Amatoxins are a subgroup of at least nine related cyclic peptide toxins found in three genera of deadly poisonous mushrooms (Amanita, Galerina and Lepiota) and one species of the genus Pholiotina. Amatoxins are very potent, as little as half a mushroom cap can cause severe liver injury if swallowed.

The compounds have a similar structure, that of eight amino-acid residues arranged in a conserved macrobicyclic motif (an overall pentacyclic structure when counting the rings inherent in the proline and tryptophan-derived residues); they were isolated in 1941 by Heinrich O. Wieland and Rudolf Hallermayer. All amatoxins are cyclic peptides that are synthesized as 35-amino-acid proproteins, from which the final eight amino acids are cleaved by a prolyl oligopeptidase. The schematic amino acid sequence of amatoxins is Ile-Trp-Gly-Ile-Gly-Cys-Asn-Pro with cross-linking between Trp and Cys via the sulfoxide (S=O) moiety and hydroxylation in variants of the molecule; enzymes for these processings steps remain unknown.

There are currently ten named amatoxins:

δ-Amanitin has been reported, but its chemical structure has not been determined.

Amanitin is very closely related to phalloidins, which are bicyclic 7-residue toxins. They both are part of the MSDIN protein family, so named after the highly conserved 5-amino-acid sequence in the preproteins. A 2014 research study determined that there exists a significant number of uncharacterized MSDIN sequences in Amanita genomes.

Amatoxins are potent and selective inhibitors of RNA polymerase II (RNA Pol II), a vital enzyme in the synthesis of messenger RNA (mRNA), microRNA, and small nuclear RNA (snRNA). Without mRNA, which is the template for protein synthesis, cell metabolism stops and apoptosis ensues. The RNA polymerase of Amanita phalloides has mutations that make it insensitive to the effects of amatoxins; thus, the mushroom does not poison itself.

Amatoxins are able to travel through the bloodstream to reach the organs in the body. While these compounds can damage many organs, damage to the liver and heart result in fatalities. At the molecular level, amatoxins cause damage to cells of these organs by causing perforations in the plasma membranes resulting in misplaced organelles that are normally in the cytoplasm to be found in the extracellular matrix. beta-Amanitin is also an inhibitor of eukaryotic RNA polymerase II and RNA polymerase III, and as a result, mammalian protein synthesis. It has not been found to inhibit RNA polymerase I or bacterial RNA polymerase. Because it inactivates the RNA polymerases, the liver is unable to repair damage and the cells of the liver die off quickly.

Alpha-amanitin (α-Amanitin) primarily affects the bridge helix of the RNA pol II complex, a highly conserved domain 35 amino acids long. At the N-terminus and the C-terminus of this region there are hinge structures that undergo significant conformational changes throughout the nucleotide addition cycle, and are essential for its progression. One of the many roles of the bridge helix is facilitating the translocation of DNA. Alpha-amanitin binds to the bridge helix of the RNA Pol II complex and it also binds to part of the complex that is adjacent to the bridge helix, while it is in one specific conformation. This binding locks the bridge helix into place, dramatically slowing its movement in translocating the DNA. The rate of pol II translocation of DNA is reduced from several thousand to a few nucleotides per minute.