articleMedChemCommJan 1, 2017HYBRID OA

A systematic analysis of atomic protein–ligand interactions in the PDB

RFRenato Ferreira de FreitasMSMatthieu Schapira

Toronto Public Health · University of Toronto · +1 more institution

PubMed
Indexed incrossrefpubmed

Abstract

As the protein databank (PDB) recently passed the cap of 123 456 structures, it stands more than ever as an important resource not only to analyze structural features of specific biological systems, but also to study the prevalence of structural patterns observed in a large body of unrelated structures, that may reflect rules governing protein folding or molecular recognition. Here, we compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins - 6444 of which have experimental binding affinity - representing 750 873 protein-ligand atomic interactions, and analyzed the frequency, geometry and impact of each interaction type. We find that hydrophobic interactions are generally…

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Topics & keywords

Topics
Keywords
  • Protein Data Bank (RCSB PDB)
  • Ligand (biochemistry)
  • Folding (DSP implementation)
  • Stacking
  • Amide
  • Hydrogen bond
  • Chemistry
  • Protein Data Bank
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