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Characterising non-covalent interactions with the Cambridge Structural Database

J P Lommerse1, R Taylor

  • 1Cambridge Crystallographic Data Centre, UK.

Journal of Enzyme Inhibition
|February 1, 1997
PubMed
Summary
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The Cambridge Structural Database (CSD) reveals insights into non-covalent interactions, aiding rational drug design. It analyzes interaction frequencies, geometries, and suggests novel targets for medicinal chemistry.

Area of Science:

  • Chemical Crystallography
  • Medicinal Chemistry
  • Drug Design

Background:

  • Non-covalent interactions are crucial in molecular recognition and drug design.
  • The Cambridge Structural Database (CSD) is a comprehensive repository of small-molecule crystal structures.

Purpose of the Study:

  • To explore the utility of the CSD for studying non-covalent interactions.
  • To identify novel interactions and potential drug targets using crystallographic data.

Main Methods:

  • Analysis of interaction frequencies and geometries within the CSD.
  • Searching the CSD for specific types of non-covalent interactions, such as hydrogen bonds and halogen bonds.
  • Evaluating the relevance of small-molecule crystal structures for protein-ligand interactions.

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Main Results:

  • Terminal oxygen atoms in phosphates frequently accept hydrogen bonds.
  • Specific geometric preferences were observed for hydrogen bonds to P-O groups and I...O contacts.
  • Novel interactions like N-H...pi hydrogen bonds and I...O contacts were identified.
  • The CSD can suggest potential binding motifs for drug design, such as electron-deficient groups interacting with tryptophan.

Conclusions:

  • The CSD is a valuable resource for understanding non-covalent interactions in rational drug design.
  • Its size, diversity, and accuracy make it ideal for identifying interaction patterns and guiding synthetic chemistry.
  • Evidence suggests that interactions observed in small-molecule crystals are relevant to protein-ligand complexes.