Scaffold hopping can be used to improve the pharmacological properties, specificity or synthesis of biologically active compounds. It identifies different core structures for ligands while retaining their bio-activity. With CSD-CrossMiner, researchers can search and retrieve novel scaffolds from world-leading databases—like the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB).


scaffold hopping wp figure

3D representation of the five-feature pharmacophore model built at the
binding site of 4MR4. The reference compound (RVX-208) is light pink, and the key residues are grey.


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Download the white paper to find out how scaffold hopping in CSD-CrossMiner was used as an alternative to the experimental approaches presented in the literature in three test cases. These examples show how the Scaffold Hopping methodology can be used to:

  • Replace a Quinazoline Core

  • Improve Metabolic Stability

  • Improve PK Profile


This fast and flexible approach obtained hits that aligned well with experimental results in all three test cases, as well as providing additional novel scaffolds that could be used in further optimization.




CSD-CrossMiner matches molecules to targets through intuitive, interactive data mining.

Learn more about CSD-CrossMiner.