I'm reasonably sure BLAST and FASTA are for looking up protein and nucleic acid sequences, not drug compounds. The Smith-Waterman process is an algorithm used for genetic similarity searches. PDB is a protein database.
ChEMBL is a database that you can use to look up drugs based on their target, or chemical structure. I haven't used ChemSpider or Drug Bank, though I believe the latter serves a similar function to ChEMBL.
Most of these also have Wikipedia pages, which you should probably look up for more information about them.