N5,N10-methenyl-5,6,7,8-tetrahydrofolateN5,N10-methenyl-5,6,7,8-tetrahydrofolate| Accession Number : KLM0000560 | 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.
Synonyms :
Config Rule :
% 'N5,N10-methenyl-5,6,7,8-tetrahydrofolate'
config('N5,N10-methenyl-5,6,7,8-tetrahydrofolate',[
substituent('N5,N10-methenyl-pteridin-N10-yl'),
substituent('1-benzoyl-4-yl'),
substituent('D-glutamate'(1,peptide,end)),
linkage(from('N5,N10-methenyl-pteridin-N10-yl',nit(10)),
to('1-benzoyl-4-yl',car(4)),
right,single),
linkage(from('1-benzoyl-4-yl',car(7)),
to('D-glutamate'(1,peptide,end),nit(1)),
trans(car(1),car(1)),cn_resonant)]).
config('N5,N10-methenyl-5,6,7,8-tetrahydrofolate',[
substituent('N5,N10-methenyl-pteridin-N10-yl'),
substituent('1-benzoyl-4-yl'),
substituent('D-glutamate'(1,peptide,end)),
linkage(from('N5,N10-methenyl-pteridin-N10-yl',nit(10)),
to('1-benzoyl-4-yl',car(4)),
right,single),
linkage(from('1-benzoyl-4-yl',car(7)),
to('D-glutamate'(1,peptide,end),nit(1)),
trans(car(1),car(1)),cn_resonant)]).
config('1-benzoyl-4-yl',[
ring([
car(1,car(7,oxy?)~)&,
car(2,hyd)&,
car(3,hyd)&,
car(4)&,
car(5,hyd)&,
car(6,hyd)&])]).
config('1-benzoyl-4-yl',[
ring([
car(1,car(7,oxy?)~)&,
car(2,hyd)&,
car(3,hyd)&,
car(4)&,
car(5,hyd)&,
car(6,hyd)&])]).
config('N5,N10-methenyl-pteridin-N10-yl',[
ring_system([
ring([
nit(1)&,
car(2,amine)&,
nit(3,hyd)&,
car(4,oxy?)&,
car(11)&,
car(12)&]),
ring([
nit(5)~,
car(6,hyd)~,
car(7,hyd&&hyd)~,
nit(8,hyd)~,
car(12)&,
car(11)~]),
ring([
(nit(5),right)~,
(car(6),up)~,
(methandiyl(9),right)~,
(nit(10),right)~,
(car(13,hyd),down)~~])],
conjugate(2,pseudopos([nit(5),car(6)]),3,pseudopos([nit(5),car(6)])),
conjugate(1,pseudopos([car(11),car(12)]),2,pseudopos([car(11),car(12)]))])]).
config('N5,N10-methenyl-pteridin-N10-yl',[
ring_system([
ring([
nit(1)&,
car(2,amine)&,
nit(3,hyd)&,
car(4,oxy?)&,
car(11)&,
car(12)&]),
ring([
nit(5)~,
car(6,hyd)~,
car(7,hyd&&hyd)~,
nit(8,hyd)~,
car(12)&,
car(11)~]),
ring([
(nit(5),right)~,
(car(6),up)~,
(methandiyl(9),right)~,
(nit(10),right)~,
(car(13,hyd),down)~~])],
conjugate(2,pseudopos([nit(5),car(6)]),3,pseudopos([nit(5),car(6)])),
conjugate(1,pseudopos([car(11),car(12)]),2,pseudopos([car(11),car(12)]))])]).
config('D-glutamate'(1,peptide,end),[
substituent(peptide_end),
substituent(ethylcarboxyl),
linkage(from(peptide_end,car(1)),
to(ethylcarboxyl,car(1)),
up,single)]).
config(ethylcarboxyl,[
top(car(1,hyd&&hyd)),
center(methandiyl),
bottom(carboxyl)]).
config(peptide_end,[
left(nit(1,hyd)),
right(hyd),
top(carboxyl),
center(car(1))]).
