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
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