9DQD image
Deposition Date 2024-09-23
Release Date 2024-12-25
Last Version Date 2025-01-29
Entry Detail
PDB ID:
9DQD
Keywords:
Title:
cryo-EM structure of human Cereblon/DDB1 in complex with a non-traditional CRBN binder
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein cereblon
Gene (Uniprot):CRBN
Chain IDs:A
Chain Length:467
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA damage-binding protein 1
Gene (Uniprot):DDB1
Mutagens:deletion of residues 396-705
Chain IDs:B
Chain Length:836
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Development of a Buchwald-Hartwig Amination for an Accelerated Library Synthesis of Cereblon Binders.
Acs Med.Chem.Lett. 16 89 95 (2025)
PMID: 39811117 DOI: 10.1021/acsmedchemlett.4c00462

Abstact

In recent years, targeted protein degradation (TPD) has emerged as a powerful therapeutic modality utilizing both heterobifunctional ligand-directed degraders (LDDs) and molecular glues (e.g., CELMoDs) to recruit E3 ligases for inducing polyubiquitination and subsequent proteasomal degradation of target proteins. The immunomodulatory drugs lenalidomide and pomalidomide bind to cereblon (CRBN), a substrate receptor of the CRL4A E3 ligase complex, to initiate degradation of neosubstrates critical for cell survival. Recently, nonlenalidomide or pomalidomide CRBN binders, known as alternate glutarimides, have gained popularity, offering potential degraders with varying physicochemical properties. Specifically, 3-substituted indazole derivatives have emerged as potent CRBN binders. We developed conditions for the direct cross-coupling of unprotected glutarimides with amines, streamlining the synthesis of alternative CRBN binders. This manuscript describes the rapid synthesis of 30 CRBN binders, their characterization as potential degraders and a cryo-EM structure of the CRBN/DDB1 with a representative compound (6).

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Primary Citation of related structures