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Medicinal Chemistry Database GDBMedChem

submitted on 26.02.2019, 13:51 and posted on 27.02.2019, 17:04 by Mahendra Awale, Finton Sirockin, Nikolaus Stiefl, Jean-Louis Reymond
The generated database GDB17 enumerates 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogens following simple chemical stability and synthetic feasibility rules, however medicinal chemistry criteria are not taken into account. Here we applied rules inspired by medicinal chemistry to exclude problematic functional groups and complex molecules from GDB17, and sampled the resulting subset evenly across molecular size, stereochemistry and polarity to form GDBMedChem as a compact collection of 10 million small molecules.

This collection has reduced complexity and better synthetic accessibility than the entire GDB17 but retains higher sp 3 - carbon fraction and natural product likeness scores compared to known drugs. GDBMedChem molecules are more diverse and very different from known molecules in terms of substructures and represent an unprecedented source of diversity for drug design. GDBMedChem is available for 3D-visualization, similarity searching and for download at


Novartis Institute for Biomedical Research (NIBR)


Email Address of Submitting Author


University of Bern



ORCID For Submitting Author


Declaration of Conflict of Interest