Fig. 6: The buried surface area (BSA) based on our predicted structures correlates with degradation potency.
From: SE(3)-equivariant ternary complex prediction towards target protein degradation
a The BSA of 22 known PROTAC-induced ternary complexes from experimental structures. b Correlation analyses between BSA and ln(KLPT) for the predicted BRD4-VHL ternary complex with various PROTACs. The quantity ln(KLPT) has been proven in previous work19 to have a positive relationship with ln(DC50). The red line represents a linear regression of the points. c Correlation analyses between BSA and linker length for predicted CRBN-BTK complexes induced by 11 different PROTACs. As PROTAC ID increases, the linker length increases. The red line shows a second-order polynomial regression. Notably, PROTACs (6–11) are associated with significant cellular knockdown, while shorter PROTACs(1–4) exhibit weak/no degradation capability. d Predicted ternary structures for CRBN-BTK complexes induced by PROTAC (1) and PROTAC (10), illustrating severe atom clashes in PROTAC (1) and increased flexibility to avoid clashes in PROTAC (10). e DeepTernary predicts ternary structures ~100 times faster than existing methods.
