Small molecule: alanine

Alanine is an alpha amino-acid. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group side chain. At pH 7.3, it exists in its zwitterionic form with its amine group protonated (as −NH3+) and its carboxyl group deprotonated (as −COO−).
The central carbon atom (Calpha) is an asymetic carbon one (a chiral center). Consequently alanine can exists as two isomers, S-alanine and R-alanine also known as L-alanine and D-alanine. The configuration of the Calpha atom defines the location of the methyl group in space.

  • The L-isomer of alanine (left-handed) is the one that is incorporated into proteins. L-alanine is one of the most frequent amino acids seen in protein sequences.
  • The right-handed form, D-alanine, is rare. It is incorporated in bacterial peptidoglycans and some bacterial peptide antibiotics.


ChEBI entries are linked by a hierarchical classification (the 'is a' relationship is only one of the multiple ChEBI relationships).


Small moleculeChEBI IDRelationships
alanineCHEBI:66916alanine is an alpha-amino-acid (CHEBI:66916 is a CHEBI:35238)
L-alanineCHEBI:57972L-alanine is an L-alpha-amino-acid (CHEBI:57972 is a CHEBI:59869)
L-alanine is an alanine (CHEBI:57972 is a CHEBI:66916)
D-alanineCHEBI:57416D-alanine is a D-alpha-amino-acid (CHEBI:57416 is a CHEBI:59871)
D-alanine is an alanine (CHEBI:57416 is a CHEBI:66916)
an alpha-amino-acidCHEBI:35238an alpha-amino-acid is an amino-acid (CHEBI:35238 is a CHEBI:33709)
an L-alpha-amino-acidCHEBI:59869an L-alpha-amino-acid is an alpha-amino-acid (CHEBI:59869 is a CHEBI:35238)
a D-alpha-amino-acidCHEBI:59871a D-alpha-amino-acid is an alpha-amino-acid (CHEBI:59871 is a CHEBI:35238)

Tips: Some of these CHEBI compounds are directly used in reactions whereas others are not, but all of them are searchable in Rhea. For instance, if you search for alanine (CHEBI:66916), even though this ChEBI entry is not a reaction participant, you will retrieve reactions with L-alanine (CHEBI:57972) and D-alanine (CHEBI:57416).

RHEA:22688 describes the oxidation of D-alanine (CHEBI:57416) liberating ammonia in the process to produce pyruvate (CHEBI:15361).
The 2D structure of the reaction participants is displayed. Hover over the name of a participant to display a tooltip allowing navigation between Rhea, ChEBI and UniProt resources. Additional information about reaction participants is also displayed in a table that can be shown or hidden._


When available, the Related reactions section displays more or less specific reactions.

  • Child reactions = more specific reactions
  • Parent reactions = less specific reactions

In the example below, we can see that RHEA:22688 is linked to RHEA:21816, a more generic reaction.


What is the relationship between RHEA:22688 and RHEA:21816 reactions?

Previously, we saw that D-alanine (CHEBI:57416) is a specific form of a D-alpha-amino acid (CHEBI:59871). Similarly, pyruvate (CHEBI:15361) is a specific form (i.e instance) of a 2-oxocarboxylate (CHEBI:35179).
As all other compounds of these two reactions are identical, we can say that RHEA:22688 is a RHEA:21816