9GJQ | pdb_00009gjq

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 
    0.209 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A dihydrouracil CRBN ligand mitigates IMiD associated safety liabilities in heterobifunctional targeted protein degrader.

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.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-70663-1
  • Primary Citation Related Structures: 
    9GJQ

  • 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.


  • Organizational Affiliation
    • Safety Sciences, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cereblon isoform 4109Magnetospirillum gryphiswaldenseMutation(s): 6 
Gene Names: MGR_0879
UniProt
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense)
Explore A4TVL0 
Go to UniProtKB:  A4TVL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4TVL0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free:  0.209 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.782α = 90
b = 82.305β = 90
c = 52.445γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-09-03 
  • Deposition Author(s): Collie, G.W.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Database references