xanthosinexanthosine| Accession Number : KLM0000408 | 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 :
% xanthosine
config(xanthosine,[
substituent(xanthinyl),
substituent('D-1-dehydroxy-ribofuranosyl'),
linkage(from('D-1-dehydroxy-ribofuranosyl',car(1)),
to(xanthinyl,nit(9)),
up,single)]).
config(xanthosine,[
substituent(xanthinyl),
substituent('D-1-dehydroxy-ribofuranosyl'),
linkage(from('D-1-dehydroxy-ribofuranosyl',car(1)),
to(xanthinyl,nit(9)),
up,single)]).
config('D-1-dehydroxy-ribofuranosyl',[
ring([
oxy,
anomeric(1,hyd),
car(2,hyd&&hydroxyl),
car(3,hyd&&hydroxyl),
car(4,hydroxymethyl&&hyd)])]).
config(xanthinyl,[
model(xanthine,[
diff(nit(9,hyd),nit(9))])]).
config(xanthinyl,[
model(xanthine,[
diff(nit(9,hyd),nit(9))])]).
config(xanthine,[
model(purine,[
diff(nit(1),nit(1,hyd)),
diff(car(2,hyd),car(2,oxy?)),
diff(nit(3),nit(3,hyd)),
diff(car(6,hyd),car(6,oxy?))])]).
config(xanthine,[
model(purine,[
diff(nit(1),nit(1,hyd)),
diff(car(2,hyd),car(2,oxy?)),
diff(nit(3),nit(3,hyd)),
diff(car(6,hyd),car(6,oxy?))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(xanthine,[
model(purine,[
diff(nit(1),nit(1,hyd)),
diff(car(2,hyd),car(2,oxy?)),
diff(nit(3),nit(3,hyd)),
diff(car(6,hyd),car(6,oxy?))])]).
config(xanthine,[
model(purine,[
diff(nit(1),nit(1,hyd)),
diff(car(2,hyd),car(2,oxy?)),
diff(nit(3),nit(3,hyd)),
diff(car(6,hyd),car(6,oxy?))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config('D-1-dehydroxy-ribofuranosyl',[
ring([
oxy,
anomeric(1,hyd),
car(2,hyd&&hydroxyl),
car(3,hyd&&hydroxyl),
car(4,hydroxymethyl&&hyd)])]).
config(xanthinyl,[
model(xanthine,[
diff(nit(9,hyd),nit(9))])]).
config(xanthinyl,[
model(xanthine,[
diff(nit(9,hyd),nit(9))])]).
config(xanthine,[
model(purine,[
diff(nit(1),nit(1,hyd)),
diff(car(2,hyd),car(2,oxy?)),
diff(nit(3),nit(3,hyd)),
diff(car(6,hyd),car(6,oxy?))])]).
config(xanthine,[
model(purine,[
diff(nit(1),nit(1,hyd)),
diff(car(2,hyd),car(2,oxy?)),
diff(nit(3),nit(3,hyd)),
diff(car(6,hyd),car(6,oxy?))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(xanthine,[
model(purine,[
diff(nit(1),nit(1,hyd)),
diff(car(2,hyd),car(2,oxy?)),
diff(nit(3),nit(3,hyd)),
diff(car(6,hyd),car(6,oxy?))])]).
config(xanthine,[
model(purine,[
diff(nit(1),nit(1,hyd)),
diff(car(2,hyd),car(2,oxy?)),
diff(nit(3),nit(3,hyd)),
diff(car(6,hyd),car(6,oxy?))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
config(purine,[
ring_system([
ring([
car(6,hyd)&,
car(5)&,
car(4)&,
nit(3)&,
car(2,hyd)&,
nit(1)&]),
ring([
nit(7)&,
car(8,hyd)&,
nit(9,hyd)&,
car(4)&,
car(5)&])],
conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).
Smiles String :
[C@2H]-1([O][C@2H]([C@2H]([OH])[C@2H]-1[OH])[C@2H2][OH])-[n]1([cH][n][c]2([c]1[_ nH][c]([nH][c]2[O-])[O-])) xanthosine
Terminal :
% xanthosine
c(1,12,(0,chiral))-[c(2,left)~,o(1,right)~,n(9,up)~,h(1,down)~],
c(2,12,(0,chiral))-[c(3,left)~,c(1,right)~,h(2,up)~,o(2,down)~],
c(3,12,(0,chiral))-[c(4,left)~,c(2,right)~,h(4,up)~,o(3,down)~],
c(4,12,(0,chiral))-[o(1,left)~,c(3,right)~,c(5,up)~,h(6,down)~],
c(5,12,(0,nonchiral))-[h(7,left)~,h(8,right)~,o(4,up)~,c(4,down)~],
c(6,12,(0,nonchiral))-[o(6,nil)?,n(3,flat)&,n(1,flat)&],
c(8,12,(0,nonchiral))-[n(3,flat)&,c(9,flat)&,n(9,flat)&],
c(9,12,(0,nonchiral))-[c(8,flat)&,c(10,flat)&,n(7,flat)&],
c(10,12,(0,nonchiral))-[o(5,nil)?,n(1,flat)&,c(9,flat)&],
c(12,12,(0,nonchiral))-[h(12,nil)~,n(7,flat)&,n(9,flat)&],
h(1,1,(0,nonchiral))-[c(1,up)~],
h(2,1,(0,nonchiral))-[c(2,down)~],
h(3,1,(0,nonchiral))-[o(2,nil)~],
h(4,1,(0,nonchiral))-[c(3,down)~],
h(5,1,(0,nonchiral))-[o(3,nil)~],
h(6,1,(0,nonchiral))-[c(4,up)~],
h(7,1,(0,nonchiral))-[c(5,right)~],
h(8,1,(0,nonchiral))-[c(5,left)~],
h(9,1,(0,nonchiral))-[o(4,nil)~],
h(10,1,(0,nonchiral))-[n(3,nil)~],
h(11,1,(0,nonchiral))-[n(1,nil)~],
h(12,1,(0,nonchiral))-[c(12,nil)~],
n(1,14,(0,nonchiral))-[h(11,nil)~,c(6,flat)&,c(10,flat)&],
n(3,14,(0,nonchiral))-[h(10,nil)~,c(8,flat)&,c(6,flat)&],
n(7,14,(0,nonchiral))-[c(9,flat)&,c(12,flat)&],
n(9,14,(0,nonchiral))-[c(1,down)~,c(12,flat)&,c(8,flat)&],
o(1,16,(0,nonchiral))-[c(1,left)~,c(4,right)~],
o(2,16,(0,nonchiral))-[h(3,nil)~,c(2,up)~],
o(3,16,(0,nonchiral))-[h(5,nil)~,c(3,up)~],
o(4,16,(0,nonchiral))-[h(9,nil)~,c(5,down)~],
o(5,16,(0,nonchiral))-[c(10,nil)?],
o(6,16,(0,nonchiral))-[c(6,nil)?]
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 xanthosine. 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!
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