LN-439A is a novel tetrahydro-β-carboline small molecule that acts as a potent catalytic inhibitor of the BAP1 deubiquitinase. It induces ubiquitination and degradation of the KLF5 transcription factor by binding to the catalytic pocket of BAP1. In basal-like breast cancer (BLBC) models, LN-439A significantly inhibits tumor cell proliferation and migration, induces G2/M phase arrest and apoptosis, and exhibits superior water solubility compared to existing BAP1 inhibitors. Furthermore, inhibition of BAP1 enzymatic activity by LN-439A also destabilizes its substrates, suggesting potential application value in inflammation-related diseases.