From owner-chemistry@ccl.net Mon Jan 16 05:09:00 2012
From: "Jose R. Valverde jrvalverde^cnb.csic.es" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: 8-oxo-GTP
Message-Id: <-46153-120116050346-6887-vw/gNbuF+bUOGeik9S1bsw+*+server.ccl.net>
X-Original-From: "Jose R. Valverde" <jrvalverde:+:cnb.csic.es>
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Date: Mon, 16 Jan 2012 11:03:37 +0100
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Sent to CCL by: "Jose R. Valverde" [jrvalverde+/-cnb.csic.es]
Hi all,

	I am interested in the structure of 8-oxo-GTP to run some calculations,
but I am having a hard time deciding which is its structure. A cursory look in
Google reveals several different structures all under the same name, viz:

PDBeChem
	http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/8GT

ChEBI
	http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1wuq&template=ligands.html&l=1.1
(this one seems to lack the H, but might be valid with appropriate double
bonds)

Jena Bioscience
	http://www.jenabioscience.com/images/2d0798249a/NU-1116.pdf
(this one puts the H on the O)

Chemical Book
	http://www.chemicalbook.com/ProductChemicalPropertiesCB6780463_EN.htm
This adds the H on a different N

PubChem
	http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=167974
This puts two H on different places as well


The problem is you can find references using any of them and calling it the
same, so any of them might be valid, but depending on where H are, the H-bonding
network on union to an enzyme would change. So, which is/should be it? Does it
make any difference? Any suggestion?

Of course I understand that for X-ray structure determination of complexes it
makes no difference as H are normally not detected nor reported, but in order
to understand the interaction mechanisms the choice might have an impact.

	Thanks.
					j
-- 
			EMBnet/CNB
		Scientific Computing Service
	Solving all your computer needs for Scientific
			Research.

		http://bioportal.cnb.csic.es
		  http://www.es.embnet.org


From owner-chemistry@ccl.net Mon Jan 16 06:08:00 2012
From: "Edward Holland hollandej]_[Cardiff.ac.uk" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: 8-oxo-GTP
Message-Id: <-46154-120116055601-29365-CtUua5fsnQ+ygFhnBWkBAg ~ server.ccl.net>
X-Original-From: Edward Holland <hollandej++Cardiff.ac.uk>
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Date: Mon, 16 Jan 2012 10:55:39 +0000
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Sent to CCL by: Edward Holland [hollandej%a%Cardiff.ac.uk]
Hi Jose,

The protonation state of molecules can depend on the pH of the environment they are in. You should be able to work out what you require from pKa data.

Yours

Ed Holland
 
On 16 Jan 2012, at 10:03, Jose R. Valverde jrvalverde^cnb.csic.es wrote:

> 
> Sent to CCL by: "Jose R. Valverde" [jrvalverde+/-cnb.csic.es]
> Hi all,
> 
> 	I am interested in the structure of 8-oxo-GTP to run some calculations,
> but I am having a hard time deciding which is its structure. A cursory look in
> Google reveals several different structures all under the same name, viz:
> 
> PDBeChem
> 	http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/8GT
> 
> ChEBI
> 	http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1wuq&template=ligands.html&l=1.1
> (this one seems to lack the H, but might be valid with appropriate double
> bonds)
> 
> Jena Bioscience
> 	http://www.jenabioscience.com/images/2d0798249a/NU-1116.pdf
> (this one puts the H on the O)
> 
> Chemical Book
> 	http://www.chemicalbook.com/ProductChemicalPropertiesCB6780463_EN.htm
> This adds the H on a different N
> 
> PubChem
> 	http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=167974
> This puts two H on different places as well
> 
> 
> The problem is you can find references using any of them and calling it the
> same, so any of them might be valid, but depending on where H are, the H-bonding
> network on union to an enzyme would change. So, which is/should be it? Does it
> make any difference? Any suggestion?
> 
> Of course I understand that for X-ray structure determination of complexes it
> makes no difference as H are normally not detected nor reported, but in order
> to understand the interaction mechanisms the choice might have an impact.
> 
> 	Thanks.
> 					j
> -- 
> 			EMBnet/CNB
> 		Scientific Computing Service
> 	Solving all your computer needs for Scientific
> 			Research.
> 
> 		http://bioportal.cnb.csic.es
> 		  http://www.es.embnet.org> 
>