Re: [ccp4bb] How to number atoms in a ligand

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CCP4bb <-- 2007 <-- October 2007 <-- 08 October 2007

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Subject: Re: How to number atoms in a ligand
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2007-10-08

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From: James Stroud jstroud {- at -} MBI {- dot -} UCLA {- dot -} EDU
Date: 2007-10-08

Subject: Re: How to number atoms in a ligand
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2007-10-08

If you want to be 'by the book' on it, you should follow IUPAC rules for
atomic numbering of chemical compounds. Unless you're an organic chemist,
these rules are pretty hard to follow, so most people number at will.

If you're dealing with a 'known' series of compounds, such as analogous
inhibitors developed in the course of a research project (say, in pharma
industry) then typically you will see people refer to specific locations by
number, and try to keep numbering consistent.

Artem

_____

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zheng
Zhou
Sent: Monday, October 08, 2007 9:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to number atoms in a ligand

Hi, all

I am a rookie in crystallography. I know this may be a little bit off topic.
I have cocrystallized several compounds with my favorite protein. I found
crystal structures for some of these chemicals. But the numbering systems
are different in those original papers for the small molecules. Some
numbering system has all the atoms from 1 to the end (C1-O3-O8-N9-C15),
while others have numbers for each individual element. (C1-C12, O1-O2, N1).
I was trying to search a unified theme for ligands in pdb. I even emailed
deposit@deposit.rcsb.org, but so far I haven't heard anything back. Could
anyone give me some suggestions? Any help would be greatly appreciated.

Thanks,

Sorry to bother others

Joe

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CCP4bb <-- 2007 <-- October 2007 <-- 08 October 2007

Previous message:
Subject: Re: How to number atoms in a ligand
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2007-10-08

Next message:
Subject: PDB Crazy or Me?
From: James Stroud jstroud {- at -} MBI {- dot -} UCLA {- dot -} EDU
Date: 2007-10-08