In this study we profiled the updated, second version of LANaPDB. The first version of the database had 12,959 NPs coming from nine different databases of six different Latin American countries. In the first version of LANaPDB was added a new database: NPDB EjeCol which is a compilation of NPs isolated and characterized in Colombia, specifically from the region known as the Coffee Region. This database is set to be published in 2024 and will be accessible through an open-data portal. Furthermore, LANaPDB was updated with new NPs from Costa Rica (NAPRORE-CR) and Mexico (BIOFACQUIM). In total, 619 new compounds were added to LANaPDB, to have a total of 13,578 NPs in the second version of the database.