- ◇ APPLICATIONS · TARGETED PROTEIN DEGRADATION
TARGETED PROTEIN
Degradation
Structural insight for PROTACs, molecular glues and degrader complex formation.
PROTACs
Molecular glues
Ternary complexes
E3 ligase recruitment
Targeted protein degradation changes the role of small molecules in drug discovery. Instead of only inhibiting or activating a protein, degraders are designed to bring disease-relevant proteins into proximity with the cellular degradation machinery.
For PROTACs, this usually means forming a ternary complex between the target protein, the PROTAC molecule and an E3 ubiquitin ligase. Structural insight helps reveal how each component is positioned, how the linker influences geometry and whether the complex is compatible with productive ubiquitination.
Molecular glues follow a different logic. They are not linker-based chimeras, but small molecules that induce or stabilize protein-protein interactions. Here, structural biology helps explain how the molecule reshapes the interaction surface and supports the formation of a degradation-relevant complex.
At BIMOVIS, we support targeted protein degradation by connecting structural biology, computational analysis and model interpretation. The goal is to make degrader hypotheses more concrete: which interactions matter, which complex arrangements are plausible and which structural questions should be addressed next.
- ◇ WHERE STRUCTURAL BIOLOGY SUPPORTS TARGETED PROTEIN DEGRADATION
Where structural biology supports targeted protein degradation.
TARGET ENGAGEMENT
Target engagement
Structural biology helps define how a ligand engages the target protein and which binding-site features need to be preserved. This supports decisions around attachment points, exit vectors and whether a target structure is suitable for a degrader strategy.
E3 ligase recruitment
E3 ligase recruitment
For PROTACs, productive degradation depends on how the E3 ligase is recruited and positioned relative to the target. Structural information can help assess recruiter binding, surface presentation and the orientation of the E3 ligase in the proposed complex.
TERNARY-COMPLEX FORMATION
Ternary-complex formation
The ternary complex is central to PROTAC activity. Experimental structures, AI-supported modelling and computational analysis can help explore whether a target-PROTAC-E3 arrangement is structurally plausible and compatible with productive ubiquitination.
LINKER GEOMETRY
Linker geometry and exit vectors
In PROTACs, the linker is not only a spacer. Its length, flexibility and exit vectors influence whether the target and E3 ligase can form a productive complex. Structural analysis can help evaluate linker hypotheses before deeper experimental testing.
MOLECULAR GLUE MECHANISMS
Molecular glue mechanisms
For molecular glues, structural biology helps reveal how the compound stabilizes or induces a protein-protein interaction. This can support interpretation of neo-substrate recognition, altered interaction surfaces and complex formation without a linker-based design.
- ◇ LET’S WORK TOGETHER
Let’s work together
Start with your structural question.
Bring us your target protein, ligand series, E3 recruiter, predicted model, structural data or degrader concept. We help identify which structural biology approach is most useful for the next design decision.
- ◇ COMPLEMENTARY SERVICES
Extend your project.
AI Structure Prediction & Model Analysis
Generate and assess structural hypotheses for target proteins, E3 ligases, binding sites and possible complex arrangements.
Molecular Dynamics Simulations
Explore flexibility, linker behaviour, binding-site dynamics and the stability of degrader-related structural models.
- ◇ RESOURCES & DOWNLOADS
Go deeper in our Knowledge Hub.
Guides, protocols, and reference materials to support your structural biology projects — free to access.