Hey all,
I've been doing a fair bit on reaction depictions recently. It's tended to
focus on organic chemistry but was wondering how much interest there would
be in specialised metabolic reaction depictions.
We do much better with the introduction of abbreviations:
SMILES:
C(C)(C)[C@@H]([C@H](C(=O)[O-])O)C(=O)[O-].C1=CC(=C[N+](=C1)[C@H]2[C@@H]([C@
> @H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@
> @H](O3)N4C=NC5=C4N=CN=C5N)O)O)O)O)C(=O)N>>CC(CC(C(=O)[O-])=O)C.C=1N=C(C2=C(N1)N(C=N2)[C@H
> ]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N.C(=O)=O
> |SgD::cdk:ReactionConditions:1.1.1.85|
CDK Depict
<http://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=C(C)(C)[C@@H]([C@H](C(=O)[O-])O)C(=O)[O-].C1=CC(=C[N%2B](=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=NC5=C4N=CN=C5N)O)O)O)O)C(=O)N%3E%3ECC(CC(C(=O)[O-])=O)C.C=1N=C(C2=C(N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N.C(=O)=O%20%7CSgD%3A%3Acdk%26%2358%3BReactionConditions%3A1.1.1.85%7C&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=none>
[image: Inline images 1]
Excluding the group abbreviations:
[image: Inline images 3]
But putting the NAD+,NADH,CO2 as side components with an arc may be more
intuitive to some.
See here: http://www.genome.jp/dbget-bin/www_bget?rn:R10052
[image: Inline images 2]
I did show this to a colleague with a background in Chemistry this morning
though and he said he couldn't tell what was going on here.
It's a moderate amount of work and I'm kind of under the impression the
current depiction is pretty good at conveying what's going on. If there is
significant demand for it though it could be something to add.
Thoughts?
John
P.S. we can display a reversible arrow and individual molecule titles (in
the reaction) but no way to put that in SMILES.
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