Crystallography Open Database
The Crystallography Open Database gathers crystal structures, the atomic-level arrangements that describe how a solid is built, for hundreds of thousands of compounds. Coverage spans organic, inorganic, and metal-organic materials.
Every record is released under CC0, which places it in the public domain, so you can use the whole database in commercial products with no attribution requirement and no licence conditions to track.
Related sources
Bio2RDF
An open-source project that pulls together a diverse set of life-sciences datasets from many providers into a single linked-data graph, with a SPARQL endpoint for querying across them. The full collection is about 11 billion triples across 35 datasets, including DrugBank, PubMed, and MeSH.
ChEBI
A dictionary of small chemical compound molecular entities, with structure files and ontology files available for download. Particularly useful as a controlled vocabulary for chemical entity linking, where you match a mention in text to a standard identifier.
ChEMBL
A manually curated database of bioactive molecules with drug-like properties, bringing together chemical, bioactivity, and genomic data to support drug discovery. Holds close to 2.5M compound records on nearly 2M unique chemical structures, extracted mainly from the medicinal chemistry literature.
Materials Project
A database of computed properties for known and predicted materials, produced through high-throughput density functional theory calculations (a physics method for modelling how electrons behave in a material). Free API access with registration.