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Synthetic Compounds with Natural Product-like Features

Natural products provide a source of substructures found in bioactive molecules. Early on, many substructures found in natural products occurred at low frequency in traditional, synthetic, drug-like compounds. Over the last 15 years, ChemBridge lead-like and drug-like compound designs have continued to evolve to incorporate a range of new features, including substructure elements more common in natural products. ChemBridge has employed a published scoring method designed to identify compounds with the most natural-product like features to create a selection of compounds with the most natural product-like features. The Natural Product-like (NPL) Library contains approximately 50,000 compounds from ChemBridge’s stock. These compounds provide a source of synthetic compounds with the highest similarity to the structural space covered by natural products.

  • Synthetic compounds with natural product-like features
  • Custom select from more than 50,000 compounds

View the Natural Product-like Library product sheet


A scoring method, published by Ertl et al (J. Chem. Inf. Model. 2008, 48, 1, 68-74), was applied to ChemBridge’s stock of small molecule lead-like and drug-like compounds to identify a subset showing a higher natural product likeness based on the presence of features more common to natural products than to traditional synthetic compounds. A cutoff of zero and higher for the natural product likeness score was selected as the majority of the natural products used in the publication had scores of zero or higher (most coming within the range 0 to 4.0), while the majority of the 1 million traditional, synthetic compounds used in the analysis had scores of -1.0 or less (see Fig. 3 in the article cited). Small percentages of both synthetic and natural product compounds scored in the -1.0 to 0 range, which indicates this range of scores was least able to discriminate between natural product and synthetic compounds.


Natural Product-like (NPL) Library compounds are lead-like and drug-like and have the following physiochemical and calculated property averages and ranges:

  • Molecular Weight: Average: 326
  • Fsp3 Average: 0.6
  • clogP Average: 2.4
  • TPSA Average: 62
  • H-bond Donor Count Average: 1.2
  • H-bond Acceptor Count Average: 4.0
  • Download structures and custom select compounds from the Natural Product-like Library SDfile
  • Compounds can be provided in 96-well and 384-well format
  • Amounts as low as 0.25 micromole (25ul of 10mM DMSO solution) available
  • Compounds are available as DMSO solutions or dry in micromole or mg amounts

For more information or a file of compound structures, please contact ChemBridge Sales