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

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

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Subject: coot-bones not showing
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-11-30

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

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

If you send a picture of this stuff to the list, I bet someone may recognize
it :)

I think it's called 'distributed computing'.

On a more serious note, a pharmacophore matching routine would do what you
need, but you'd have to convert from E.D. to a 'blank' pharmacophore with
all property parameters set exactly to 1. Unfortunately, I don't know of any
non-commercial programs for that stuff...

Artem

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Ronaldo Alves Pinto Nagem
Sent: Friday, November 30, 2007 7:47 PM
To: CCP4BB@JISCMAIL.AC.UK
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.

CCP4bb navigation

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

Previous message:
Subject: coot-bones not showing
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-11-30

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