Het-PDB Navi

NAR Molecular Biology Database Collection entry number 360
Yamaguchi, A.1, Tomoda, S.2, Yura, K.3, Go, M.1
1Department of Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266, Tamura-cho, Nagahama, Shiga, 526-0829, JAPAN
2Department of Electronic and Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki, 036-8560, JAPAN
3Quantum Bioinformatics Group, Center for Promotion of Computational Science and Engineering, Japan Atomic Energy Research Institute, 8-1 Umemidai, Kizu-cho, Souraku-gun, Kyoto, 619-0215, JAPAN

Database Description

Het-PDB Navi is a database that collects small molecules found in Protein Data Bank (PDB). An atomic reality of protein function is based on interactions between a protein and another molecule. One of the approaches to assume protein functions from the genome sequences is to predict interactions between proteins and the molecules. Toward that goal, we have searched through interactions of proteins and other molecules in PDB to survey molecules of which interaction modes are available. In PDB, the molecules that interact with proteins are mainly small molecules except for DNA and RNA. Amongst about 21,000 entries in PDB, about 4,260 groups of small molecules are found to interact with proteins. Small molecules most often found in PDB are metal ions, such as magnesium, calcium and zinc. Sugar molecules are the next top small molecules found in PDB. Those molecules are known to act as cofactors for enzymes and/or stabilizers of the proteins. Understanding the interactions between those molecules and proteins is necessary to predict functions of proteins. The data is collected in the database and is freely available.


This work was supported by Grant-in-Aid for Scientific Research on Priority Areas (C) Genome Information Science from the Ministry of Education, Culture, Sports, Science and Technology of Japan and by grant for Research and Development for Applying Advanced Computational Science and Technology of Japan Science and Technology Corporation.


A. Yamaguchi, K. Iida, N. Matsui, S. Tomoda, K. Yura, M. Go (2004). Het-PDB Navi. : A database for protein-small molecule interactions. J. Biochem (Tokyo), 135: 79-84

Subcategory: Small molecules

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