FTP site for downloading PubChem Substance, Compound, and BioAssay Data. There are over 230 million substance, 90 million compound, and 1 million BioAssay records. Data is available in SDF and XML format. Download via FTP (Services > Download Facility > Bulk Data Download.
FTP site is available for downloading ChEMBL data focused on small molecules and related bioactivity data. There are over 2 million compound records, 1 million assays, and 11,000 targets. Data is available as SDF, Oracle, and SQL.