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Welcome to sc-PDB-Frag

sc-PDB-Frag is a database of protein-bound fragments that assists you
in selecting truly bioisosteric scaffolds

The database allows you to:
  • Search your favorite fragment among PDB ligands or sketch it;
  • Define similarity rules to retrieve potential bioisosteres;
  • Score bioisosteres according to interaction pattern similarity;
  • Align bioisosteres to your reference scaffold;
  • Visualize the proposed alignment.

Citing sc-PDB-Frag

Desaphy, J. and and Rognan, D.
sc-PDB-Frag: A Database of Protein-Ligand Interaction Patterns for Bioisosteric Replacements
J. Chem. Inf. Model. 2014, 54, 1908-1918


8,077 protein-ligand complexes
2,377 proteins
5,233 ligands
12,000 fragments
15 million pair-wise fragment comparisons

© Copyright 2013. Structural Chemogenomics Group - UMR7200