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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-05-22 14:17:30 UTC

Update Date

2021-09-14 15:18:56 UTC

HMDB ID

HMDB0001983

Secondary Accession Numbers

HMDB01983

Metabolite Identification

Common Name

5'-Deoxyadenosine

Description

5'-Deoxyadenosine is an oxidized nucleoside found in the urine of normal subjects. Oxidized nucleosides represent excellent biomarkers for determining the extent of damage in genetic material, which has long been of interest in understanding the mechanism of aging, neurodegenerative diseases, and carcinogenesis. (PMID 15116424 ). The normal form of deoxyadenosine used in DNA synthesis and repair is 2'-deoxyadenosine where the hydroxyl group (-OH) is at the 2' position of its ribose sugar moiety. 5'-deoxyadenosine has its hydroxyl group at the 5' position of the ribose sugar.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0001983
     RDKit          3D
5'-Deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
   -3.5821   -0.2285   -1.5338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6570   -0.5382   -0.3915 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4046   -0.9559   -0.8088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6726   -1.0021    0.3807 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7502   -0.9763    0.1435 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5572   -2.0691    0.0983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8109   -1.6467   -0.1429 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8099   -0.3087   -0.2507 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7953    0.6347   -0.4896 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1332    0.1912   -0.6750 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4548    1.9282   -0.5376 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1908    2.3382   -0.3618 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2280    1.4290   -0.1294 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5209    0.1051   -0.0710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1603    0.1063    1.2534 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7892   -0.4122    2.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3046    0.6907    0.4145 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3360    1.1482    1.1901 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629    0.4693   -2.2747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5169    0.1831   -1.0946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8760   -1.2098   -1.9826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1014   -1.3272    0.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9421   -1.9920    0.8513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2107   -3.0957    0.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3157   -0.3939   -1.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    0.4505    0.0173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9941    3.3989   -0.4148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4190    0.8599    1.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5289   -1.3720    2.5030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8497    1.4379   -0.2510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3239    2.1571    1.1406 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  4 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  2  1  0
 14  5  1  0
 14  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
  4 23  1  1
  6 24  1  0
 10 25  1  0
 10 26  1  0
 12 27  1  0
 15 28  1  1
 16 29  1  0
 17 30  1  6
 18 31  1  0
M  END

  Mrv1652309042000252D          

 18 20  0  0  0  0            999 V2000
    6.0924    1.6396    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0924    0.8146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3780    0.4021    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3779   -0.4229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0923   -0.8354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.8069   -0.4229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8069    0.4021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5915    0.6570    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.0765   -0.0105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5915   -0.6778    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8465   -1.4626    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.3615   -2.1300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8464   -2.7976    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.5914   -3.5822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6310   -2.5425    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.2985   -3.0276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6311   -1.7176    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.2985   -1.2326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  7  2  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6 10  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 11 10  1  1  0  0  0
 11 12  1  0  0  0  0
 11 17  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0001983

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O3/c1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15/h2-4,6-7,10,16-17H,1H3,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1

> <INCHI_KEY>
XGYIMTFOTBMPFP-KQYNXXCUSA-N

> <FORMULA>
C10H13N5O3

> <MOLECULAR_WEIGHT>
251.2419

> <EXACT_MASS>
251.101839307

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
24.30241412668001

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-methyloxolane-3,4-diol

> <ALOGPS_LOGP>
-0.52

> <JCHEM_LOGP>
-1.0440539050000002

> <ALOGPS_LOGS>
-1.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.04065367928522

