Sphingomyelin

290px-sphingomyelin-core-structure-colored.svg.png

Sphingomyelin is a type of fat molecule that is found in the membranes of animal cells. It is especially important for the formation and maintenance of the myelin sheath, which insulates nerve cells and helps them to send signals quickly. Sphingomyelin is also involved in other cellular processes, such as cell signaling, membrane trafficking, and apoptosis (programmed cell death).

Deficiency in sphingomyelin can lead to a number of health problems, including multiple sclerosis, Niemann-Pick disease, and Krabbe disease.

Sphingomyelin is a fat molecule that is important for nerve cells and other cells in the body. It helps to protect nerve cells and send signals quickly. Too little sphingomyelin can cause health problems.


This work is released into the public domain; please see our release statement.
Doug Markham has contributed a molecular mechanics computation of the structure! See below for the details.

Config Rule :

 

% sphingomyelin


config(sphingomyelin,[
        substituent('sphingosine-N-yl-O-yl'),
        substituent(stearyl),
        substituent('choline-phosphoryl'),
        linkage(from('sphingosine-N-yl-O-yl',attach_to([oxy(2),car(1)])),
                to('choline-phosphoryl',pho(1)),
                nil,single),
        linkage(from('sphingosine-N-yl-O-yl',nit(1)),
                to(stearyl,car(1)),
                nil,single)]).

config('choline-phosphoryl',[
        substituent(cholyl),
        substituent(oxy),
        substituent(phosphodiyl),
        linkage(from(phosphodiyl,pho(1)),
                to(oxy,oxy),
                nil,single),
        linkage(from(oxy,oxy),
                to(cholyl,car(1)),
                nil,single)]).

config(cholyl,[
        chain([
                car(1,hyd&&hyd;),
                methandiyl,
                nit(1,methyl&&methyl;&&methyl;)])]).

config(cholyl,[
        chain([
                car(1,hyd&&hyd;),
                methandiyl,
                nit(1,methyl&&methyl;&&methyl;)])]).

config('sphingosine-N-yl-O-yl',[
        chain([
                car(1,hyd&&hyd;&& (oxy~)),
                car(2,hyd&& (nit(1,hyd)~)),
                car(3,hyd&&hydroxyl;),
                car(4,hyd)~~,
                car(5,hyd),
                num(methandiyl,12),
                methyl]),
        trans(car(3),car(6),bond(car(4),car(5)))]).

config(stearyl,[
        chain([
                ketyl(1),
                num(methandiyl,16),
                methyl])]).

Smiles String :

 

[C@2H2]([O][P@2](=[O])([O-])[O][C@2H2][C@2H2][N@2+]([CH3])([CH3])[CH3])[C@2H]([C@2H](/[CH]=[CH]/[C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][CH3])[OH])[NH][C]([C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][C@2H2][CH3])=[O]

 

The Terminals for all the Config Rules are in Prolog Definite Clause Grammar (DCG) form.They can be checked in the Manual here.

The compound's PDB file can be seen here.

Doug Markham of the Institute for Cancer Research, Fox Chase Cancer Center,Philadelphia, PA, has contributed the following structure for sphingomyelin. He computed this structure in sdf format using MacroModel, a molecular mechanics program. We have used Babel to convert the .sdf format to PDB format. You'll find it interesting to compare these structures to those computed using CONCORD.

Many thanks Doug!