I'd like to be able to find the crystal structures of drugs, for example at the moment I want to find the crystal structure of (R)-fluoxetine so that I can use Jmol to create an accurate 3D model of it. This is so I can then upload it to Wikimedia Commons so it may be used alongside Benjah-bmm27's structure of (S)-fluoxetine on the Wikipedia page for fluoxetine. I have tried this database [1] but when I searched for the SMILES of (R)-fluoxetine, CNCCC@HOC2=CC=C(C=C2)C(F)(F)F (from ChemSpider [2]), I obtained no search results.


I think my first question is why you need the crystal structure?

For organic molecules, the definitive resource is the proprietary (and fairly expensive) Cambridge Structure Database.

The Crystallographic Open Database which you linked is fairly new and expanding, but does not have the many, many molecular crystals in the CSD. For example, American Chemical Society journals required submission to the CSD for publication.

My suggestion would be to start with the NIH Chemical Resolver or PubChem. The latter has a 3D computed structure of (R)-fluoxetine, which I'm sure is pretty decent. Jmol should be able to load these directly, or you could save SDF files and open them in Jmol.

I'll point out that Avogadro can also do these tasks, but since I'm the creator, I'm biased.

  • 1
    $\begingroup$ Avogadro with UFF performs fine for simple cases. Some special cases, including atoms with unusual coordination and/or delocalized structure do not work, one need QC software and good initial guess to get adequate structure in the case. $\endgroup$ – permeakra Oct 25 '14 at 7:24

Consider http://www.rcsb.org/pdb/home/home.do , that contains structures for proteing-drug complexes and http://www.drugbank.ca/ . Also, don't drop plain google searches


Are there any crystal structures of the free base?

The structure of the hydrochloride was published by D. W. Robertson and co-workers in J. Med. Chem., 1988, 31, 185–189 (DOI).

The structure of 1:1 co-crystals of the hydrochloride with different acids was published by S. L. Childs and co-workers in J. Am. Chem. Soc., 2004, 126, 13335–13342 (DOI).

The CIF of the 1:1 co-crystal of the hydrochloride with benzoic acid is freely available.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.