Identification of an allosteric site on the E3 ligase adapter cereblon
Summary
This Nature paper reports the discovery of a previously unrecognised allosteric site on the E3 ligase adapter cereblon (CRBN). Through X-ray crystallography and cryo-EM, the authors show that the small molecule SB-405483 binds this site and shifts CRBN conformation. Biochemical and cellular assays demonstrate that SB-405483 allosterically modulates substrate recruitment and potentiates degradation by both monovalent molecular glues and PROTACs. Global proteomics and targeted validation identify new CRBN-dependent neosubstrates (including Wee1) and reveal that allosteric engagement can tune degradation specificity and potency.
Key Points
- Crystal structures and cryo-EM maps identify a conserved allosteric pocket on human CRBN that binds SB-405483.
- SB-405483 binding shifts CRBN conformational populations (closed/open/intermediate), observed by cryo-EM.
- Allosteric binding modulates orthosteric ligand (lenalidomide and others) activity — in many cases potentiating target degradation.
- Functional assays used include TR-FRET, ASMS, thermal-shift, NanoBRET, HiBiT degradation reporters, and cellular viability tests.
- Proteomics reveals DEG-47 and other degraders have altered substrate spectra in the presence of SB-405483; Wee1 emerges as a validated CRBN neosubstrate.
- SB-405483 broadly potentiates PROTAC-mediated target degradation across multiple reporter systems, indicating a general mechanism.
- Mechanistic model: allosteric ligand biases CRBN toward conformations that favour recruitment/ubiquitination of particular neosubstrates.
Content summary
The team combined structural biology (X-ray crystallography, cryo-EM) with orthogonal binding and functional assays to locate and characterise an allosteric site on CRBN. SB-405483 was shown to bind at this site with clear electron density and to be biochemically distinguishable from orthosteric phthalimide-based ligands.
Cellular thermal-shift, NanoBRET and affinity-purification experiments confirmed target engagement and demonstrated that SB-405483 alters CRBN’s stability and ubiquitin ligase behaviour in cells. In degradation assays, SB-405483 potentiated the activity of monovalent degraders (molecular glues) and improved PROTAC efficacy across several target reporter lines.
Global proteomics (multiple PXD datasets) identified changes in the degradome when SB-405483 was present; targeted follow-up validated CK1α and Wee1 among others as CRBN-dependent neosubstrates of interest. The authors propose an allosteric modulation model where SB-405483 biases CRBN conformation to favour recruitment of some substrates while diminishing others.
Context and relevance
CRBN is a central E3 ligase hub for thalidomide analogues, molecular glues and many PROTACs. Finding an allosteric site that reliably tunes substrate recruitment is a big deal for targeted protein degradation research: it offers a new lever to alter potency, selectivity and perhaps safety profiles of degrader programmes. This work links structural insight to cellular and proteome-wide outcomes, so it matters both for basic mechanistic understanding and practical degrader design.
Why should I read this?
Short version: they found a knob you can turn on CRBN. If you care about designing better molecular glues or PROTACs — or about avoiding unwanted degradation — this paper shows a concrete way to tweak CRBN’s behaviour. It’s packed with structures, assays and proteomics so you can see how the mechanism plays out from molecule to cell.
Author style
Punchy: the authors combine high-resolution structures with robust cellular validation to argue that allosteric modulation of CRBN is real, controllable and druggable. If you’re working on degraders, the mechanistic detail is worth digging into — it could change how you think about ligand design and selectivity.
Source
Article Date: 21 January 2026