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.
Het-PDB Navi2 is developed by Sippakorn Widsankun, who is a internship student from Kasetsart University at 2015, and Masafumi Shionyu.
Development of this database is supported by JSPS KAKENHI Grant Numbers JP15K00411 and Platform Project for Supporting Drug Discovery and Life Science Research（Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS )) from Japan Agency for Medical Research and Development (AMED).
In citing Het-PDB Navi. please refer to:
A. Yamaguchi, K. Iida, N. Matsui, S. Tomoda, K. Yura, M. Go: Het-PDB Navi. : A database for protein-small molecule interactions. J. Biochem (Tokyo), 135, pp.79-84 (2004)