SMILES

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

You may launch ChemAxon's Marvin for JavaScript Chemical structure editor to provide or edit a SMILES string expression

SMILES (Simplified Molecular Input Line Entry Specification) is a linear notation for describing chemical structures.

The SMILES search supports four search types:


Search type Query Result
Exact query result
Substructure query result
Superstructure query result
Similar result query

  • Exact - finds an exact structure match

  • Substructure - finds ligands that contain the specified structure as a substructure

  • Superstructure - finds ligands that are substructures (fragments) of the specified structure

  • Similar - finds structures that bind similar ligands. Specify a similarity threshold to change the degree of similarity in the [0...1] range: 0 - dissimilar ... 1 identical.
    The similarity is based on the number of chemical features in common between the query and the target molecule.
    Similarity is calculated using the Tanimoto Coefficient.


Polymeric type option

The polymeric type option can be used to specify the context where the chemical component is used:

  • Free: in entries where it is not part of a polymeric chain of a protein or nucleic acid

  • Polymeric: in entries where it is part of a chain.

  • Any: in any of the cases listed above


SMILES Examples

  1. Similarity with similarity threshold of 0.8

    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.

  5. Substructure match where polymeric type is Polymeric (modified residues or proteins or nucleic acid)

    c1ccccc1

    This query returns structures that contain a benzene ring in a non-standard modified residue of their polymer chains