N5-methyl-5,6,7,8-tetrahydrofolate

Accession Number : KLM0000564

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 :

5-methyltetrahydrofolate
5-methyl-THF
N5-methyl-THF
N5-methyl-5,6,7,8-THF
5-methyl-5,6,7,8-THF

Config Rule :

% 'N5-methyl-5,6,7,8-tetrahydrofolate'


config('N5-methyl-5,6,7,8-tetrahydrofolate',[
        substituent('1-benzoyl-4-yl'),
        substituent('N5-methyl-pteridin-N10-yl'),
        substituent('D-glutamate'(1,peptide,end)),
        linkage(from('N5-methyl-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-methyl-5,6,7,8-tetrahydrofolate',[
        substituent('1-benzoyl-4-yl'),
        substituent('N5-methyl-pteridin-N10-yl'),
        substituent('D-glutamate'(1,peptide,end)),
        linkage(from('N5-methyl-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-methyl-pteridin-N10-yl',[
        ring_system([
                ring([
                        nit(1)&,
                        car(2,amine)&,
                        nit(3,hyd)&,
                        car(4,oxy?)&,
                        car(11)&,
                        car(12)&]),
                ring([
                        nit(5,methyl(13)~)~,
                        car(6,(car(9,hyd&&hyd&& (nit(10,hyd)~))~)&&hyd)~,
                        car(7,hyd&&hyd)~,
                        nit(8,hyd)~,
                        car(12)&,
                        car(11)~])],
                conjugate(1,pseudopos([car(11),car(12)]),2,pseudopos([car(11),car(12)]))])]).

config('N5-methyl-pteridin-N10-yl',[
        ring_system([
                ring([
                        nit(1)&,
                        car(2,amine)&,
                        nit(3,hyd)&,
                        car(4,oxy?)&,
                        car(11)&,
                        car(12)&]),
                ring([
                        nit(5,methyl(13)~)~,
                        car(6,(car(9,hyd&&hyd&& (nit(10,hyd)~))~)&&hyd)~,
                        car(7,hyd&&hyd)~,
                        nit(8,hyd)~,
                        car(12)&,
                        car(11)~])],
                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-methyl-pteridin-N10-yl',[
        ring_system([
                ring([
                        nit(1)&,
                        car(2,amine)&,
                        nit(3,hyd)&,
                        car(4,oxy?)&,
                        car(11)&,
                        car(12)&]),
                ring([
                        nit(5,methyl(13)~)~,
                        car(6,(car(9,hyd&&hyd&& (nit(10,hyd)~))~)&&hyd)~,
                        car(7,hyd&&hyd)~,
                        nit(8,hyd)~,
                        car(12)&,
                        car(11)~])],
                conjugate(1,pseudopos([car(11),car(12)]),2,pseudopos([car(11),car(12)]))])]).

config('N5-methyl-pteridin-N10-yl',[
        ring_system([
                ring([
                        nit(1)&,
                        car(2,amine)&,
                        nit(3,hyd)&,
                        car(4,oxy?)&,
                        car(11)&,
                        car(12)&]),
                ring([
                        nit(5,methyl(13)~)~,
                        car(6,(car(9,hyd&&hyd&& (nit(10,hyd)~))~)&&hyd)~,
                        car(7,hyd&&hyd)~,
                        nit(8,hyd)~,
                        car(12)&,
                        car(11)~])],
                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@2H]([N@2]2[CH3])[C@2H2][NH]-[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-methyl-5,6,7,8-tetrahydrofolate'

Terminal :

