Did you had an inhibitor present in your purification ? Complete tablets ?
Can you derive from the chemical environment perhaps if some of the atoms are nitrogens or oxygens ? Then you could sketch your putative molecule and search in the NCI database for homologous structures to your sketch.
Here's the link: http://dtp.nci.nih.gov Juergen Ronaldo Alves Pinto Nagem wrote:
Dear crystallographers, I hope someone could give me a hint to solve this problem. I have collected five datasets from the same protein and all of them, including the highest resolution data set (1.6 angstrons), display at the active site of the enzyme a very clear electron density with boundaries well defined. The problem is that I have already tried to fit all kinds of molecules present in the purification and crystallization conditions and none of them fit well into the density. Here are my questions: Is there any program available that could take a small volume of the electron density map (obviously the unidentified electron density ligand) and try to fit a list of known compounds (a list that I do not have, by the way) for potential ligands? Or, is there any website or program that could give me a list of compounds based only in the backbone of the ligand I could sketch from the density (by backbone I mean the plane shape of the compound – I do not know its atom composition)? I hope someone could help. Thanks Ronaldo.
-- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
