Het-PDB Navi. A Database for Protein-Small Molecule Interactions

Akihiro Yamaguchi, Kei Iida, Nobuaki Matsui, Shirou Tomoda, Kei Yura, Mitiko Go*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

37 Citations (Scopus)


The genomes of more than 100 species have been sequenced, and the biological functions of encoded proteins are now actively being researched. Protein function is based on interactions between proteins and other molecules. One approach to assuming protein function based on genomic sequence is to predict interactions between an encoded protein and other molecules. As a data source for such predictions, knowledge regarding known protein-small molecule interactions needs to be compiled. We have, therefore, surveyed interactions between proteins and other molecules in Protein Data Bank (PDB), the protein three-dimensional (3D) structure database. Among 20,685 entries in PDB (April, 2003), 4,189 types of small molecules were found to interact with proteins. Biologically relevant small molecules most often found in PDB were metal ions, such as calcium, zinc, and magnesium. Sugars and nucleotides were the next most common. These molecules are known to act as cofactors for enzymes and/or stabilizers of proteins. In each case of interactions between a protein and small molecule, we found preferred amino acid residues at the interaction sites. These preferences can be the basis for predicting protein function from genomic sequence and protein 3D structures. The data pertaining to these small molecules were collected in a database named Het-PDB Navi., which is freely available at http:// daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html and linked to the official PDB home page.

Original languageEnglish
Pages (from-to)79-84
Number of pages6
JournalJournal of biochemistry
Issue number1
Publication statusPublished - 2004 Jan
Externally publishedYes


  • Co-factor
  • Database
  • Metal
  • Nucleotide
  • Protein 3D-structure
  • Protein function
  • Sugar

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


Dive into the research topics of 'Het-PDB Navi. A Database for Protein-Small Molecule Interactions'. Together they form a unique fingerprint.

Cite this