NLDB: a database for 3D protein–ligand interactions in enzymatic reactions

Yoichi Murakami, Satoshi Omori, Kengo Kinoshita

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


NLDB (Natural Ligand DataBase; URL: is a database of automatically collected and predicted 3D protein–ligand interactions for the enzymatic reactions of metabolic pathways registered in KEGG. Structural information about these reactions is important for studying the molecular functions of enzymes, however a large number of the 3D interactions are still unknown. Therefore, in order to complement such missing information, we predicted protein–ligand complex structures, and constructed a database of the 3D interactions in reactions. NLDB provides three different types of data resources; the natural complexes are experimentally determined protein–ligand complex structures in PDB, the analog complexes are predicted based on known protein structures in a complex with a similar ligand, and the ab initio complexes are predicted by docking simulations. In addition, NLDB shows the known polymorphisms found in human genome on protein structures. The database has a flexible search function based on various types of keywords, and an enrichment analysis function based on a set of KEGG compound IDs. NLDB will be a valuable resource for experimental biologists studying protein–ligand interactions in specific reactions, and for theoretical researchers wishing to undertake more precise simulations of interactions.

Original languageEnglish
Pages (from-to)101-110
Number of pages10
JournalJournal of Structural and Functional Genomics
Issue number4
Publication statusPublished - 2016 Dec 1


  • Database
  • Docking
  • Enzymatic reactions
  • Protein–ligand interactions
  • Variant residues


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