We prepared a database of 49 compounds. Their detailed list is available in Additional File 1. The majority of these compounds are drugs or plant metabolites, of which 44 have documented synthesis. Our database contains a wide variety of compounds, starting from easily synthesizable, via complex syntheses of low yield, to non-synthesizable. All compounds have their structure encoded in SMILES notation from PubChem with incorporating stereo orientation. Molecules from this database were further input dataset of AiZynthFinder tool and synthetic accessibility scores for their analysis.