Secondary Metabolites Search

About SMS

Historically, natural products have been recognized as the foundation of medicines, cosmetics and foods. Today, they continue to be an important resource for technological and socioeconomic development and for maintaining human well-being. In this scenario, secondary metabolites play a fundamental role, mainly thanks to their great chemical diversity.

Here we present the Secondary Metabolites Search (S.M.S.). The database collects more than 5000 compounds isolated from plants growing in Italy and describes them considering both their 2D and 3D structure. The producing organism is also reported, linked to FlorItaly, the portal to the Italian flora, for a full botanical description. The easy download of all the contained data would greatly simplify research on natural products in different fields and allow computational applications.

Data sources and citations

  • RDKit — 2D structure drawings and 3D models (ETKDG conformers, MMFF94-optimised), generated from the SMILES in the database. RDKit: Open-source cheminformatics. www.rdkit.org
  • 3Dmol.js — interactive 3D viewer. Rego N, Koes D. 3Dmol.js: molecular visualization with WebGL. Bioinformatics. 2015;31(8):1322–1324. doi:10.1093/bioinformatics/btu829
  • PubChem — compound identifiers. Compounds found in PubChem link to their record. Kim S, et al. PubChem 2025 update. Nucleic Acids Res. 2025;53(D1):D1516–D1525. doi:10.1093/nar/gkae1059
  • NPClassifier — chemical classification of natural products (pathway, superclass, class), predicted from the structure. Kim HW, et al. NPClassifier: a deep neural network-based structural classification tool for natural products. J Nat Prod. 2021;84(11):2795–2807. doi:10.1021/acs.jnatprod.1c00399
  • LOTUS — data model: every record is a structure–organism pair documented by a reference, with compounds identified by InChIKey. The whole database can be downloaded in LOTUS format from the API. Rutz A, et al. The LOTUS initiative for open knowledge management in natural products research. eLife. 2022;11:e70780. doi:10.7554/eLife.70780
  • Dryades — plant photographs, University of Trieste. Author and owner are credited under each photo. dryades.units.it
  • FlorItaly — the portal to the flora of Italy, for plant names and botanical descriptions. dryades.units.it/floritaly