I am trying to collect an extensive list of databases capturing chemical compound interactions with other biological structures. I already have KEGG, HMDB, and WikiPathways
Which resources would you consider to be essential in the context of integrating biological knowledge?
The databases that you have listed seem to be focused on metabolites. One obvious database that you should probably include is MetaCyc. If you are also interested in the small-molecule drugs, there is a long list of other databases to include:
I probably forgot some more databases that others will point out :-)
Here are some that Lars missed (great list though!)
I would like to add two important resources: