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We performed a large scale analysis of the Protein Data Bank and systematically characterized the binding mode of fragments and drug-like ligands.

Explore drug-like ligand and fragment binding modes over 235 proteins to answer these questions:

• Does a fragment always bind a protein pocket in a similar way ?
• Is the binding mode between a fragment and its drug-like superstructure conserved ?
• Is there an influence of fragment size on binding mode conservation ?
• Is there a minimal dataset size to observe interaction pattern similarity between fragment and ligand complexes ?

General conclusions from the analysis are given in the article:

Drwal, M. N.; Bret, G.; Perez, C.; Jacquemard, C.; Desaphy, J. and Kellenberger, E. Structural insights on fragment binding mode conservation J. Med. Chem. 2018, 61(14), 5963-5973, DOI: https://doi.org/10.1021/acs.jmedchem.8b00256.

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This work was supported by the University of Strasbourg, the LabEx Medalis and Eli Lilly and Compagny through the Lilly Research Award Program (LRAP).