Dear CCP4bb users,
I attached a sketch of my ligand. I realized it could be a di-peptide
GlySer, but still, other potential ligands are possible and I have not a
clue. The crystallization condition contains MIB buffer (sodium malonate,
imidazole and boric acid) and PEG. As far as I know none inhibitor were
present during purification. One important point about the ligand is that
I believe the position occupied by the serine carboxylic group (in the
di-peptide scheme) is indeed a charged group. Apart of that all positions
and configurations might be possible (only using C, N, O and H – I did not
see the presence of sulfur nor heavy atoms).
Thanks again for all tips and suggestions and we will probably try
mass-spectroscopy.
Here is the summary (so far) for my previous question.
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)?
1) from [log in to unmask]
Send a picture to the BB and someone might recognize it.
2) from [log in to unmask]
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...
---------------------------------------------------------
Prof. Dr. Ronaldo Alves Pinto Nagem
Universidade Federal de Minas Gerais
Instituto de Ciências Biológicas
Departamento de Bioquímica e Imunologia
Av. Antônio Carlos, 6627 - Caixa Postal 486
Bairro Pampulha - CEP: 31270-901
Belo Horizonte, MG - Brasil
Tel: +55 31 3499-2626
Fax: +55 31 3499-2614
E-mail: [log in to unmask]
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