SMILES

Searches for structures containing a chemical component (ligand) using a SMILES string .

The SMILES search supports three types of queries:

  • Similar - finds structures that bind similar ligands. Specify a dissimilarity threshold to change the degree of dissimilarity in the [0...1] range: 0 - identical ... 1 dissimilar. The dissimilarity is based on the number of chemical features in common between the query and the target molecule. Dissimilarity is defined as 1 - Tanimoto Coefficient.
  • Exact - finds an exact structure match
  • Substructure - finds ligands that contain the specified structure as a substructure

Examples

  1. Dissimilarity with dissimilarity threshold of 0.2

    C1C2C(C(S1)CCCCC(=O)O)NC(=O)N2 - SMILES string for biotin

    This query returns structures containing biotin, its steroisomers, and various biotin derivatives including: BTN (biotin), BTQ (epi-biotin), BSO (biotin-d-sulfoxide), IMI (2-iminobiotin), SHM (homobiotin), SNR (norbiotin), etc.

  2. Exact match (without stereochemistry)

    C1C2C(C(S1)CCCCC(=O)O)NC(=O)N2 - SMILES string for biotin

    This query returns structures containing BTN (biotin) and its stereoisomer BTQ (epi-biotin).

  3. Exact match (with complete stereochemistry specified in SMILES string)

    C1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(= O)N2 - isomeric SMILES string for BTN (biotin)

    This query only returns structures containing a single stereoisomer: BTN (biotin).

    C1[C@H]2[C@@H]([C@H](S1)CCCCC(=O)O)NC(=O )N2 - isomeric SMILES string for BTQ (epi-biotin)

    This query only returns structures containing a single stereoisomer: BTQ (epi-biotin)

  4. Substructure match

    C1C2C(C(S1)CCCCC(=O)O)NC(=O)N2

    This query returns structures that contain ligands with a biotin substructure, i.e. biotin-d-sulfoxide and biotinyl-5-amp.

    C1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(= O)N2 - isomeric SMILES string for biotin

    This query returns structures that contain ligands with a biotin substructure which have the same stereochemistry within the substructure. For example the stereoisomer epi-biotin is not found by this query.