Secondary metabolites can be classified by their chemical structure or physical properties into one or more of the following groups: alkaloids, terpenoids, polyketides, aliphatic, aromatic, and heteroaromatic organic acids, phenols, iridoids, steroids, saponins, peptides, ethereal oils, resins and balsams.
Most of the secondary metabolites of interest to humankind fit into categories which classify secondary metabolites based on their biosynthetic origin. Since secondary metabolites are often created by modified primary metabolite synthases, or "borrow" substrates of primary metabolite origin, these categories should not be interpreted as saying that all molecules in the category are secondary metabolites (for example the steroid category), but rather that there are secondary metabolites in these categories
Alkaloids
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Codeine | Morphine | Cocaine | Tetrodotoxin | Atropine
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Flavonoids
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Naringenin | Genistein
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Terpenoids
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Azadirachtin, (Neem tree) tetrahydrocannabinol, present in cannabis sativa
Steroids (Terpenes with a particular ring structure)
Saponins (plant steroids, often glycosylated)
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Monoterpenoids
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Limonene | Pinene
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Diterpenoids
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Taxol, Pimaradiene
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Antibiotics
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Penicillin | Streptomycin | Tetracycline
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Glycosides (heavily modified sugar molecules)
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Glucosinolates
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Phenols:
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Resveratrol
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Phenazines:
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Pyocyanin
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Non-"small molecules" - DNA, RNA, ribosome, or polysaccharide "classical" biopolymers
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Ribosomal peptides: Microcin-J25
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