9SAI image
Deposition Date 2025-08-07
Release Date 2025-10-29
Last Version Date 2025-10-29
Entry Detail
PDB ID:
9SAI
Keywords:
Title:
Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.66 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA damage-binding protein 1
Gene (Uniprot):DDB1
Chain IDs:B (auth: A)
Chain Length:836
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein cereblon
Gene (Uniprot):CRBN
Chain IDs:A (auth: B)
Chain Length:442
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bromodomain-containing protein 4
Gene (Uniprot):BRD4
Chain IDs:C
Chain Length:127
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Enzyme-Activated Sugar-Coated Bifunctional Degraders.
J.Am.Chem.Soc. 147 34672 34680 (2025)
PMID: 40937862 DOI: 10.1021/jacs.5c09843

Abstact

Targeted protein degradation with compounds like proteolysis targeting chimeras (PROTACs) directs disease-associated proteins to the E3 ligase ubiquitin-proteasome system for removal. However, commonly employed E3 ligases such as cereblon (CRBN) are broadly expressed. To metabolically gate PROTAC activity, we developed an enzymatic activation strategy by integrating an O-GlcNAc modification to the cyclimids, ligands derived from the natural motifs recognized by CRBN. These sugar-coated PROTACs (SCPs) were designed using structural analyses of representative cyclimid degraders complexed with CRBN and target protein BRD4. We found that glycosylation of the cyclimid reduced CRBN binding and complex formation with BRD4 until enzymatic removal of the O-GlcNAc moiety by O-GlcNAcase (OGA). The requirement for enzymatic activation is demonstrated by in vitro biochemical binding, cellular degradation, and cell viability assays in engineered and native cell lines. O-GlcNAc is thus an effective mechanism to gate targeted protein degradation modalities that motivates the development of similar strategies to enhance selectivity with other protein modifications.

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Protein

Chemical

Disease

Primary Citation of related structures