Chloroeremomycin is composed of seven amino acids (three non-proteinogenic, and four proteinogenic) and three saccharide units. From N-terminus to C-terminus, the order is: Me--Leu, -Tyr, -Asn, -4-hydroxyphenylglycine (HPG), -HPG, -Tyr, and -3,5-dihydroxyphenylglycine (DHPG). When referring to specific amino acids, this article will reference the amino acid in the order it appears within the heptapeptide. Chloroeremomycin is glycosylated at aa4 with a Glc-(2→α1)-epivancosamine disaccharide and at aa6 with a -BHT-(→α1)-epivancosamine saccharide.
Some amino acids are modified prior to the completion of the heptapeptide (in cis) and some are modified after the heptapeptide is formed (in trans). During the synthesis of the heptapeptide, the stereocenters of aa3, aa4, aa6, and aa7 are changed from L to D. Both Tyr residues are hydroxylated and chlorinated after the amino acids have been incorporated to the growing polypeptide to form 4-chloro-β-hydroxytyrosine (BHT). The now-BHT residues are then crosslinked to the aa4 HPG through aryl-ether linkages. An aryl-aryl bond is formed between aa5 and aa7 at the aa5-C3 and aa7-C2 positions on the aromatic rings. Finally, the N-terminus Leu is methylated.
In addition to the presence of -amino acids, the molecule has atropisomer chemistry. The orientations of the chloro-substituted phenyl rings add another aspect of stereochemistry to the molecule.