Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17
Open accessAbstract
Drug molecules consist of a few tens of atoms connected by covalent bonds. How many such molecules are possible in total and what is their structure? This question is of pressing interest in medicinal chemistry to help solve the problems of drug potency, selectivity, and toxicity and reduce attrition rates by pointing to new molecular series. To better define the unknown chemical space, we have enumerated 166.4 billion molecules of up to 17 atoms of C, N, O, S, and halogens forming the chemical universe database GDB-17, covering a size range containing many drugs and typical for lead compounds. GDB-17 contains millions of isomers of known drugs, including analogs with high shape similarity to the parent drug. Compared to known molecules in PubChem, GDB-17 molecules are much richer in nonaromatic heterocycles, quaternary centers, and stereoisomers, densely populate the third dimension in shape space, and represent many more scaffold types.
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The GDB-17 set of organic molecules of up to 17 heavy atoms with a limited number of elements contains 66 billion compounds.
“The GDB-17 (35) set of organic molecules of up to 17 heavy atoms with a limited number of elements (i.e., C, N, O, S and halogens) contains 66 billion compounds”
From Machine Learning for the Discovery, Design, and Engineering of Materials. (2022) · cites this paper as [35]
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- Authors
- Ruddigkeit, L., van Deursen, R., Blum, L. C., & Reymond, J.-L.
- Affiliations
- University of Bern (CH)
- Ecole Polytechnique Fédérale de Lausanne Biomolecular Screening Facility, NCCR Chemical Biology, School of Life Sciences, , 1015 Lausanne, Switzerland
- Corresponding author
- Reymond, Jean-Louis
- ORCID
- Reymond, Jean-Louis
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-10-22
- Volume
- 52
- Issue
- 11
- Pages
- 2864-2875
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W2114704115
- Cited by
- 1,505
- References
- 47
- Citations by year
- 2026: 115 · 2025: 202 · 2024: 192 · 2023: 178 · 2022: 174 · 2021: 177 · 2020: 148 · 2019: 100 · 2018: 54 · 2017: 41 · 2016: 36 · 2015: 33 · 2014: 34 · 2013: 19 · 2012: 2
- FWCI
- 30.17
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of Chemical Information and Modeling (publishedVersion, cc-by)
- PubMed (publishedVersion)
- BORIS (University Library Bern) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Chemistry › Organic Chemistry › Synthesis and Characterization of Heterocyclic Compounds
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Keywords
- small organic molecules, chemical space, drug-like molecules, lead compounds, molecular geometry, isomers, quaternary centers, stereoisomers, scaffolds
- MeSH terms
- Computer Simulation, Models, Chemical, Stereoisomerism, Structure-Activity Relationship, Drug Design, Molecular Structure, Prescription Drugs, Databases, Chemical, Databases, Pharmaceutical
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