Choose for the target
Rank ligases against target geometry, candidate anchor sites, tissue context and the biology that must be preserved or removed.
BraidEra · E3 Ligase Opportunity Atlas
The field has roughly 600 E3 ligases. It builds almost everything with two.
BraidEra maps the recruiter landscape beyond CRBN and VHL—prioritizing noncanonical E3 opportunities, identifying candidate binding sites and carrying selected ligases into target-specific, falsifiable validation programs.
371catalytic E3 ligases screened
14CRL adaptors included
243computationally prioritized
677recruiter-anchor hypotheses
A narrow toolkit is holding back a broad biological system.
The opportunity is not another list of proteins. It is a better decision about which ligase to build with.
Only about 1% of the approximately 600 human E3 ligases has been used in targeted protein degradation, while CRBN-recruiting compounds dominate clinical PROTAC research. That concentration constrains tissue fit, resistance strategy, target geometry, recruiter IP and program differentiation.
Expand the recruiter space
Move beyond repeated CRBN/VHL scaffolds toward differentiated covalent and cryptic-pocket starting points.
Spend experiments deliberately
Focus protein production, screening and cellular assays on a bounded set of hypotheses with explicit negatives and stop gates.
Start with the map. Go as deep as the program requires.
Four commercial paths, from evaluation data to an exclusive recruiter asset.
E3 Opportunity Map
A curated 10–25-ligase package with candidate sites, anchor hypotheses, evidence, limitations and the experiments that would change the decision.
Target- and tissue-specific ligase sprint
A ranked E3 shortlist that integrates recruiter opportunity, tissue fit, target geometry, safety liabilities, resistance logic and validation design.
Private enterprise atlas
A versioned atlas, per-E3 dossiers, query access and private deployment for teams that need sensitive target and chemistry work kept inside their boundary.
Exclusive recruiter program
Advance a selected E3 from anchor hypothesis through chemistry, biochemical engagement, cellular validation and target-specific degrader design.
What is different about the BraidEra approach?
Existing resources answer valuable questions. BraidEra connects them to a decision and a program.
| Approach | What it answers | What the buyer still needs |
|---|---|---|
| Expression and tissue atlases | Where an E3 is expressed and which target relationships may be relevant. | A recruiter opportunity, target fit and experimental plan. |
| Structure and pocket databases | Which structures, pockets and known ligands exist. | Prioritized residue-level chemistry and program context. |
| Published PROTAC databases | What compounds and recruiter systems have already been reported. | New proprietary opportunities beyond the established toolkit. |
| BraidEra | Which noncanonical E3 opportunities to pursue, why, where an anchor may bind and what to test next. | Prospective biochemical and cellular validation—the explicit next gate. |
The boundary is part of the product.
We distinguish computational prioritization from experimental proof.
What the atlas provides
- Family-wide computational triage
- Positive and negative prioritization
- Candidate residue-level anchor sites
- Candidate warhead and recruiter starting points
- Confidence, provenance and validation gates
What still requires validation
- Biochemical binding and selectivity
- Cellular target engagement
- Productive ternary-complex geometry
- Ubiquitination and target degradation
- Pharmacology, safety and in-vivo exposure
Scientific context
Primary literature and public resources supporting the opportunity landscape.
- Proteome-wide ligandability maps of drugs with diverse cysteine-reactive chemotypes ↗Nature Communications, 2025 · Reports that only about 1% of approximately 600 E3 ligases had been used in TPD.
- IKZF2 Degradation: It’s Time to Take It Into Account When Designing Cereblon-Based PROTACs ↗ChemBioChem, 2024 · Describes the concentration of clinical PROTAC research around CRBN.
- E3Atlas ↗Public E3 structure, expression, PPI and ligandability context.
- ELiAH: the atlas of E3 ligases in human tissues ↗Public tissue-expression and E3–target relationship resource spanning 614 E3 ligases.
- PROTAC-DB 3.0 ↗Published PROTAC, E3-ligand and experimental records.
Bring us a target—or an E3 no one has learned to use.
We will define the computational opportunity, the evidence boundary and the smallest experiment capable of changing the decision.
Request an E3 evaluationContact hello@8braid.com.