Deoxyadenosine

Deoxyadenosine (represented as dA or dAdo) is a critical deoxyribonucleoside that plays a fundamental role in the DNA structure. It is derived from the nucleoside adenosine, distinguished by the absence of a hydroxyl group (-OH) and the presence of hydrogen (-H) at the 2′ position of its ribose sugar moiety. Deoxyadenosine, known as the DNA nucleoside A, forms pairs with deoxythymidine (T) in double-stranded DNA.

In cases where adenosine deaminase (ADA) is absent, deoxyadenosine tends to accumulate in T lymphocytes, resulting in their demise. This build-up is associated with the onset of a genetic disorder referred to as adenosine deaminase severe combined immunodeficiency disease (ADA-SCID).

Accession Number : KLM0000106 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.

MBS1224195 | Recombinant Lactobacillus acidophilus Deoxyadenosine kinase (LBA1949)
MBS170430 | 2'-Deoxyadenosine 5'-Monophosphate Disodium Salt (dAMP)
MBS256095 | 3'- Amino- 3'- deoxyadenosine (3'-AdA)
MBS256362 | 2'- Deoxyadenosine- 3', 5'- cyclic monophosphate (2'-dcAMP)
MBS256447 | 2'- Amino- 2'- deoxyadenosine (2'-AdA)
MBS545434 | 2'-DEOXYADENOSINE, MONOHYDRATE
MBS576858 | 2'-Deoxyadenosine monohydrate
MBS651491 | Puromycin Aminonucleoside (3'-Dimethylamino-3'-deoxyadenosine)
MBS657833 | 2'-Deoxyadenosine Monohydrate
MBS1322412 | Recombinant Lactobacillus johnsonii Deoxyadenosine kinase (LJ_1824)
MBS1380152 | Recombinant Dictyostelium discoideum Deoxyadenosine kinase (dak)
MBS6022813 | 2-Methoxy 2'-Deoxyadenosine
MBS6061696 | 1-Hydroxyethyl-2'-deoxyadenosine
MBS6103100 | 1-Hydroxy(ethyl-d4)-2'-deoxyadenosine
MBS6106837 | 5'-Iodo-5'-deoxyadenosine
MBS6111103 | N6-(2-Hydroxyethyl-d4)-2'-deoxyadenosine
MBS6115900 | N6-(2-Hydroxyethyl)-2'-deoxyadenosine
MBS3608095 | 2-Deoxyadenosine monohydrate
MBS3609641 | 2-Deoxyadenosine 5-monophosphate
MBS3609747 | 5'-DEOXYADENOSINE

deoxyadenosine-3d.gif

Config Rule :

 

% deoxyadenosine


config(deoxyadenosine,[
        substituent(adenyl),
        substituent('D-1-dehydroxy-2-deoxy-5-oxy-ribofuranosyl'),
        linkage(from('D-1-dehydroxy-2-deoxy-5-oxy-ribofuranosyl',car(1)),
                to(adenyl,nit(9)),
                up,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(adenyl,[
        model(adenine,[
                diff(nit(9,hyd),nit(9))])]).

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)]))])]).

Smiles String :

 

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

deoxyadenosine

Terminal :

% deoxyadenosine

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))-[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)&],
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))-[c(6,nil)~],
h(12,1,(0,nonchiral))-[c(12,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)~],
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))-[c(5,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 deoxyadenosine. 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!