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NLDB: Natural Ligand DataBase - A database of protein-ligand interactions in three-dimension.
The ligand in the database is a “natural ligand” generated by the knowledge of enzymatic reactions appeared in KEGG combined with a three-dimensional data of protein-analog interactions in PDB.
Natural Complex
122,804
Experimentally determined structures
Analog Complex
current: 32,875
obsolete: 4,084
Transformation of a natural ligand to its analog, and then the local optimization of the embedded ligand
Ab initio Complex
current: 67,692
obsolete: 5,120
Docking of a natural ligand to predicted ligand-binding sites, and then the local optimization of the embedded ligand
(Last Update: 15-Mar-2026)
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