9GJQ image
Deposition Date 2024-08-22
Release Date 2025-09-03
Last Version Date 2026-04-01
Entry Detail
PDB ID:
9GJQ
Keywords:
Title:
Crystal structure of humanised cereblon from Magnetospirillum gryphiswaldense bound by dihydrouracil-indole compound [1-(1H-indol-6-yl)dihydro-2,4(1H,3H)-pyrimidinedione].
Biological Source:
Source Organism(s):
Expression System(s):
Method Details:
Experimental Method:
Resolution:
1.39 Å
R-Value Free:
0.20
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
C 2 2 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cereblon isoform 4
Gene (Uniprot):MGR_0879
Mutagens:A52H, M54Y, F56H, F77H, Y101F, R117A
Chain IDs:A
Chain Length:109
Number of Molecules:1
Biological Source:Magnetospirillum gryphiswaldense
Primary Citation

Abstact

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.

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Primary Citation of related structures
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