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J Struct Funct Genomics. 2016 Dec;17(4):101-110. doi: 10.1007/s10969-016-9206-0. Epub 2016 Aug 16.

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

Author information

Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8575, Japan.
Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Saito-Asagi 7-6-8, Ibaraki-city, Osaka, 567-0085, Japan.
Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8575, Japan.
Institute of Development, Aging and Cancer, Tohoku University, Seiryo-machi 4-1, Aoba-ku, Sendai, 980-8575, Japan.
Tohoku Medical Megabank Organization, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8573, Japan.


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.


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

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