I learned from an earlier CCP4BB post of a routine in Phenix that
searches a database of small molecules from (I think) 200 protein-small
molecule complex structures. Some of the small molecules seemed
redundant; however, they may be in different conformations in the
different structures that are used.
From the Phenix GUI, click on the "Strategies" menu, and then go to the
ligand sub-menu, and choose "ligand identification".
Gregg
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Gregg Crichlow
Department of Pharmacology
Yale University
Box 208066
New Haven, CT 06520-8066
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-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Ronaldo Alves Pinto Nagem
Sent: Friday, November 30, 2007 7:47 PM
To: [email protected]
Subject: [ccp4bb] Unidentified ligand (electron density) found at active
site
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.
