NAD+NAD+| Accession Number : KLM0000284 | 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 :
% 'NAD+'
config('NAD+',[
substituent('nicotinamide-1-yl'),
substituent('D-1-dehydroxy-5-oxy-ribofuranosyl'),
substituent('ADP-yl'),
linkage(from('ADP-yl',pho(2)),
to('D-1-dehydroxy-5-oxy-ribofuranosyl',attach_to([oxy,car(5)])),
nil,single),
linkage(from('D-1-dehydroxy-5-oxy-ribofuranosyl',car(1)),
to('nicotinamide-1-yl',nitp(1)),
up,single)]).
config('ADP-yl',[
substituent('D-1-dehydroxy-5-oxy-ribofuranosyl'),
substituent(diphosphopentaoxygen),
substituent(adenyl),
linkage(from('D-1-dehydroxy-5-oxy-ribofuranosyl',car(1)),
to(adenyl,nit(9)),
up,single),
linkage(from('D-1-dehydroxy-5-oxy-ribofuranosyl',attach_to([oxy,car(5)])),
to(diphosphopentaoxygen,attach_to([pho(1)])),
nil,single)]).
config('ADP-yl',[
substituent('D-1-dehydroxy-5-oxy-ribofuranosyl'),
substituent(diphosphopentaoxygen),
substituent(adenyl),
linkage(from('D-1-dehydroxy-5-oxy-ribofuranosyl',car(1)),
to(adenyl,nit(9)),
up,single),
linkage(from('D-1-dehydroxy-5-oxy-ribofuranosyl',attach_to([oxy,car(5)])),
to(diphosphopentaoxygen,attach_to([pho(1)])),
nil,single)]).
config('D-1-dehydroxy-5-oxy-ribofuranosyl',[
ring([
oxy,
anomeric(1,hyd),
car(2,hyd&&hydroxyl),
car(3,hyd&&hydroxyl),
car(4,oxymethyl&&hyd)])]).
config(adenyl,[
model(adenine,[
diff(nit(9,hyd),nit(9))])]).
config(adenyl,[
model(adenine,[
diff(nit(9,hyd),nit(9))])]).
config(adenine,[
model(purine,[
diff(car(6,hyd),car(6,amine(10)))])]).
config(adenine,[
model(purine,[
diff(car(6,hyd),car(6,amine(10)))])]).
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(adenine,[
model(purine,[
diff(car(6,hyd),car(6,amine(10)))])]).
config(adenine,[
model(purine,[
diff(car(6,hyd),car(6,amine(10)))])]).
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-5-oxy-ribofuranosyl',[
ring([
oxy,
anomeric(1,hyd),
car(2,hyd&&hydroxyl),
car(3,hyd&&hydroxyl),
car(4,oxymethyl&&hyd)])]).
config(adenyl,[
model(adenine,[
diff(nit(9,hyd),nit(9))])]).
config(adenyl,[
model(adenine,[
diff(nit(9,hyd),nit(9))])]).
config(adenine,[
model(purine,[
diff(car(6,hyd),car(6,amine(10)))])]).
config(adenine,[
model(purine,[
diff(car(6,hyd),car(6,amine(10)))])]).
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(adenine,[
model(purine,[
diff(car(6,hyd),car(6,amine(10)))])]).
config(adenine,[
model(purine,[
diff(car(6,hyd),car(6,amine(10)))])]).
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-5-oxy-ribofuranosyl',[
ring([
oxy,
anomeric(1,hyd),
car(2,hyd&&hydroxyl),
car(3,hyd&&hydroxyl),
car(4,oxymethyl&&hyd)])]).
config('nicotinamide-1-yl',[
ring([
nitp(1)&,
car(2,hyd)&,
car(3,carboxamide(7))&,
car(4,hyd)&,
car(5,hyd)&,
car(6,hyd)&])]).
