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Structure paper

TitleStructural and Biophysical Methods for the Assessment of Cereblon Binders for PROTACs
Journal, issue, pagesTo Be Published
Publish dateJul 31, 2025 (structure data deposition date)
AuthorsRutter ZJ / Cowan AD / McAulay K / Ciulli A
External linksSearch PubMed
MethodsEM (single particle) / X-ray diffraction
Resolution2.36 - 4.23 Å
Structure data

EMDB-54624: Consensus map of CRBN bound to spirocyclic ligand in the open conformation
Method: EM (single particle) / Resolution: 2.51 Å

EMDB-54644: Locally refined map of CRBN TBD bound to spirocyclic ligand in the open conformation
Method: EM (single particle) / Resolution: 3.46 Å

EMDB-55057: Consensus map of CRBN bound to dihydrouracil ligand in the closed conformation
Method: EM (single particle) / Resolution: 3.66 Å

EMDB-55058: Locally refined map of CRBN bound to dihydrouracil ligand in the closed conformation
Method: EM (single particle) / Resolution: 4.23 Å

EMDB-55059: Consensus map of CRBN bound to dihydrouracil ligand in the open conformation
Method: EM (single particle) / Resolution: 3.33 Å

EMDB-55060: Locally refined map of CRBN TBD bound to dihydrouracil ligand in the open conformation
Method: EM (single particle) / Resolution: 4.23 Å

55257

9svg

EMDB-55257, PDB-9svg:
Cryo-EM structure of CRBN bound to 2-[5-chloro-1-(4-piperidyl)indol-4-yl]-2,5-diazaspiro[3.4]octan-6-one in the open conformation
Method: EM (single particle) / Resolution: 2.51 Å

55258

9svh

EMDB-55258, PDB-9svh:
Cryo-EM structure of CRBN bound to 1-[1-(4-piperidyl)indol-4-yl]hexahydropyrimidine-2,4-dione in the closed conformation
Method: EM (single particle) / Resolution: 3.66 Å

55259

9svi

EMDB-55259, PDB-9svi:
Cryo-EM structure of CRBN bound to 1-[1-(4-piperidyl)indol-4-yl]hexahydropyrimidine-2,4-dione in the open conformation
Method: EM (single particle) / Resolution: 3.33 Å

PDB-9sun:
Crystal structure of CRBN-midi in complex with 1-(1-(piperidin-4-yl)-1H-indol-4-yl)dihydropyrimidine-2,4(1H,3H)-dione
Method: X-RAY DIFFRACTION / Resolution: 2.36 Å

Chemicals

PDB-1jp8:
Sperm Whale met-Myoglobin (room temperature; high pressure)

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

PDB-1jqz:
Human Acidic Fibroblast Growth Factor. 141 Amino Acid Form with Amino Terminal His Tag.

Source
  • homo sapiens (human)
KeywordsLIGASE / E3 ligase / PROTAC / molecular glue / targeted protein degradation / E3 ubiquitin ligase

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