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].

• PDB DOI: https://doi.org/10.2210/pdb9GJQ/pdb

• Classification: LIGASE
• Organism(s): Magnetospirillum gryphiswaldense
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-08-22 Released: 2025-09-03 
• Deposition Author(s): Collie, G.W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.209 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

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 

• PubMed: 41876537 
• 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.

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Organizational Affiliation: 
• Safety Sciences, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK.
Assays, Profiling & Cell Sciences, Discovery Sciences, R&D, AstraZeneca, Boston, MA, USA.
Protein, structure and biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK.
Protein, structure and biophysics, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
Assays, Profiling & Cell Sciences, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK.
Assays, Profiling & Cell Sciences, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
Data Sciences & Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Boston, MA, USA.
Integrated Bioanalysis, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK.
Pharmaron Beijing Co., Ltd, 100176, Beijing, People's Republic of China.
Animal Science & Technologies, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK.
Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuicals R&D, AstraZeneca, Gothenburg, Sweden.
DMPK, Oncology R&D, AstraZeneca, Cambridge, UK.
Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK.
Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK. [e-mail].
Safety Sciences, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.34 kDa 
• Atom Count: 981 
• Modeled Residue Count: 109 
• Deposited Residue Count: 109 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cereblon isoform 4	A	109	Magnetospirillum gryphiswaldense	Mutation(s): 6  Gene Names: MGR_0879
UniProt
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense) Explore A4TVL0  Go to UniProtKB:  A4TVL0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IMN	B [auth A]	1-(1H-indol-6-yl)-1,3-diazinane-2,4-dione C12 H11 N3 O2 RYEZBXXJPZGMGF-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.209 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.782	α = 90
b = 82.305	β = 90
c = 52.445	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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