9GJQ

Crystal structure of humanised cereblon from Magnetospirillum gryphiswaldense bound by dihydrouracil-indole compound [1-(1H-indol-6-yl)dihydro-2,4(1H,3H)-pyrimidinedione].

This is a non-PDB format compatible entry.

Summary for 9GJQ

• Entry DOI: 10.2210/pdb9gjq/pdb
• Descriptor: Cereblon isoform 4, 1-(1H-indol-6-yl)-1,3-diazinane-2,4-dione, ZINC ION, ... (4 entities in total)
• Functional Keywords: cereblon, crbn, inhibitor, dihydrouracil, ligase
• Biological source: Magnetospirillum gryphiswaldense
• Total number of polymer chains: 1
• Total formula weight: 12338.19

Authors

Collie, G.W. (deposition date: 2024-08-22, release date: 2025-09-03, Last modification date: 2026-04-01)

Primary citation

Rodrigo-Brenni, M.C.,Komen, J.C.,Hamza, G.M.,Bohin, N.,Adomavicius, T.,Andres, A.,Blaho, S.,Borjesson, U.,Collie, G.W.,De Donatis, G.M.,Eisele, F.,Gao, N.,Gohlke, A.,Grebner, C.,Gustafsson, F.,Hock, A.,Kankkonen, C.,Kumar, P.,Leonard, E.,Li, X.,Macdonald, R.,Madeyski-Bengtson, K.,Miele, E.,Nevin, P.,Overman, J.,Pachl, F.,Pathe, C.,Perry, M.W.D.,Phillips, C.,Pike, A.,Purvis, I.,Rasmusson, T.,Regan, S.,Reilly, L.,Rose, J.,Storer, R.I.,Wang, J.,Zhai, X.,Michaelides, I.N.,Moreau, K.
A dihydrouracil CRBN ligand mitigates IMiD associated safety liabilities in heterobifunctional targeted protein degrader.
Nat Commun, 2026

PubMed Abstract: Immunomodulatory imide drugs (IMiDs) like lenalidomide and pomalidomide are effective in treating multiple myeloma (MM) but pose hematotoxicity risks by degrading neosubstrates Ikaros (IKZF1) and Aiolos (IKZF3). When these IMiD scaffolds are integrated into proteolysis targeting chimeras (PROTACs), they can inadvertently lead to the degradation of these neosubstrates alongside the intended protein of interest (POI), raising safety concerns. This study profiles existing PROTACs and reveals instances of undesired degradation of IMiD-associated neosubstrates. We have developed in vitro hematopoietic assays to scrutinize the IMiD effects and describe the mechanistic insights on cell differentiation rewiring towards megakaryocytes together with an activation of the interferon response that is phenocopied by an Ikaros knock-out model. Moreover, we have identified a CRBN ligand that mitigates these safety liabilities and can be effectively incorporated into PROTACs. This advancement provides a promising path toward safer preclinical development of PROTACs, especially as the field expands into chronic disease treatments beyond oncology.

PubMed: 41876537
DOI: 10.1038/s41467-026-70663-1

Experimental method

X-RAY DIFFRACTION (1.393 Å)