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Fluorine Fragment Library

It was demonstrated that ¹⁹F NMR ligand-based fragment screening could be used as a very efficient tool for rapid and sensitive detection of fragment hits in fragment-based lead discovery (FBLD) [1]. As shown, although the fraction of chemical space covered by fluorine-labeled fragments may be limited compared to that covered by non-fluorinated fragments, similar hit rates are obtained applying both methods. At the same time, fragment screening with a simple one-dimensional ¹⁹F NMR experiment (with ¹H decoupling) is significantly faster and, in many ways, more robust than traditional ¹H-based NMR screening.

An in-house developed method focuses on the use of a fluorine nucleus as a detection tool. After a ¹⁹F fragment screen, protonated analogs of hit compounds can be mined and pursued in initial hit expansion. This approach can significantly add to the chemical space explored and also provide valuable information and early-stage SAR to chemists.

The Life Chemicals Fluorine Fragment Library comprises over 6,800 drug-like fluorinated compounds from the General Fragment Stock Collection.

In addition, we have designed a Diversity Screening Set of 1,600 structurally-diverse fluorinated fragments to provide the most-promising drug-like screening compounds in a convenient manner. These fluorine-containing fragment-like molecules possess a wide range of chemical structure dissimilarity and are compliant with in-house MedChem and PAINS structural filters [6-7].

 No metal or reactive compounds, no undesired chemotypes, no salts are present in the Library, and the PAINS filters were applied. All compounds are available from stock.

The compound selection can be customized based on your requirements, cherry picking is available.

Please, contact us at for any additional information and price quotations.

For a pre plated set based on this Screening Library, please explore our Pre-plated Fragment Screening Sets.

Distribution of differently fluorine-substituted fragments

Figure 1. Distribution of differently fluorine-substituted fragments

Single-fluorine Fragments

Mono-fluorine Subsituted Fragments

Difluoromethyl- and difluoromethylene (CF2) substituted Fragments 

CF2-substituted Fragments

Trifluoromethyl-substituted (CF3) Fragments

CF3-substituted Fragments

Figure 2. Representative fluorine-containing fragments from Fluorine Fragment Library

Figure 3. Predicted “fragment space” coverage of Life Chemicals fluorinated fragments (in red) is similar to the coverage of >100k commercially available fluorine-containing fragment-like molecules from eMolecules (in blue).


  1. Jordan J. B. et al. J. Med. Chem. 2012, 55, 678−687.
  2. Vulpetti A, Dalvit C. Drug Discov Today. 2012 Aug;17(15-16):890-7. 
  3. Nagatoishi S, Yamaguchi S et al. Bioorg Med Chem. 2018 May 1;26(8):1929-1938. 
  4. Norton RS, Leung EW et al. Molecules. 2016 Jul 16; 21(7). pii: E860.
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