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Homocysteine is a sulfur-containing, non-proteinogenic amino acid with the side chain $-\mathrm{C}{\mathrm{H}}_2\mathrm{C}{\mathrm{H}}_2\mathrm{SH}$. Its neutral-form molecular formula is ${\mathrm{C}}_4{\mathrm{H}}_9\mathrm{N}{\mathrm{O}}_2\mathrm{S}$. The terminal $-\mathrm{SH}$ is a thiol group. The name without a stereochemical qualifier does not itself distinguish the possible configurations; L-homocysteine specifies the biologically important L form.^[ref]

A concrete metabolic connection is the reaction catalyzed by adenosylhomocysteinase:Thus homocysteine is not another name for S-adenosylhomocysteine: hydrolysis separates the sulfur-linked adenosyl portion from the amino-acid portion. The accepted IUBMB entry is now EC 3.13.2.1.^[ref]

An atom-inventory check makes the separation clear: the 14 carbons in S-adenosylhomocysteine partition into the four-carbon homocysteine portion and ten-carbon adenosine portion, $14=4+10$. This checks one part of the stoichiometry; it does not establish the equilibrium position or net reaction direction in a living cell.

L-homocysteine is the L-configured form of homocysteine, a sulfur-containing amino acid. ChEBI specifies its systematic name as (2S)-2-amino-4-sulfanylbutanoic acid. The neutral representation has molecular formula ${\mathrm{C}}_4{\mathrm{H}}_9\mathrm{N}{\mathrm{O}}_2\mathrm{S}$, but the formula alone does not specify the stereochemistry.^[ref]

Its stereocenter has four different attachments: hydrogen, an amino group, a carboxyl group and the side chain $-\mathrm{C}{\mathrm{H}}_2\mathrm{C}{\mathrm{H}}_2\mathrm{SH}$. A mirror-image arrangement can retain the same atom inventory and connectivity while differing in configuration. This makes L-homocysteine a concrete example of why a molecular formula cannot distinguish enantiomers.

The stereochemical qualifier also matters in biochemical reaction notation. The accepted adenosylhomocysteinase reaction names L-homocysteine as one product of hydrolyzing S-adenosylhomocysteine. That explicit identity is more precise than reporting only a sulfur-containing product. Protonation and configuration remain separate descriptors: a record of a conjugate acid or base is not, merely for that reason, a different enantiomer.^[ref]