Searches for a chemical component (ligand) using a SMILES
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:
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.
is calculated using the Tanimoto Coefficient.
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
Similarity with similarity threshold of 0.8
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.
Exact match (without stereochemistry)
This query returns structures containing BTN (biotin) and its stereoisomer BTQ (epi-biotin).
Exact match (with complete stereochemistry specified in SMILES string)
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 -
This query only returns structures containing a single stereoisomer: BTQ (epi-biotin)
This query returns structures that contain ligands with a biotin substructure, i.e. biotin-d-sulfoxide and biotinyl-5-amp.
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.
Substructure match where polymeric type is Polymeric (modified residues or proteins or nucleic acid)
This query returns structures that contain a benzene ring in a non-standard modified residue of their polymer chains
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.