Het-PDB Navi. is a navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms.

PDB is a database for protein three-dimensional structures, but the data in PDB are often obtained with bound non-standard components such as DNA, RNA, ATP, GTP, PLP and so forth. As number of proteins in PDB increases, we realized that a wealth of information for small molecule-protein interactions is buried in PDB.

The interactions found in PDB can be treated as a general template for interaction between a protein and a small molecule, such as ATP, GTP and drugs.

We have, hereby, launched Het-PDB Navi. as a starter for classification and data retrieval system of protein-small molecule interactions from PDB.

The database is focused on small molecules and does not treat macromolecules such as DNA and RNA. The database was initially developed at Nagoya University in 1999, and transferred to Nagahama Institute of Bio-Science and Technology in 2003.