Understanding the biological phenomena of sequence, structure, function, metabolism, and molecular interactions of species is crucial to identify or analyze the biological problems in the ideal way. Integration of all data facilitates unified access to the key problem. PDTDB (Phytochemical and Drug Target DataBase) is anintegrative structural database, which contains information about the plants (secondary metabolites, plant anatomy, side effects, and medicinal properties), ligands (3D molecular structure, SMILES string, side effects, and medicinal properties), therapeutic drug targets (3D molecular structure, sequence, mechanism of the drug target, disease nature, and disease symptoms), molecular dockings (target-ligand complex interaction, drug action, home remedies, and docking results), and structure activity relationship between diseases, therapeutic targets, plants, and phytochemicals. The database provides keyword or accession number search, similar phytochemical structures search using SMILES string or by sketching the structure in the chemical structure editor, phytochemical structures with similar molecular formula search, binding structure search, and browse and/or search database entries from the sortable table. It supports predicting physicochemical properties of sequence and structures, and interactive visualization of structures in various models. PDTDB is freely accessible at https://pdt.biogem.org.