Deoxyguanosine monophosphate (dGMP)

also known as deoxyguanylic acid or deoxyguanylate is a crucial derivative of guanosine triphosphate (GTP), a ubiquitous nucleic acid. It is characterized by the absence of the hydroxyl group (-OH) on the 2' carbon of the nucleotide's pentose, denoted by the prefix "deoxy-." In the realm of DNA, it serves as a fundamental monomer.

Accession Number : KLM0000113 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 :

deoxyguanosine monophosphate
deoxyguanosine 5'-monophosphate
5' deoxyguanylate monophosphate
5' dGMP

Config Rule :

% dGMP


config(dGMP,[
        substituent('D-1-dehydroxy-2-deoxy-5-oxy-ribofuranosyl'),
        substituent(guanyl),
        substituent(phosphoryl),
        linkage(from('D-1-dehydroxy-2-deoxy-5-oxy-ribofuranosyl',car(1)),
                to(guanyl,nit(9)),
                up,single),
        linkage(from(phosphoryl,pho(1)),
                to('D-1-dehydroxy-2-deoxy-5-oxy-ribofuranosyl',attach_to([oxy,car(5)])),
                nil,single)]).

config('D-1-dehydroxy-2-deoxy-5-oxy-ribofuranosyl',[
        ring([
                oxy,
                anomeric(1,hyd),
                car(2,hyd&&hyd;),
                car(3,hyd&&hydroxyl;),
                car(4,oxymethyl&&hyd;)])]).

config(guanyl,[
        model(guanine,[
                diff(nit(9,hyd),nit(9))])]).

config(guanine,[
        model(purine,[
                diff(nit(1),nit(1,hyd)),
                diff(car(2,hyd),car(2,amine(10))),
                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)]))])]).

Smiles String :

[C@2H]-1([O][C@2H]([C@2H]([OH])[C@2H2]-1)[C@2H2][O][P@2](=[O])([O-])[O-])-[n]1(_
[cH][n][c]2([c]1[n][c]([nH][c]2[O-])[NH2]))

dGMP

Terminal :

% dGMP

c(1,12,(0,chiral))-[c(2,left)~,o(1,right)~,n(9,up)~,h(1,down)~],
c(2,12,(0,nonchiral))-[c(3,left)~,c(1,right)~,h(2,up)~,h(3,down)~],
c(3,12,(0,chiral))-[c(4,left)~,c(2,right)~,h(4,up)~,o(2,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(3,up)~,c(4,down)~],
c(6,12,(0,nonchiral))-[n(10,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(4,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))-[c(2,up)~],
h(4,1,(0,nonchiral))-[c(3,down)~],
h(5,1,(0,nonchiral))-[o(2,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))-[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))-[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(6,nil)~],
o(1,16,(0,nonchiral))-[c(1,left)~,c(4,right)~],
o(2,16,(0,nonchiral))-[h(5,nil)~,c(3,up)~],
o(3,16,(0,nonchiral))-[p(1,right)~,c(5,down)~],
o(4,16,(0,nonchiral))-[c(10,nil)?],
o(5,16,(-6.666666666666666E-01,nonchiral))-[p(1,left)?],
o(6,16,(-6.666666666666666E-01,nonchiral))-[p(1,up)?],
o(7,16,(-6.666666666666666E-01,nonchiral))-[p(1,down)?],
p(1,31,(0,nonchiral))-[o(3,left)~,o(5,right)?,o(7,up)?,o(6,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 dGMP. 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!