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.482511642166756

> <JCHEM_PKA_STRONGEST_BASIC>
3.9212963575149358

> <JCHEM_POLAR_SURFACE_AREA>
119.30999999999999

> <JCHEM_REFRACTIVITY>
61.6519

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.88e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5'-deoxyadenosine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001983
     RDKit          3D
5'-Deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
   -3.5821   -0.2285   -1.5338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6570   -0.5382   -0.3915 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4046   -0.9559   -0.8088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6726   -1.0021    0.3807 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7502   -0.9763    0.1435 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5572   -2.0691    0.0983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8109   -1.6467   -0.1429 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8099   -0.3087   -0.2507 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7953    0.6347   -0.4896 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1332    0.1912   -0.6750 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4548    1.9282   -0.5376 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1908    2.3382   -0.3618 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2280    1.4290   -0.1294 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5209    0.1051   -0.0710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1603    0.1063    1.2534 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7892   -0.4122    2.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3046    0.6907    0.4145 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3360    1.1482    1.1901 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629    0.4693   -2.2747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5169    0.1831   -1.0946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8760   -1.2098   -1.9826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1014   -1.3272    0.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9421   -1.9920    0.8513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2107   -3.0957    0.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3157   -0.3939   -1.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    0.4505    0.0173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9941    3.3989   -0.4148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4190    0.8599    1.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5289   -1.3720    2.5030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8497    1.4379   -0.2510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3239    2.1571    1.1406 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  4 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  2  1  0
 14  5  1  0
 14  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
  4 23  1  1
  6 24  1  0
 10 25  1  0
 10 26  1  0
 12 27  1  0
 15 28  1  1
 16 29  1  0
 17 30  1  6
 18 31  1  0
M  END

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0      11.372   3.061   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      11.372   1.521   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      10.039   0.751   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      10.039  -0.789   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      11.372  -1.559   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      12.706  -0.789   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.706   0.751   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      14.171   1.226   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      15.076  -0.020   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      14.171  -1.265   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      14.647  -2.730   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      13.741  -3.976   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      14.647  -5.222   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      14.171  -6.687   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      16.111  -4.746   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      17.357  -5.652   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      16.111  -3.206   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      17.357  -2.301   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    2    6    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    6    9   11                                                  
CONECT   11   10   12   17                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   11   15   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0001983
HETATM    1  C1  UNL     1      -3.582  -0.228  -1.534  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.657  -0.538  -0.392  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.405  -0.956  -0.809  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.673  -1.002   0.381  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.750  -0.976   0.144  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.557  -2.069   0.098  1.00  0.00           C  
HETATM    7  N2  UNL     1       2.811  -1.647  -0.143  1.00  0.00           N  
HETATM    8  C5  UNL     1       2.810  -0.309  -0.251  1.00  0.00           C  
HETATM    9  C6  UNL     1       3.795   0.635  -0.490  1.00  0.00           C  
HETATM   10  N3  UNL     1       5.133   0.191  -0.675  1.00  0.00           N  
HETATM   11  N4  UNL     1       3.455   1.928  -0.538  1.00  0.00           N  
HETATM   12  C7  UNL     1       2.191   2.338  -0.362  1.00  0.00           C  
HETATM   13  N5  UNL     1       1.228   1.429  -0.129  1.00  0.00           N  
HETATM   14  C8  UNL     1       1.521   0.105  -0.071  1.00  0.00           C  
HETATM   15  C9  UNL     1      -1.160   0.106   1.253  1.00  0.00           C  
HETATM   16  O2  UNL     1      -1.789  -0.412   2.409  1.00  0.00           O  
HETATM   17  C10 UNL     1      -2.305   0.691   0.414  1.00  0.00           C  
HETATM   18  O3  UNL     1      -3.336   1.148   1.190  1.00  0.00           O  
HETATM   19  H1  UNL     1      -3.163   0.469  -2.275  1.00  0.00           H  
HETATM   20  H2  UNL     1      -4.517   0.183  -1.095  1.00  0.00           H  
HETATM   21  H3  UNL     1      -3.876  -1.210  -1.983  1.00  0.00           H  
HETATM   22  H4  UNL     1      -3.101  -1.327   0.219  1.00  0.00           H  
HETATM   23  H5  UNL     1      -0.942  -1.992   0.851  1.00  0.00           H  
HETATM   24  H6  UNL     1       1.211  -3.096   0.238  1.00  0.00           H  
HETATM   25  H7  UNL     1       5.316  -0.394  -1.533  1.00  0.00           H  
HETATM   26  H8  UNL     1       5.856   0.451   0.017  1.00  0.00           H  
HETATM   27  H9  UNL     1       1.994   3.399  -0.415  1.00  0.00           H  
HETATM   28  H10 UNL     1      -0.419   0.860   1.509  1.00  0.00           H  
HETATM   29  H11 UNL     1      -1.529  -1.372   2.503  1.00  0.00           H  
HETATM   30  H12 UNL     1      -1.850   1.438  -0.251  1.00  0.00           H  
HETATM   31  H13 UNL     1      -3.324   2.157   1.141  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3   17   22
CONECT    3    4
CONECT    4    5   15   23
CONECT    5    6   14
CONECT    6    7    7   24
CONECT    7    8
CONECT    8    9    9   14
CONECT    9   10   11
CONECT   10   25   26
CONECT   11   12   12
CONECT   12   13   27
CONECT   13   14   14
CONECT   15   16   17   28
CONECT   16   29
CONECT   17   18   30
CONECT   18   31
END