config('1-benzoyl-4-yl',[
ring([
car(1,car(7,oxy?)~)&,
car(2,hyd)&,
car(3,hyd)&,
car(4)&,
car(5,hyd)&,
car(6,hyd)&])]).
config('1-benzoyl-4-yl',[
ring([
car(1,car(7,oxy?)~)&,
car(2,hyd)&,
car(3,hyd)&,
car(4)&,
car(5,hyd)&,
car(6,hyd)&])]).
config('N5,N10-methenyl-pteridin-N10-yl',[
ring_system([
ring([
nit(1)&,
car(2,amine)&,
nit(3,hyd)&,
car(4,oxy?)&,
car(11)&,
car(12)&]),
ring([
nit(5)~,
car(6,hyd)~,
car(7,hyd&&hyd)~,
nit(8,hyd)~,
car(12)&,
car(11)~]),
ring([
(nit(5),right)~,
(car(6),up)~,
(methandiyl(9),right)~,
(nit(10),right)~,
(car(13,hyd),down)~~])],
conjugate(2,pseudopos([nit(5),car(6)]),3,pseudopos([nit(5),car(6)])),
conjugate(1,pseudopos([car(11),car(12)]),2,pseudopos([car(11),car(12)]))])]).
config('N5,N10-methenyl-pteridin-N10-yl',[
ring_system([
ring([
nit(1)&,
car(2,amine)&,
nit(3,hyd)&,
car(4,oxy?)&,
car(11)&,
car(12)&]),
ring([
nit(5)~,
car(6,hyd)~,
car(7,hyd&&hyd)~,
nit(8,hyd)~,
car(12)&,
car(11)~]),
ring([
(nit(5),right)~,
(car(6),up)~,
(methandiyl(9),right)~,
(nit(10),right)~,
(car(13,hyd),down)~~])],
conjugate(2,pseudopos([nit(5),car(6)]),3,pseudopos([nit(5),car(6)])),
conjugate(1,pseudopos([car(11),car(12)]),2,pseudopos([car(11),car(12)]))])]).
config('D-glutamate'(1,peptide,end),[
substituent(peptide_end),
substituent(ethylcarboxyl),
linkage(from(peptide_end,car(1)),
to(ethylcarboxyl,car(1)),
up,single)]).
config(ethylcarboxyl,[
top(car(1,hyd&&hyd)),
center(methandiyl),
bottom(carboxyl)]).
config(peptide_end,[
left(nit(1,hyd)),
right(hyd),
top(carboxyl),
center(car(1))]).
Smiles String :
[c]1([nH][c]([c]2([c]([NH][C@2H2][C@1H]3([C@2H2][N]([CH]=[N@1+]23)-[c]2([cH][cH_ ][c]([cH][cH]2)/[C](/[O])=[NH]/[C@2H]([C](=[O])[O-])[C@2H2][C@2H2][C](=[O])[O-]_ )))[n]1))[O-])[NH2] 'N5,N10-methenyl-5,6,7,8-tetrahydrofolate'
Terminal :
% 'N5,N10-methenyl-5,6,7,8-tetrahydrofolate'
c(2,12,(0,nonchiral))-[n(2,nil)~,n(1,flat)&,n(3,flat)&],
c(4,12,(0,nonchiral))-[o(1,nil)?,n(3,flat)&,c(24,flat)&],
c(6,12,(0,chiral))-[c(7,left)~,n(5,right)~,c(9,up)~,h(1,down)~],
c(7,12,(0,nonchiral))-[n(8,left)~,c(6,right)~,h(2,up)~,h(3,down)~],
c(9,12,(0,nonchiral))-[h(5,left)~,n(10,right)~,h(6,up)~,c(6,down)~],
c(13,12,(0,nonchiral))-[n(10,left)~,h(7,nil)~,n(5,down)~~],
c(24,12,(0,nonchiral))-[n(5,left)~,c(25,flat)&,c(4,flat)&],
c(25,12,(0,nonchiral))-[n(8,right)~,n(1,flat)&,c(24,flat)&],
c(26,12,(0,nonchiral))-[c(32,(nil,isomeric(up)))~,c(31,flat)&,c(27,flat)&],
