Low MW Fragment Library

Many vendors are offering libraries for FBDD, mainly being guided by the well-known Rule of Three in their design. However, in most of these libraries, the physicochemical parameters of the compounds tend to be closer to their upper limits (MW = 300, ClogP = 3).

Notably, recent tendencies in drug discovery shift towards aiming at leads with lower molecular weight and higher hydrophilicity. It is not surprising, therefore, that even more meticulous criteria must be applied to fragment libraries. In particular, lowering the upper molecular weight cut-off value (200 – 240 instead of 300) is strived for by many companies employing the FBDD approach and HTS campaigns in their research.

To meet these principles, Life Chemicals has designed its Low MW Fragment Library applying several physicochemical filters [1, 2] to its General Fragment Collection. Although the molecular weight is the main parameter which was controlled strictly, other physicochemical characteristics were also well monitored (e. g., more than 80 % of the Library has ClogP < 2). Finally, the compounds were passed through MedChem [3] and PAINS [4] structural filters. Over 7,100 small-molecule compounds were selected for the Library.

Additionally, an advanced subset of over 3,400 drug-like fragments was generated employing more rigorous structural filters. 





Average Values

Low MW Fragment Library

Advanced Low MW Fragment Subset


100 - 225




-3 - 3




0 - 100 Å2

51 Å2

45 Å2

Rotatable bonds

≤ 2




≤ 3




≤ 6



Ring count

1 - 3




Cherry-picking is available. Please, contact us at orders@lifechemicals.com for any details and quotations.

Representative fragments with low molecular weight

Figure 1. Representative compounds from Low MW Fragment Library


  1. Wenlock M. C. et al. J. Med. Chem. 2003, 46, 1250–1256.
  2. Hann M. M. Part of the Series: NATO Science for Peace and Security, Series A: Chemistry and Biology. 2015, 183–196.
  3. Bruns R. F.; Watson I. A. J. Med. Chem. 2012, 55, 9763–9772.
  4. Baell J. B.; Holloway G. A. J. Med. Chem. 2010, 53, 2719–2740.
  5. Thien TV et al. Dokl Biochem Biophys. 2017 Sep;476(1):316-319.
  6. Chen Y et al. Chemosphere. 2018 May;198:226-237.
  7. Lazzarino G et al. Hum Reprod. 2018 Oct 1;33(10):1817-1828.
  8. O'Reilly M. Drug Discov Today. 2019 May;24(5):1081-1086.  
This site uses cookies. Some of these cookies are essential, while others help us improve your experience by providing insights into how the site is being used. By using our website, you accept our conditions of use of cookies to track data and create content (including advertising) based on your interest. Accept