This is the main site for protein pdb files"...This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data..."https://www.rcsb.org
Structures in Pdb files. "...Dictionary of chemical components (ligands, small molecules and monomers) referred to in PDB entries and maintained by wwPDB. It provides comprehensive search facilities for finding a particular component, or determining components in structure entries or vice versa...." https://www.ebi.ac.uk/pdbe-srv/pdbechem/
"...PubChem is the world's largest collection of freely accessible chemical information. Search chemicals by name, molecular formula, structure, and other identifiers. Find chemical and physical properties, biological activities, safety and toxicity information, patents, literature citations and more..." https://pubchem.ncbi.nlm.nih.gov/source/ChemBank
"...Established in 1965, the CSD is the world's repository for small-molecule organic and metal-organic crystal structures. Containing over one million structures from x-ray and neutron diffraction analyses, this unique database of accurate 3D structures has become an essential resource to scientists around the world.....Every structure is enriched with chemical representations, as well as bibliographic, chemical and physical property information, adding further value to the raw structural data..." https://www.ccdc.cam.ac.uk/solutions/csd-core/components/csd/
Small molecule drugs and Biotech Drugs... 3D files in sdf, pdb and mol types. https://go.drugbank.com/
"...This is one of the longest running chemistry webpages on the internet. Each month since January 1996 a new molecule has been added to the list on this page, which makes this one of the longest running Chemical websites on the internet! The links will take you to a page at one of the Web sites at a University Chemistry Department or commercial site in the UK, the US, or anywhere in the world, where useful (and hopefully entertaining!), information can be found about a particularly interesting molecule..." http://www.chm.bris.ac.uk/motm/motm.htm
"...LIPID MAPS® Lipidomics Gateway was created in 2003 via an NIH "Glue Grant" to provide access to lipid nomenclature, databases, tools, protocols, standards, tutorials, meetings, publications, and other resources and serving the international lipid research community. .."https://www.lipidmaps.org/data/structure/