Re: [ccp4bb] Unidentified ligand (electron density) found at active site

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Unidentified ligand (electron density) found at active site
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2007-11-30

Next message:
Subject: Re: Unidentified ligand (electron density) found at active site
From: gerrit {- at -} EMBL-HAMBURG {- dot -} DE gerrit {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-11-30

Subject: Re: Unidentified ligand (electron density) found at active site
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-11-30

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 â€“ I do not know its atom
>composition)?
>
>I hope someone could help.
>
>Thanks
>
>Ronaldo.
>
>
>

--
JÃ¼rgen 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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Unidentified ligand (electron density) found at active site
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2007-11-30

Next message:
Subject: Re: Unidentified ligand (electron density) found at active site
From: gerrit {- at -} EMBL-HAMBURG {- dot -} DE gerrit {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-11-30