HMDB0001983
     RDKit          3D
5'-Deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
   -3.5821   -0.2285   -1.5338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6570   -0.5382   -0.3915 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4046   -0.9559   -0.8088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6726   -1.0021    0.3807 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7502   -0.9763    0.1435 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5572   -2.0691    0.0983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8109   -1.6467   -0.1429 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8099   -0.3087   -0.2507 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7953    0.6347   -0.4896 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1332    0.1912   -0.6750 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4548    1.9282   -0.5376 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1908    2.3382   -0.3618 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2280    1.4290   -0.1294 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5209    0.1051   -0.0710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1603    0.1063    1.2534 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7892   -0.4122    2.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3046    0.6907    0.4145 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3360    1.1482    1.1901 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629    0.4693   -2.2747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5169    0.1831   -1.0946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8760   -1.2098   -1.9826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1014   -1.3272    0.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9421   -1.9920    0.8513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2107   -3.0957    0.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3157   -0.3939   -1.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    0.4505    0.0173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9941    3.3989   -0.4148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4190    0.8599    1.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5289   -1.3720    2.5030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8497    1.4379   -0.2510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3239    2.1571    1.1406 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  4 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  2  1  0
 14  5  1  0
 14  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
  4 23  1  1
  6 24  1  0
 10 25  1  0
 10 26  1  0
 12 27  1  0
 15 28  1  1
 16 29  1  0
 17 30  1  6
 18 31  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
5'-Deoxy-adenosine	HMDB
5'-DAdo nucleoside	MeSH, HMDB

Chemical Formula

C₁₀H₁₃N₅O₃

Average Molecular Weight

251.2419

Monoisotopic Molecular Weight

251.101839307

IUPAC Name

(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-methyloxolane-3,4-diol

Traditional Name

5'-deoxyadenosine

CAS Registry Number

4754-39-6

SMILES

C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12

InChI Identifier

InChI=1S/C10H13N5O3/c1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15/h2-4,6-7,10,16-17H,1H3,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1

InChI Key

XGYIMTFOTBMPFP-KQYNXXCUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

5'-deoxyribonucleosides

Sub Class

Not Available

Direct Parent

5'-deoxyribonucleosides

Alternative Parents

Substituents

5'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
6-aminopurine
Purine
Imidazopyrimidine
Aminopyrimidine
Imidolactam
Pyrimidine
N-substituted imidazole
Azole
Heteroaromatic compound
Imidazole
Tetrahydrofuran
1,2-diol
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Alcohol
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Amine
Primary amine
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

adenosines (CHEBI:17319 )
5'-deoxyribonucleoside (CHEBI:17319 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0001983)

Excreta

Biofluid or Excreta

Urine (PMID: 15116424)

Cellular substructure

Extracellular (HMDB: HMDB0001983)
Cytoplasm (HMDB: HMDB0001983)

Organelle

Mitochondrion (HMDB: HMDB0001983)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0001983)

Source

Endogenous

Endogenous (HMDB: HMDB0001983)

Plant

Animal

Animal (HMDB: HMDB0001983)

Exogenous

Food

Food (HMDB: HMDB0001983)

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Herb and spice mixture

Curry powder (FooDB: FOOD00678)

Herbs and Spices (FooDB: FOOD00866)

Vegetable

Cabbage

Onion-family vegetable

Allium (FooDB: FOOD00005)
Garden onion (FooDB: FOOD00006)
Leek (FooDB: FOOD00007)
Garden onion (var.) (FooDB: FOOD00226)
Shallot (FooDB: FOOD00243)
Wild leek (FooDB: FOOD00396)
Red onion (FooDB: FOOD00962)
Green onion (FooDB: FOOD00963)
Onion-family vegetables (FooDB: FOOD00855)

