The nomenclature of isoprenoids and their derivatives is somewhat confusing. Here are some guidelines for understanding these names:
Isoprenoids are composed of repeating isoprene units. The units can be attached in either a trans conformation (the two carbons are on opposite sides of the double bond) or a cis conformation (the two carbons are on the same side of the double bond). It is common to use E and Z instead of trans and cis , respectively.
The numbering of carbons in the molecule starts from the carbon attached to the hydroxyl or phosphate group. The isoprene unit furthest from the C1 carbon is called the ω unit. Unlike all other isoprene units, the ω unit is not a stereo center since the last carbon is attached to two identical methyl groups.
There are two widely used naming systems, and unfortunately they refer to the isoprene units in opposite order. One method describes the molecule starting with the unit with the lowest carbon number (ie the one furthest from the ω unit), naming each of the stereo-active carbons by its number, followed by its stereo designation. For example, this molecule is referred to as 2,6-cis,10-trans-tetraprenyl diphosphate or (2Z,6Z,10E)-tetraprenyl diphosphate. According to the other method, the molecule is described by the stereoconfiguration of the molecule starting with the ω unit. For example (2Z,6Z,10E)-tetraprenyl diphosphate is referred to as ω,E,Z,Z tetraprenyl diphosphate.
On top of this, many of the shorter molecules have trivial names that are commonly used. Some of these names are specific for a particular stereoisomer and some are used for all stereoisomer. For example, geranylgeranyl diphosphate is commonly used for the all-trans isomer of the molecule with four isoprene units, while farnesyl diphosphate is used for all four isomers of the molecule with three isoprene units - (2E,6E)-farnesyl diphosphate, (2Z,6E)-farnesyl diphosphate, (2Z,6Z)-farnesyl diphosphate and (2E,6Z)-farnesyl diphosphate.
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