In this work, we introduce MetAP DB, the first open access and oriented metal-based approved drug database, which contains 61 compounds classified according to their clinical uses in five categories: "metallodrug", "imagenology", "radioimagenology", "radiotherapy" and "photodynamic". We also introduce three versions of a metal-based fingerprint that encodes information related to the presence of metals, their valence and oxidation state, the presence of specific functional groups, and the atom connectivity of metal-based compounds. The newly developed fingerprints open up new perspectives on rational molecular design with applications in medicinal chemistry or materials development, which offer a low-computational cost solution to the systematic study of small and large metal-based datasets, for example, been applied on virtual screening campaigns, chemical space analysis, and artificial intelligence applications. The Metal-FP3 shows the best performance to differentiate metal-based compounds according to inter- and intra-Jaccard distance metrics and the t-SNE analysis, however additional studies using the most robust datasets will be necessary to confirm their descriptive power.