Root vegetable

Shoot vegetable

Leaf vegetable

Common beet (FooDB: FOOD00025)
Endive (FooDB: FOOD00048)
Rocket salad (ssp.) (FooDB: FOOD00077)
Swamp cabbage (FooDB: FOOD00091)
Lettuce (FooDB: FOOD00095)
Garden cress (FooDB: FOOD00099)
Spinach (FooDB: FOOD00178)
Swiss chard (FooDB: FOOD00237)
Chicory leaves (FooDB: FOOD00250)
Garland chrysanthemum (FooDB: FOOD00333)
Corn salad (FooDB: FOOD00340)
Jute (FooDB: FOOD00389)
Lambsquarters (FooDB: FOOD00394)
Malabar spinach (FooDB: FOOD00404)
New Zealand spinach (FooDB: FOOD00415)
Yautia (FooDB: FOOD00510)
Ostrich fern (FooDB: FOOD00556)
Romaine lettuce (FooDB: FOOD00888)
Iceberg lettuce (FooDB: FOOD00973)
Pea shoots (FooDB: FOOD00975)
Yau choy (FooDB: FOOD00976)
Water spinach (FooDB: FOOD00977)
Rocket salad (FooDB: FOOD00244)
Green vegetables (FooDB: FOOD00872)

Fruit vegetable

Pepper (FooDB: FOOD00040)
Olive (FooDB: FOOD00121)
Avocado (FooDB: FOOD00130)
Garden tomato (FooDB: FOOD00171)
Cherry tomato (FooDB: FOOD00172)
Garden tomato (var.) (FooDB: FOOD00173)
Eggplant (FooDB: FOOD00174)
Pepper (C. baccatum) (FooDB: FOOD00231)
Pepper (C. chinense) (FooDB: FOOD00232)
Pepper (Capsicum) (FooDB: FOOD00233)
Groundcherry (FooDB: FOOD00371)
Pepper (C. frutescens) (FooDB: FOOD00428)
Mexican groundcherry (FooDB: FOOD00491)
Pepper (C. pubescens) (FooDB: FOOD00849)
Green bell pepper (FooDB: FOOD00877)
Yellow bell pepper (FooDB: FOOD00878)
Orange bell pepper (FooDB: FOOD00879)
Red bell pepper (FooDB: FOOD00880)
Italian sweet red pepper (FooDB: FOOD00881)
Jalapeno pepper (FooDB: FOOD00955)
Cubanelle pepper (FooDB: FOOD00971)

Tuber

Stalk vegetable

Other vegetable

Giant butterbur (FooDB: FOOD00314)
Carob (FooDB: FOOD00321)
Chinese water chestnut (FooDB: FOOD00332)
Horseradish tree (FooDB: FOOD00379)
Sacred lotus (FooDB: FOOD00402)
Nopal (FooDB: FOOD00416)
Okra (FooDB: FOOD00420)
Sesbania flower (FooDB: FOOD00469)
Agave (FooDB: FOOD00563)
Narrowleaf cattail (FooDB: FOOD00564)
Heart of palm (FooDB: FOOD00718)
Tree fern (FooDB: FOOD00797)

Mushroom

Castanospermum australe (FooDB: FOOD00893)
Gentiana lutea (FooDB: FOOD00894)
Juniperus communis (FooDB: FOOD00895)
Albizia gummifera (FooDB: FOOD00896)

Brassica

Brassicas (FooDB: FOOD00857)

Fruit

Tropical fruit

Citrus

Lime (FooDB: FOOD00053)
Lemon (FooDB: FOOD00054)
Pummelo (FooDB: FOOD00055)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)
Sweet orange (FooDB: FOOD00057)
Grapefruit/Pummelo hybrid (FooDB: FOOD00255)
Grapefruit (FooDB: FOOD00256)
Persian lime (FooDB: FOOD00543)
Sour orange (FooDB: FOOD00918)
Mikan (FooDB: FOOD00932)
Clementine (FooDB: FOOD00959)
Citrus (FooDB: FOOD00859)

