its application to targeted protein ubiquitination.
Chem Sci 16 10432 10443 (2025)
PMID: 40365055 DOI: 10.1039/d5sc01540e

Abstact

The tripartite motif (TRIM) family of RING-type E3 ligases catalyses the formation of many different types of ubiquitin chains, and as such, plays important roles in diverse cellular functions, ranging from immune regulation to cancer signalling pathways. Few ligands have been discovered for TRIM E3 ligases, and these E3s are under-represented in the rapidly expanding field of induced proximity. Here we present the identification of a novel covalent ligand for the PRYSPRY substrate binding domain of TRIM25. We employ covalent fragment screening coupled with high-throughput chemistry direct-to-biology optimisation to efficiently elaborate covalent fragment hits. We demonstrate that our optimised ligand enhances the in vitro auto-ubiquitination activity of TRIM25 and engages TRIM25 in live cells. We also present the X-ray crystal structure of TRIM25 PRYSPRY in complex with this covalent ligand. Finally, we incorporate our optimised ligand into heterobifunctional proximity-inducing compounds and demonstrate the in vitro targeted ubiquitination of a neosubstrate by TRIM25.

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