Smiles String :
[C@2H]-1([O][C@2H]([C@2H]([OH])[C@2H]-1[OH])[C@2H2][O][P@2]([O][P@2](=[O])([O][_ C@2H2][C@1H]1([C@2H]([OH])[C@2H]([OH])[C@2H]([O]1)-[n+]1([cH][c]([cH][cH][cH]1)_ [C]([O-])=[NH2])))[O-])([O-])=[O])-[n]1([cH][n][c]2([c]1[n][cH][n][c]2[NH2])) 'NAD+'
Terminal :
% 'NAD+'
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))-[h(11,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))-[n(10,nil)~,n(1,flat)&,c(9,flat)&],
c(12,12,(0,nonchiral))-[h(12,nil)~,n(7,flat)&,n(9,flat)&],
c(13,12,(0,chiral))-[c(14,left)~,o(10,right)~,n(11,up)~,h(13,down)~],
c(14,12,(0,chiral))-[c(15,left)~,c(13,right)~,h(14,up)~,o(11,down)~],
c(15,12,(0,chiral))-[c(16,left)~,c(14,right)~,h(16,up)~,o(12,down)~],
c(16,12,(0,chiral))-[o(10,left)~,c(15,right)~,c(17,up)~,h(18,down)~],
c(17,12,(0,nonchiral))-[o(13,left)~,h(19,right)~,h(20,up)~,c(16,down)~],
c(18,12,(0,nonchiral))-[h(21,nil)~,n(11,flat)&,c(19,flat)&],
c(19,12,(0,nonchiral))-[c(23,nil)~,c(18,flat)&,c(20,flat)&],
c(20,12,(0,nonchiral))-[h(24,nil)~,c(19,flat)&,c(21,flat)&],
c(21,12,(0,nonchiral))-[h(25,nil)~,c(20,flat)&,c(22,flat)&],
c(22,12,(0,nonchiral))-[h(26,nil)~,c(21,flat)&,n(11,flat)&],
c(23,12,(0,nonchiral))-[o(14,nil)?,n(12,nil)#,c(19,nil)~],
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))-[n(10,nil)~],
h(10,1,(0,nonchiral))-[n(10,nil)~],
h(11,1,(0,nonchiral))-[c(6,nil)~],
h(12,1,(0,nonchiral))-[c(12,nil)~],
h(13,1,(0,nonchiral))-[c(13,up)~],
h(14,1,(0,nonchiral))-[c(14,down)~],
h(15,1,(0,nonchiral))-[o(11,nil)~],
h(16,1,(0,nonchiral))-[c(15,down)~],
h(17,1,(0,nonchiral))-[o(12,nil)~],
h(18,1,(0,nonchiral))-[c(16,up)~],
h(19,1,(0,nonchiral))-[c(17,left)~],
h(20,1,(0,nonchiral))-[c(17,down)~],
h(21,1,(0,nonchiral))-[c(18,nil)~],
h(22,1,(0,nonchiral))-[n(12,nil)~],
h(23,1,(0,nonchiral))-[n(12,nil)~],
h(24,1,(0,nonchiral))-[c(20,nil)~],
h(25,1,(0,nonchiral))-[c(21,nil)~],
h(26,1,(0,nonchiral))-[c(22,nil)~],
n(1,14,(0,nonchiral))-[c(6,flat)&,c(10,flat)&],
n(3,14,(0,nonchiral))-[c(6,flat)&,c(8,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)&],
n(10,14,(0,nonchiral))-[h(9,nil)~,h(10,nil)~,c(10,nil)~],
n(11,14,(1,nonchiral))-[c(13,down)~,c(18,flat)&,c(22,flat)&],
n(12,14,(0,nonchiral))-[h(22,nil)~,h(23,nil)~,c(23,nil)#],
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))-[p(1,right)~,c(5,down)~],
o(5,16,(0,nonchiral))-[p(1,left)~,p(2,right)~],
o(6,16,(-5.0E-01,nonchiral))-[p(1,up)?],
o(7,16,(-5.0E-01,nonchiral))-[p(1,down)?],
o(8,16,(-5.0E-01,nonchiral))-[p(2,left)?],
o(9,16,(-5.0E-01,nonchiral))-[p(2,down)?],
o(10,16,(0,nonchiral))-[c(13,left)~,c(16,right)~],
o(11,16,(0,nonchiral))-[h(15,nil)~,c(14,up)~],
o(12,16,(0,nonchiral))-[h(17,nil)~,c(15,up)~],
o(13,16,(0,nonchiral))-[c(17,right)~,p(2,up)~],
o(14,16,(0,nonchiral))-[c(23,nil)?],
p(1,31,(0,nonchiral))-[o(4,left)~,o(5,right)~,o(7,up)?,o(6,down)?],
p(2,31,(0,nonchiral))-[o(5,left)~,o(8,right)?,o(9,up)?,o(13,down)~]
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 NAD+. 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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