ZINC Biogenic compounds - commercially available primary and secondary metabolites (natural products), based on ZINC catalogs ending in np
Zbc (ZINC Biogenic Compounds) is the database of all biogenic molecules you can buy as pure compounds. This includes secondary metabolites (commonly called natural products) and primary metabolites (commonly called simply metabolites).
Our information about what is natural and what is not is drawn from both vendor catalogs and public domain sources, including but not limited to wikipedia and google. One source of errors is that many source databases fail to completely specify chirality. Since ZINC is a 3D database, we are obliged to guess the correct stereochemistry. We take up to four guesses per ambiguous molecule. Thus for molecules with more than 2 stereocenters, caveat emptor.
If you find an error, please let us know and we will endeavor to fix it.
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:
Tanimoto Cutoff Level | 100% |
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Number of Representatives | Not Available |
We compute the physical properties of each molecule in the subset, and graph them below.
Download Calculated Physical Properties
Format | Reference(pH 7) | Mid(pH 6-8) | High(pH 8-9.5) | Low(pH 4.5-6) | Download Unix | Download Windows |
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SMILES | Not Available | Not Available | Not Available | Not Available | ||
MOL2 | Not Available | Not Available | Not Available | Not Available | ||
SDF | Not Available | Not Available | Not Available | Not Available | ||
Flexibase | Not Available | Not Available | Not Available | Not Available |