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.
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!