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Two organic-inorganic hybrids based on sodium peroxidomolybdates(VI) and 3,5-dicarboxylic pyridine acid (Na-35dcpa) or N-oxide isonicotinic acid (Na-isoO) have been synthesized and characterized. All compounds contain inorganic parts: a pentagonal bipyramid with molybdenum center, and an organic part containing 3,5-dicarboxylic pyridine acid or N-oxide isonicotinic acid moieties. The type of organic part used in the synthesis influences the crystal structure of obtained compounds. This aspect can be interesting for crystal engineering. Crystal structures were determined using powder X-ray diffraction or single crystal diffraction for compounds Na-35dcpa and Na-isoO, respectively. Elemental analysis was used to check the purity of the obtained compounds, while X-ray Powder Diffraction (XRPD) vs. temp. was applied to verify their stability. Moreover, all the compounds were examined by Infrared (IR) spectroscopy. Their catalytic activity was tested in the Baeyer–Villiger (BV) oxidation of cyclohexanone to ε-caprolactone in the oxygen-aldehyde system. The highest catalytic activity in the BV oxidation was observed for Na-35dcpa. The compounds were also tested for biological activity on human normal cells (fibroblasts) and colon cancer cell lines (HT-29, LoVo, SW 620, HCT 116). All compounds were cytotoxic against tumor cells with metastatic characteristics, which makes them interesting and promising candidates for further investigations of specific anticancer mechanisms.