See what the database offers in a nutshell.

The aim of the database

  • Provide downloadable binding sites ready for docking and inverse docking (last update on Feb 8 2021, contains PDBs till Jul 31 2020)
  • Enable PDB-wide drug discovery and intra and cross-organism selectivity prediction
  • Classify binding sites as primary (orthosteric in most cases) and secondary (allosteric/orthosteric/other)
  • Rank binding sites according to their druggability

The database is searchable by

  • PDB ID and Chain ID
  • Source organism or taxonomic group
  • Medically interesting protein classes, such as kinases or cancer-related proteins
  • Binding site type, e.g. substrate/agonist-binding, cofactor-binding, etc.
  • See tutorial for more query options

Binding sites consist of

  • Centroids that accurately describe the various, often convoluted, shapes of binding sites
  • Receptor, a biologically relevant single chain protein or a multi-chain protein complex
  • Accessory ligands, i.e., cofactors, metal ions, conserved waters, and covalently attached glycans
  • Predicted ligands from similar binding sites obtained by the ProBiS approach
  • Bounding box representing outer limits of a binding site

Binding sites are classified as

  • Compound sites containing substrate/agonist-competitive ligands
  • Cofactor sites containing known cofactors and cofactor-competitive ligands
  • Primary sites (rank 1), each being the most druggable site on a protein
  • Secondary sites (rank >1), other sites

Download the binding sites as

  • Individual or multiple selected binding sites based on user query (see tutorial for how to efficiently use the search bar on top of the page)
  • Prepared binding site datasets for different organisms, taxonomic groups or diseases

This database does not

  • Solve all the problems related to preparation of binding sites for docking as many other tools exist for this. Examples include:
    • Adding hydrogens
    • Assigning protonation states
    • Adding missing residues