Smiles Arbitrary Target Specification - Examples of SMARTS

Examples of SMARTS

A number of illustrative examples of SMARTS have been assembled by Daylight.

The definitions of hydrogen bond donors and acceptors used to apply Lipinski's Rule of Five . are easily coded in SMARTS. Donors are defined as nitrogen or oxygen atoms that have at least one directly bonded hydrogen atom:

or (aromatic oxygen cannot have a bonded hydrogen)

Acceptors are defined as nitrogen or oxygen:

or

A simple definition of aliphatic amines that are likely to protonate at physiological pH can be written as the following recursive SMARTS:

),$(),$)]

In real applications the CX4 atoms would need to be defined more precisely to prevent matching against electron withdrawing groups such as CF3 that would render the amine insufficiently basic to protonate at physiological pH.

SMARTS can be used to encode pharmacophore elements such as anionic centers. In the following example, recursive SMARTS notation is used to combine acid oxygen and tetrazole nitrogen in a definition of oxygen atoms that are likely to be anionic under normal physiological conditions.

=O),$(1nnnc1)]

The SMARTS above would only match the acid hydroxyl and the tetrazole NH. When a carboxylic acid deprotonates the negative charge is delocalised over both oxygen atoms and it may be desirable to designate both as anionic. This can achieved using the following SMARTS.

)C=O),$(O=C)]