Harmonized Drug Dataset (abbreviated as HDD) integrates comprehensive metadata for small‑molecule compounds, combining structural, physicochemical, regulatory, toxicological, and experimental assay information from PubChem, LINCS, Cell Painting, DeepChem resources, and multiple toxicology databases. It includes curated binding affinities, bioassay outcomes, adverse drug reactions, toxicity measurements, and machine‑learning‑ready molecular fingerprints. The dataset is designed to support large‑scale modeling, compound characterization, and toxicology prediction workflows.