Bitter DB


BitterDB is a free repository of bitter molecules. It contains information on compounds that were documented to taste bitter to humans or to activate bitter taste receptors in-vitro.


To cite BitterDB, please reference: BitterDB: a database of bitter compounds. Nucleic Acids Res. 2012 Wiener A, Shudler M, Levit A, Niv MY.
View on NAR website


Information about activation of human bitter taste receptors by bitter molecules can be found in BitterDB as described in the above paper, and for example by using this link: http://bitterdb.agri.huji.ac.il/bitterdb/dbbitter.php#receptorBrowse

We are grateful to the authors for allowing us to incorporate the molecular structrues of this database in ZINC.

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Chemical Diversity and Clustering

We assess the chemical diversity of a subset by clustering the molecules. First, we sort ligands by increasing molecular weight. Then, we use the SUBSET 1.0 algorithm ( Voigt JH, Bienfait B, Wang S, Nicklaus MC. JCICS, 2001, 41, 702-12) to progressively select compounds that differ from those previously selected by at least the Tanimoto cutoff, using ChemAxon default fingerprints. The resulting representatives have two interesting properties:

  • 1) Each representative differs from all the others by at least the Tanitmoto cutoff and
  • 2) All the molecules in the subset are within the Tanimoto cutoff of at least one representative.
Thus the representatives can be said to "cover" the chemical space of the subset at a given Tanimoto level. N/A indicates that clustering is pending.

Tanimoto Cutoff Level 60% 70% 80% 90% 100%
Number of Representatives 216 301 363 436 686

Physical Property Distributions

We compute the physical properties of each molecule in the subset, and graph them below.   Download Calculated Physical Properties

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Format Reference(pH 7) Mid(pH 6-8) High(pH 8-9.5) Low(pH 4.5-6) Download
SMILES All All All All
MOL2 All All All All Single Usual Metals All Single Usual Metals All
SDF All All All All Single Usual Metals All Single Usual Metals All
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