Pome

Berry

Black crowberry (FooDB: FOOD00075)
Strawberry (FooDB: FOOD00083)
Black huckleberry (FooDB: FOOD00084)
Sea-buckthornberry (FooDB: FOOD00087)
Mulberry (FooDB: FOOD00116)
Black mulberry (FooDB: FOOD00117)
Black chokeberry (FooDB: FOOD00136)
Blackcurrant (FooDB: FOOD00155)
Redcurrant (FooDB: FOOD00156)
Gooseberry (FooDB: FOOD00157)
Cloudberry (FooDB: FOOD00161)
Red raspberry (FooDB: FOOD00162)
Black raspberry (FooDB: FOOD00163)
Black elderberry (FooDB: FOOD00166)
Rowanberry (FooDB: FOOD00176)
Vaccinium (Blueberry, Cranberry, Huckleberry) (FooDB: FOOD00188)
Lowbush blueberry (FooDB: FOOD00189)
Sparkleberry (FooDB: FOOD00190)
Highbush blueberry (FooDB: FOOD00191)
American cranberry (FooDB: FOOD00192)
Bilberry (FooDB: FOOD00193)
Lingonberry (FooDB: FOOD00194)
Muscadine grape (FooDB: FOOD00203)
Common grape (FooDB: FOOD00204)
Arctic blackberry (FooDB: FOOD00207)
Bayberry (FooDB: FOOD00209)
Elliott's blueberry (FooDB: FOOD00210)
Canada blueberry (FooDB: FOOD00211)
Bog bilberry (FooDB: FOOD00212)
Buffalo currant (FooDB: FOOD00213)
European cranberry (FooDB: FOOD00217)
Deerberry (FooDB: FOOD00218)
Cascade huckleberry (FooDB: FOOD00220)
Oval-leaf huckleberry (FooDB: FOOD00221)
Evergreen huckleberry (FooDB: FOOD00222)
Red huckleberry (FooDB: FOOD00223)
Summer grape (FooDB: FOOD00227)
Fox grape (FooDB: FOOD00228)
Half-highbush blueberry (FooDB: FOOD00248)
Jostaberry (FooDB: FOOD00257)
Sweet rowanberry (FooDB: FOOD00265)
Skunk currant (FooDB: FOOD00267)
Squashberry (FooDB: FOOD00344)
Elderberry (FooDB: FOOD00358)
Grape (FooDB: FOOD00369)
Alaska blueberry (FooDB: FOOD00380)
Loganberry (FooDB: FOOD00400)
Ohelo berry (FooDB: FOOD00419)
Salmonberry (FooDB: FOOD00456)
Strawberry guava (FooDB: FOOD00482)
Boysenberry (FooDB: FOOD00542)
Chinese bayberry (FooDB: FOOD00852)
Saskatoon berry (FooDB: FOOD00884)
Nanking cherry (FooDB: FOOD00885)
Rabbiteye blueberry (FooDB: FOOD00898)
Blackberry (FooDB: FOOD00906)
Partridge berry (FooDB: FOOD00931)
Green grape (FooDB: FOOD00964)
Red grape (FooDB: FOOD00965)
Black plum (FooDB: FOOD00966)
Black raisin (FooDB: FOOD00968)
Chinese plum (FooDB: FOOD00978)
Green plum (FooDB: FOOD00979)
Wampee (FooDB: FOOD00980)
Goji (FooDB: FOOD00982)
Monk fruit (FooDB: FOOD00983)
Hawthorn (FooDB: FOOD00985)
Lantern fruit (FooDB: FOOD00986)
Cape gooseberry (FooDB: FOOD00988)
Rubus (Blackberry, Raspberry) (FooDB: FOOD00160)

Other fruit

Fig (FooDB: FOOD00081)
Date (FooDB: FOOD00135)
Jujube (FooDB: FOOD00388)

Drupe

Prunus (Cherry, Plum) (FooDB: FOOD00143)
Apricot (FooDB: FOOD00144)
Sweet cherry (FooDB: FOOD00145)
Sour cherry (FooDB: FOOD00146)
European plum (FooDB: FOOD00147)
Peach (FooDB: FOOD00149)
Nectarine (FooDB: FOOD00229)
Peach (var.) (FooDB: FOOD00230)
Common chokecherry (FooDB: FOOD00562)

Fruits (FooDB: FOOD00871)

Nut

Cashew nut (FooDB: FOOD00011)
Peanut (FooDB: FOOD00016)
Brazil nut (FooDB: FOOD00024)
Pecan nut (FooDB: FOOD00044)
Chestnut (FooDB: FOOD00045)
Common hazelnut (FooDB: FOOD00062)
Black walnut (FooDB: FOOD00093)
Common walnut (FooDB: FOOD00094)
Pine nut (FooDB: FOOD00138)
Pistachio (FooDB: FOOD00140)
Almond (FooDB: FOOD00148)
Macadamia nut (M. tetraphylla) (FooDB: FOOD00225)
Japanese walnut (FooDB: FOOD00240)
Acorn (FooDB: FOOD00282)
Beech nut (FooDB: FOOD00299)
Butternut (FooDB: FOOD00316)
Chinese chestnut (FooDB: FOOD00331)
European chestnut (FooDB: FOOD00363)
Hazelnut (FooDB: FOOD00376)
Hickory nut (FooDB: FOOD00377)
Japanese chestnut (FooDB: FOOD00385)
Pili nut (FooDB: FOOD00432)
Colorado pinyon (FooDB: FOOD00433)
Macadamia nut (FooDB: FOOD00525)
Walnut (FooDB: FOOD00608)
Mixed nuts (FooDB: FOOD00771)
Nuts (FooDB: FOOD00869)

