Re: [ccp4bb] few organophophates coordiantes

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

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Subject: few organophophates coordiantes
From: U Sam us_x {- at -} HOTMAIL {- dot -} COM
Date: 2007-09-05

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From: Joel Guenther guenthej {- at -} GMAIL {- dot -} COM
Date: 2007-09-05

Subject: Re: few organophophates coordiantes
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-09-05

Hi Sam:

You can define a SMILES string, put that in coot, and it will create coordinates.

Similarly, within phenix, you can do this with elbow.builder and then optimize is either with built-in forcefields or with an external QM program. It will give you a reasonable (usually) cif file that you can then use for refinements in phenix or refmac.

Do you actually keep ligands of mass destruction on hand in the lab? Cool.

Bill

On Wed, 5 Sep 2007 19:21:45 +0000
U Sam wrote:

Hi,
Thanks for the reply to my earlier query.

I am looking for the coordinates of few organophosphates which can bond covalently to protein as follows .

1) Para-oxon: O,O-Diethyl-O-para-nitrophenyl phosphate
2) Sarin: 2-(fluoro-methyl-phosphoryl)oxypropane
3) Soman: 3-(fluoro-methyl-phosphoryl)oxy-2,2-dimethyl-butane
4) Tabun: Ethyl N,N-dimethylphosphoramidocyanidate
5) DFP: 2-(fluoro-(1-methylethoxy)phosphoryl)oxypropane
6) VX: O-ethyl-S-[2(diisopropylamino)ethyl] methylphosphonothiolate

I would like to know if anybody know the correct "hiccup' site. I searched a similar site though google, but I did not find any good hit.

JL Susman and Charles Millard groups did some studies with few of these organophosphates, but I donot see any complete structure of the organophosphates in their submitted PDBs.

Appreciate suggestion/notes.
Sam
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CCP4bb navigation

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

Previous message:
Subject: few organophophates coordiantes
From: U Sam us_x {- at -} HOTMAIL {- dot -} COM
Date: 2007-09-05

Next message:
Subject: Re: MS for verification of protein constructs
From: Joel Guenther guenthej {- at -} GMAIL {- dot -} COM
Date: 2007-09-05