dAMP


Accession Number : KLM0000100 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.

MBS170430 | 2'-Deoxyadenosine 5'-Monophosphate Disodium Salt (dAMP)
MBS256025 | 2'- Deoxy- 3'- O- (N'- methylanthraniloyl)adenosine- 5'- O- monophosphate (MANT-5'-dAMP)
MBS256161 | 2'- Deoxy- 1, N6- ethenoadenosine- 5'- O- monophosphate (epsilon-5'-dAMP)
MBS256312 | 7- Deaza- 2'- deoxyadenosine- 5'- O- monophosphate (7-CH-5'-dAMP / 5'-dTuMP)
MBS256465 | 2'- Deoxyadenosine- 5'- O- monophosphorothioate (5'-dAMPS)
MBS545802 | 2'-Deoxyadenosine 5'-monophosphate (dAMP) free acid
MBS6024831 | 7-Cyano DAMPA Ethyl Ester
MBS6042886 | N,N'-Diacetyl DAMPA Ethyl Ester
MBS6074732 | DAMPA
MBS6085610 | DAMPA Ethyl Ester
MBS6087749 | 7-Hydroxy DAMPA Methyl Ester
MBS6101341 | DAMPA Methyl Ester
MBS7078318 | Recombinant Dampiera diversifolia NAD (P) H-quinone oxidoreductase subunit 5, chloroplastic (ndhF), partial

damp-3d.gif

Synonyms :

 

  • deoxyadenosine monophosphate
  • deoxyadenosine 5'-monophosphate
  • 5' deoxyadenylate monophosphate
  • 5' dAMP

 

Config Rule :

 

% dAMP


config(dAMP,[
        substituent('D-1-dehydroxy-2-deoxy-5-oxy-ribofuranosyl'),
        substituent(adenyl),
        substituent(phosphoryl),
        linkage(from('D-1-dehydroxy-2-deoxy-5-oxy-ribofuranosyl',car(1)),
                to(adenyl,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(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][P@2](=[O])([O-])[O-])-[n]1(_
[cH][n][c]2([c]1[n][cH][n][c]2[NH2]))

dAMP

Terminal :

% dAMP

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))-[p(1,right)~,c(5,down)~],
o(4,16,(-6.666666666666666E-01,nonchiral))-[p(1,left)?],
o(5,16,(-6.666666666666666E-01,nonchiral))-[p(1,up)?],
o(6,16,(-6.666666666666666E-01,nonchiral))-[p(1,down)?],
p(1,31,(0,nonchiral))-[o(3,left)~,o(4,right)?,o(6,up)?,o(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 dAMP. 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!