Cereal and cereal product

Cereal

Cereal product

Dough

Sourdough (FooDB: FOOD00275)

Leavened bread

Flat bread

Other bread

Potato bread (FooDB: FOOD00811)
Other bread (FooDB: FOOD00269)

Sweet bread

Raisin bread (FooDB: FOOD00817)

Cereals and cereal products (FooDB: FOOD00858)

Pulse

Pea

Lentil

Lentils (FooDB: FOOD00098)

Other pulse

Lupine (FooDB: FOOD00104)
White lupine (FooDB: FOOD00403)

Bean

Green lentil (FooDB: FOOD00970)
Pulses (FooDB: FOOD00867)

Gourd

Watermelon (FooDB: FOOD00052)
Muskmelon (FooDB: FOOD00064)
Cucumber (FooDB: FOOD00065)
Cucurbita (FooDB: FOOD00066)
Bitter gourd (FooDB: FOOD00115)
Winter squash (FooDB: FOOD00283)
Butternut squash (FooDB: FOOD00317)
Calabash (FooDB: FOOD00318)
Chayote (FooDB: FOOD00325)
Towel gourd (FooDB: FOOD00492)
Wax gourd (FooDB: FOOD00499)
Tinda (FooDB: FOOD00559)
Horned melon (FooDB: FOOD00761)
Sunburst squash (pattypan squash) (FooDB: FOOD00874)
Green zucchini (FooDB: FOOD00875)
Yellow zucchini (FooDB: FOOD00876)
Japanese pumpkin (FooDB: FOOD00886)
Acorn squash (FooDB: FOOD00972)
Cantaloupe melon (FooDB: FOOD00984)

Coffee and coffee product

Coffee

Arabica coffee (FooDB: FOOD00059)
Robusta coffee (FooDB: FOOD00060)

Soy

Soy bean (FooDB: FOOD00085)

Soy product

Dish

Other dish

Taco shell (FooDB: FOOD00991)
Tostada shell (FooDB: FOOD00992)

Tea

Herbal tea

Hibiscus tea (FooDB: FOOD00723)
Greenthread tea (FooDB: FOOD00820)

Baking good

Wrapper

Wonton wrapper (FooDB: FOOD00818)

Abalone (FooDB: FOOD00279)
Conch (FooDB: FOOD00611)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Porphyrin Metabolism (PathBank: SMP0000953)
Lipoic Acid Metabolism (PathBank: SMP0121070)
Lipoate Biosynthesis and Incorporation I (PathBank: SMP0122263)
Biotin Metabolism (PathBank: SMP0000785)
Thiamin Diphosphate Biosynthesis (PathBank: SMP0122222)
Tyrosine Biosynthesis (PathBank: SMP0000826)
Thiazole Biosynthesis I (PathBank: SMP0002055)
Molybdenum Cofactor Biosynthesis (PathBank: SMP0012017)
Thio-Molybdenum Cofactor Biosynthesis (PathBank: SMP0012046)

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	213.0 - 214.5 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Baker	160.19	30932474
[M-H]-	MetCCS_train_neg	151.905	30932474
[M+H]+	Baker	162.1	30932474
[M-H]-	Not Available	155.5	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000131
[M+H]+	Not Available	162.1	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000131