% 'N5-methyl-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(11,flat)&],
c(6,12,(0,chiral))-[c(7,left)~,n(5,right)~,c(9,up)~,h(4,down)~],
c(7,12,(0,nonchiral))-[n(8,left)~,c(6,right)~,h(8,up)~,h(9,down)~],
c(9,12,(0,nonchiral))-[h(5,left)~,h(6,right)~,n(10,up)~,c(6,down)~],
c(11,12,(0,nonchiral))-[n(5,left)~,c(12,flat)&,c(4,flat)&],
c(12,12,(0,nonchiral))-[n(8,right)~,n(1,flat)&,c(11,flat)&],
c(13,12,(0,nonchiral))-[h(11,left)~,h(12,right)~,h(13,up)~,n(5,down)~],
c(14,12,(0,nonchiral))-[c(20,(nil,isomeric(up)))~,c(19,flat)&,c(15,flat)&],
c(15,12,(0,nonchiral))-[h(14,nil)~,c(14,flat)&,c(16,flat)&],
c(16,12,(0,nonchiral))-[h(15,nil)~,c(15,flat)&,c(17,flat)&],
c(17,12,(0,nonchiral))-[n(10,nil)~,c(18,flat)&,c(16,flat)&],
c(18,12,(0,nonchiral))-[h(16,nil)~,c(17,flat)&,c(19,flat)&],
c(19,12,(0,nonchiral))-[h(17,nil)~,c(18,flat)&,c(14,flat)&],
c(20,12,(0,nonchiral))-[c(14,(nil,isomeric(down)))~,o(2,(nil,isomeric(up)))?,n(11,trans)#], c(21,12,(0,chiral))-[n(11,(left,isomeric(down)))~,h(18,right)~,c(23,up)~,c(22,down)~],
c(22,12,(0,nonchiral))-[o(3,nil)?,o(4,nil)?,c(21,up)~],
c(23,12,(0,nonchiral))-[c(24,left)~,h(22,right)~,h(23,up)~,c(21,down)~],
c(24,12,(0,nonchiral))-[c(25,left)~,c(23,right)~,h(21,up)~,h(20,down)~],
c(25,12,(0,nonchiral))-[o(5,nil)?,c(24,right)~,o(6,nil)?],
h(1,1,(0,nonchiral))-[n(2,nil)~],
h(2,1,(0,nonchiral))-[n(2,nil)~],
h(3,1,(0,nonchiral))-[n(3,nil)~],
h(4,1,(0,nonchiral))-[c(6,up)~],
h(5,1,(0,nonchiral))-[c(9,right)~],
h(6,1,(0,nonchiral))-[c(9,left)~],
h(7,1,(0,nonchiral))-[n(10,nil)~],
h(8,1,(0,nonchiral))-[c(7,down)~],
h(9,1,(0,nonchiral))-[c(7,up)~],
h(10,1,(0,nonchiral))-[n(8,nil)~],
h(11,1,(0,nonchiral))-[c(13,right)~],
h(12,1,(0,nonchiral))-[c(13,left)~],
h(13,1,(0,nonchiral))-[c(13,down)~],
h(14,1,(0,nonchiral))-[c(15,nil)~],
h(15,1,(0,nonchiral))-[c(16,nil)~],
h(16,1,(0,nonchiral))-[c(18,nil)~],
h(17,1,(0,nonchiral))-[c(19,nil)~],
h(18,1,(0,nonchiral))-[c(21,left)~],
h(19,1,(0,nonchiral))-[n(11,(nil,isomeric(up)))~],
h(20,1,(0,nonchiral))-[c(24,up)~],
h(21,1,(0,nonchiral))-[c(24,down)~],
h(22,1,(0,nonchiral))-[c(23,left)~],
h(23,1,(0,nonchiral))-[c(23,down)~],
n(1,14,(0,nonchiral))-[c(12,flat)&,c(2,flat)&],
n(2,14,(0,nonchiral))-[h(1,nil)~,h(2,nil)~,c(2,nil)~],
n(3,14,(0,nonchiral))-[h(3,nil)~,c(2,flat)&,c(4,flat)&],
n(5,14,(0,nonchiral))-[c(6,left)~,c(11,right)~,c(13,up)~],
n(8,14,(0,nonchiral))-[c(12,left)~,c(7,right)~,h(10,nil)~],
n(10,14,(0,nonchiral))-[h(7,nil)~,c(17,nil)~,c(9,down)~],
n(11,14,(0,nonchiral))-[h(19,(nil,isomeric(down)))~,c(21,(right,isomeric(up)))~,c(20,trans)#], o(1,16,(0,nonchiral))-[c(4,nil)?],
o(2,16,(0,nonchiral))-[c(20,(nil,isomeric(down)))?],
o(3,16,(-5.0E-01,nonchiral))-[c(22,nil)?],
o(4,16,(-5.0E-01,nonchiral))-[c(22,nil)?],
o(5,16,(-5.0E-01,nonchiral))-[c(25,nil)?],
o(6,16,(-5.0E-01,nonchiral))-[c(25,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-methyl-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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