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How to get the InChI and InChIKey of a molecule

Tutorial · macOS and Windows

The InChI is IUPAC's standard text identifier for a chemical structure, and the InChIKey is its fixed-length, 27-character hash, ideal for searching databases such as PubChem and ChemSpider. ChemPencil computes both with the official InChI library, so the identifiers match what the databases use.

Copy the InChI or InChIKey

  1. Draw the molecule, or insert it from SMILES.
  2. On Mac choose Structure › Copy InChI or Structure › Copy InChIKey. On Windows they are in Edit › Copy As.
  3. Paste into your notebook, a spreadsheet or a database search box.
The Structure menu with Copy InChI, Copy InChIKey and Copy SMILES
Identifiers in the Structure menu (Mac).

Example: L-alanine

For L-alanine drawn with a wedge to the amine, ChemPencil gives:

InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 QNAYBMKLOCPYGJ-REOHCLBHSA-N

The /t2-/m0/s1 layer and the REOHCLBHSA block of the key encode the stereocentre. Flip the wedge to a hash and you get D-alanine, with a different key: enantiomers are told apart. Without any wedge the key ends in UHFFFAOYSA-N, the code for "no stereo given".

Look the compound up

Paste the InChIKey into the search box of PubChem. An exact key match takes you straight to the compound page; for aspirin, BSYNRYMUTXBXSQ-UHFFFAOYSA-N finds acetylsalicylic acid.

Copy InChI and Copy InChIKey use the first molecule in the document. For a whole reaction or a mixture, use Copy SMILES, which covers every molecule.

Try it yourself. ChemPencil runs on macOS 12 and later and on Windows 10 and 11.

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