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A complete small molecule dataset from the protein data bank.

Howard J Feldman1, Kevin A Snyder, Amy Ticoll

  • 1The Blueprint Initiative, Suite 101, 200 Elm Street, Toronto, Ont., Canada M5T 1K4.

FEBS Letters
|February 24, 2006
PubMed
Summary

A new dataset of 6300 small molecule ligands, including cyclic polypeptides and branched polysaccharides, is now available in PubChem. This comprehensive ligand resource enhances structural accuracy and nomenclature for research.

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Area of Science:

  • Chemical Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Small molecule ligands are crucial for understanding biological processes.
  • Existing ligand databases often lack comprehensive structural diversity and accurate nomenclature.
  • The Protein Data Bank (PDB) contains valuable ligand information but requires curation.

Purpose of the Study:

  • To create a curated and comprehensive dataset of small molecule ligands from the PDB.
  • To improve ligand representation by including diverse structures like cyclic polypeptides and branched polysaccharides.
  • To establish an unambiguous nomenclature and accurate structural data for deposited ligands.

Main Methods:

  • Extraction of 6300 small molecule ligands from the Protein Data Bank.

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  • Inclusion of cyclic polypeptides and branched polysaccharides.
  • Development of an unambiguous nomenclature system.
  • Data curation to correct errors and determine bond order/aromaticity using a perception algorithm.
  • Establishment of a PubChem data source named 'SMID'.

    • Main Results:

    • A complete set of 6300 small molecule ligands was compiled and deposited in PubChem as 'SMID'.
    • The dataset uniquely incorporates cyclic polypeptides and branched polysaccharides with clear nomenclature.
    • Best examples of each ligand structure were retained, with a separate dataset for all structural examples.
    • Ambiguous atomic elements and common errors were corrected.

    Conclusions:

    • The 'SMID' dataset provides a significant advancement in small molecule ligand resources.
    • This comprehensive and accurate ligand dataset will facilitate drug discovery and biochemical research.
    • Improved ligand data enhances the reliability of structural biology studies.