Re: [ccp4bb] elbow and compound library

- Protein crystallography

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

Previous message:
Subject: shape complementarity calculations
From: "Oganesyan, Vaheh" OganesyanV {- at -} MEDIMMUNE {- dot -} COM
Date: 2009-03-03

Next message:
Subject: Re: shape complementarity calculations
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2009-03-03

Subject: Re: elbow and compound library
From: Judith Murray-Rust judith {- dot -} murray-rust {- at -} CANCER {- dot -} ORG {- dot -} UK
Date: 2009-03-03

But beware of chiral centres. You need the isomeric SMILES - otherwise you may take your chances on what is generated. If in doubt see wikipedia for ref to staurosporine structure determination.
HTH
J
-------------------
Judith Murray-Rust
Structural Biology Lab
Cancer Research UK

-----Original Message-----
From: CCP4 bulletin board on behalf of William G. Scott
Sent: Tue 03-Mar-09 9:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] elbow and compound library

Hi Eric:

You could try generating a SMILES string for your compound using this: http://www.molinspiration.com/cgi-bin/properties

(or search to see if one is available) and feed that into elbow, eg:

elbow.builder --
smiles
=
"CC12C
(C(CC(O1)N3C4=CC=CC=C4C5=C6C(=C7C8=CC=CC=C8N2C7=C53)C(NC6=O)O)NC)OC"

I got the smiles string here:
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=14717161

Here is the resulting cif file generated by the above command:

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CCP4bb navigation

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

Previous message:
Subject: shape complementarity calculations
From: "Oganesyan, Vaheh" OganesyanV {- at -} MEDIMMUNE {- dot -} COM
Date: 2009-03-03

Next message:
Subject: Re: shape complementarity calculations
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2009-03-03