Search Rhea using chemical structures (InChIKey)
Some experimental analysis provide only structure data encoded as InChIKey (see What are InChI and InChIKey?). The Rhea search allows you to retrieve reactions based on such format.
- Simple search: use the prefix "inchikey:".
- Advanced search: click the red All button and select the InChIKey topic.
Let's use "HVYWMOMLDIMFJA-DPAQBDIFSA-N", the InChIKey of cholesterol (CHEBI:16113) as an example.
If you search for inchikey:HVYWMOMLDIMFJA-DPAQBDIFSA-N, you will get all reactions involving this steroid.
The search always returns the ChEBI compounds that correspond to the major microspecies at pH 7.3. The charge is encoded by the third part of the InChIKey.
If you query Rhea with an InChIKey which describes a neutral structure whereas Rhea uses the charged one, the search engine will bypass this constraint and returns the reaction for the structure used in Rhea.
For example, by searching for inchikey:OIWCYIUQAVBPGV-DAQGAKHBSA-N, you will retrieve reactions that involve CHEBI:75029 (1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-L-serine). The InChIKey of CHEBI:75029 is "OIWCYIUQAVBPGV-DAQGAKHBSA-M", it differs from our query by its third section (N: neutral in the query and M: charge=-1 in the result).
Note that you would obtain the same result if you had searched for the partial inchikey:OIWCYIUQAVBPGV-DAQGAKHBSA (i.e the third part of the InChIKey is omitted).
You can search Rhea using only the first part of the InChIKey which encodes the connectivity of a molecule if the stereochemistry of the molecules are not relevant for your search (remember that the stereochemistry is encoded by the second part of an InChIKey).
For instance, the query inchikey:JUGXQEJPWDYOJV will return reactions with participants having JUGXQEJPWDYOJV-CCDZVGGQSA-N ((3β)-hydroxy-cholest-5-en-26-al) or JUGXQEJPWDYOJV-YSQMORBQSA-N ((25R)-3β-hydroxy-5-cholesten-26-al ) as InChIKey. These two compounds differ by the stereochemistry of C25 which is not defined in the first case whereas it has the configuration (R) in the second case.