c(27,12,(0,nonchiral))-[h(11,nil)~,c(26,flat)&,c(28,flat)&],
c(28,12,(0,nonchiral))-[h(12,nil)~,c(27,flat)&,c(29,flat)&],
c(29,12,(0,nonchiral))-[n(10,nil)~,c(30,flat)&,c(28,flat)&],
c(30,12,(0,nonchiral))-[h(13,nil)~,c(29,flat)&,c(31,flat)&],
c(31,12,(0,nonchiral))-[h(14,nil)~,c(30,flat)&,c(26,flat)&],
c(32,12,(0,nonchiral))-[c(26,(nil,isomeric(down)))~,o(2,(nil,isomeric(up)))?,n(11,trans)#],
c(33,12,(0,chiral))-[n(11,(left,isomeric(down)))~,h(15,right)~,c(35,up)~,c(34,down)~],
c(34,12,(0,nonchiral))-[o(3,nil)?,o(4,nil)?,c(33,up)~],
c(35,12,(0,nonchiral))-[c(36,left)~,h(19,right)~,h(20,up)~,c(33,down)~],
c(36,12,(0,nonchiral))-[c(37,left)~,c(35,right)~,h(18,up)~,h(17,down)~],
c(37,12,(0,nonchiral))-[o(5,nil)?,c(36,right)~,o(6,nil)?],
h(1,1,(0,nonchiral))-[c(6,up)~],
h(2,1,(0,nonchiral))-[c(7,down)~],
h(3,1,(0,nonchiral))-[c(7,up)~],
h(4,1,(0,nonchiral))-[n(8,nil)~],
h(5,1,(0,nonchiral))-[c(9,right)~],
h(6,1,(0,nonchiral))-[c(9,down)~],
h(7,1,(0,nonchiral))-[c(13,nil)~],
h(8,1,(0,nonchiral))-[n(2,nil)~],
h(9,1,(0,nonchiral))-[n(2,nil)~],
h(10,1,(0,nonchiral))-[n(3,nil)~],
h(11,1,(0,nonchiral))-[c(27,nil)~],
h(12,1,(0,nonchiral))-[c(28,nil)~],
h(13,1,(0,nonchiral))-[c(30,nil)~],
h(14,1,(0,nonchiral))-[c(31,nil)~],
h(15,1,(0,nonchiral))-[c(33,left)~],
h(16,1,(0,nonchiral))-[n(11,(nil,isomeric(up)))~],
h(17,1,(0,nonchiral))-[c(36,up)~],
h(18,1,(0,nonchiral))-[c(36,down)~],
h(19,1,(0,nonchiral))-[c(35,left)~],
h(20,1,(0,nonchiral))-[c(35,down)~],
n(1,14,(0,nonchiral))-[c(25,flat)&,c(2,flat)&],
n(2,14,(0,nonchiral))-[h(8,nil)~,h(9,nil)~,c(2,nil)~],
n(3,14,(0,nonchiral))-[h(10,nil)~,c(2,flat)&,c(4,flat)&],
n(5,14,(1,nonchiral))-[c(6,left)~,c(24,right)~,c(13,up)~~],
n(8,14,(0,nonchiral))-[c(25,left)~,c(7,right)~,h(4,nil)~],
n(10,14,(0,nonchiral))-[c(9,left)~,c(13,right)~,c(29,nil)~],
n(11,14,(0,nonchiral))-[h(16,(nil,isomeric(down)))~,c(33,(right,isomeric(up)))~,c(32,trans)#],
o(1,16,(0,nonchiral))-[c(4,nil)?],
o(2,16,(0,nonchiral))-[c(32,(nil,isomeric(down)))?],
o(3,16,(-5.0E-01,nonchiral))-[c(34,nil)?],
o(4,16,(-5.0E-01,nonchiral))-[c(34,nil)?],
o(5,16,(-5.0E-01,nonchiral))-[c(37,nil)?],
o(6,16,(-5.0E-01,nonchiral))-[c(37,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 N5,N10-methenyl-5,6,7,8-tetrahydrofolate. 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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