Modern drug discovery and pharmaceutics are benefited from nature. Natural products (NPs) are used as a source of therapeutic agents with beneficial uses. Nowadays, there is considerable interest in the exploration of NPs for drug discovery, and continuous investigations on the therapeutic claims and mechanisms of herbal medicines. Currently, about a million NPs have been isolated and subjected to experimental assays to evaluate quantitative biological activities. This makes necessary the use of an integrated database to assemble and correlate this valuable information from literature, experimental studies and databases. In the present work, using state of the art in silico techniques of chemoinformatics including data mining, machine learning, and unsupervised clustering, the available accessible information related to NPs was collected, analyzed and stored in the Hippo(crates) database. Part of the Openscreen-gr project, the portal is developed to provide a user-friendly access interface, integrating annotated information of species sources, biological activities, physicochemical properties, linear and 3D chemical structure and many other relative terms that can describe the chemical compounds and their use. The Hippo database in the current version (V1.0) provides 45300 NPs, NP derivatives and synthetic compounds, which are separated into 32 major categories including biological or medicinal properties. In the database 22830 NP source organisms are correlated, with more than 100000 terms including biological pathways, target organisms, target diseases, target types, target proteins and pathogens, and 6070 three dimensional structures of NP target proteins. For each entry, a cluster with similar compounds and a ligand-based or structure-based pharmacophore model is provided. The portal is designed as an easy to use tool where the user can easily search, extract and correlate information and data for natural product chemical compounds through various fields such as categories, keywords, targets, species or two-dimensional or three-dimensional similarity structure in the Hippo(crates), atlas of NPs database.