What is Binding MOAD?
We have created a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. Hence, we call it the Mother of All Databases (MOAD).
Binding MOAD's goal is to be the largest collection of well resolved protein crystal structures with clearly identified biologically relevant ligands annotated with experimentally determined binding data extracted from literature.

Binding MOAD Criteria for inclusion:
  ...biologically relevant ligands...
Ligands may be a
  • peptide of 10 amino acids or less
  • oligonucleotide of 4 nucleotides or less
  • small organic molecule (e.g. ibuprofen)
  • cofactor (e.g. NADPH)
Ligands are not:
  • crystallographic additives (e.g. polythylene glycol)
  • salts (Cl-, phosphates)
  • buffers (e.g. Tris, CHAPS)
  • metals (e.g. Rb+, Zn2+)
  • metallic catalytic centers (e.g. FeS, NiFe)
  • solvents (e.g. DMSO)
  ...well resolved...
has a resolution of 2.5 Å or better
  ...binding data extracted from literature
We've searched through the primary reference of each PDB entry looking for Kd, Ki, and IC50 data. If we've got something wrong or if you have something to add, Please let us know - we'll correct it, and give you credit.
- We have gone through all the single HET group ligands and updated the SMILES to the current PDB Component Dictionary OpenEye Cannonical form.
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  • Cite Binding MOAD:
    1) L Hu, ML Benson, RD Smith, MG Lerner, HA Carlson. Binding MOAD (Mother Of All Databases).Proteins 2005, 60, 333-40.
    2) A Ahmed, RD Smith, JJ Clark, JB Dunbar Jr., HA Carlson. Recent improvements to Binding MOAD: a resource for proteinligand binding affinities and structures. Nucl. Acids Res. 2014,43, D465-D469.
    3) RD Smith, JJ Clark, A Ahmed, ZJ Orban, JB Dunbar Jr., HA Carlson. Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing. J. Mol. Biol. 2019,431, 2423-2433.
  • Additional Reference:
    ML Benson, RD Smith, NA Khazanov, B Dimcheff, J Beaver, P Dresslar, J Nerothin, and HA Carlson. Binding MOAD, A high-quality protein-ligand database. Nucleic Acids Research 2008, 36, D674-D678.

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