Predicted Molecular Properties

Property	Value	Source
Water Solubility	9.88 g/L	ALOGPS
logP	-0.52	ALOGPS
logP	-1	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	12.48	ChemAxon
pKa (Strongest Basic)	3.92	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	119.31 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	61.65 m³·mol⁻¹	ChemAxon
Polarizability	24.3 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	158.734	31661259
DarkChem	[M-H]-	152.575	31661259
AllCCS	[M+H]+	157.613	32859911
AllCCS	[M-H]-	156.631	32859911
DeepCCS	[M-2H]-	185.181	30932474
DeepCCS	[M+Na]+	160.022	30932474
AllCCS	[M+H]+	157.6	32859911
AllCCS	[M+H-H2O]+	154.0	32859911
AllCCS	[M+NH4]+	161.0	32859911
AllCCS	[M+Na]+	162.0	32859911
AllCCS	[M-H]-	156.6	32859911
AllCCS	[M+Na-2H]-	156.3	32859911
AllCCS	[M+HCOO]-	156.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5'-Deoxyadenosine	C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12	3367.2	Standard polar	33892256
5'-Deoxyadenosine	C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12	2091.8	Standard non polar	33892256
5'-Deoxyadenosine	C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12	2379.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5'-Deoxyadenosine,1TMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O	2427.0	Semi standard non polar	33892256
5'-Deoxyadenosine,1TMS,isomer #2	C[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@H](O)[C@@H]1O[Si](C)(C)C	2446.6	Semi standard non polar	33892256
5'-Deoxyadenosine,1TMS,isomer #3	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O	2464.4	Semi standard non polar	33892256
5'-Deoxyadenosine,2TMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2412.7	Semi standard non polar	33892256
5'-Deoxyadenosine,2TMS,isomer #2	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O	2417.7	Semi standard non polar	33892256
5'-Deoxyadenosine,2TMS,isomer #3	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O[Si](C)(C)C	2440.0	Semi standard non polar	33892256
5'-Deoxyadenosine,2TMS,isomer #4	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O	2439.7	Semi standard non polar	33892256
5'-Deoxyadenosine,3TMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2449.8	Semi standard non polar	33892256
5'-Deoxyadenosine,3TMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2551.3	Standard non polar	33892256
5'-Deoxyadenosine,3TMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	3507.0	Standard polar	33892256
5'-Deoxyadenosine,3TMS,isomer #2	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O	2446.2	Semi standard non polar	33892256
5'-Deoxyadenosine,3TMS,isomer #2	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O	2599.4	Standard non polar	33892256
5'-Deoxyadenosine,3TMS,isomer #2	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O	3306.0	Standard polar	33892256
5'-Deoxyadenosine,3TMS,isomer #3	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O[Si](C)(C)C	2457.2	Semi standard non polar	33892256
5'-Deoxyadenosine,3TMS,isomer #3	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O[Si](C)(C)C	2591.0	Standard non polar	33892256
5'-Deoxyadenosine,3TMS,isomer #3	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O[Si](C)(C)C	3214.5	Standard polar	33892256
5'-Deoxyadenosine,4TMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2500.4	Semi standard non polar	33892256
5'-Deoxyadenosine,4TMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2641.3	Standard non polar	33892256
5'-Deoxyadenosine,4TMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2979.4	Standard polar	33892256
5'-Deoxyadenosine,1TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2672.4	Semi standard non polar	33892256
5'-Deoxyadenosine,1TBDMS,isomer #2	C[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2701.6	Semi standard non polar	33892256
5'-Deoxyadenosine,1TBDMS,isomer #3	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O	2648.3	Semi standard non polar	33892256
5'-Deoxyadenosine,2TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2848.0	Semi standard non polar	33892256
5'-Deoxyadenosine,2TBDMS,isomer #2	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2807.2	Semi standard non polar	33892256
5'-Deoxyadenosine,2TBDMS,isomer #3	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2824.4	Semi standard non polar	33892256
5'-Deoxyadenosine,2TBDMS,isomer #4	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O	2817.2	Semi standard non polar	33892256
5'-Deoxyadenosine,3TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3010.4	Semi standard non polar	33892256
5'-Deoxyadenosine,3TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3221.0	Standard non polar	33892256
5'-Deoxyadenosine,3TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3638.6	Standard polar	33892256
5'-Deoxyadenosine,3TBDMS,isomer #2	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2978.5	Semi standard non polar	33892256
5'-Deoxyadenosine,3TBDMS,isomer #2	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3254.2	Standard non polar	33892256
5'-Deoxyadenosine,3TBDMS,isomer #2	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3455.2	Standard polar	33892256
5'-Deoxyadenosine,3TBDMS,isomer #3	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2996.4	Semi standard non polar	33892256
5'-Deoxyadenosine,3TBDMS,isomer #3	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3247.4	Standard non polar	33892256
5'-Deoxyadenosine,3TBDMS,isomer #3	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3382.6	Standard polar	33892256
5'-Deoxyadenosine,4TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3183.4	Semi standard non polar	33892256
5'-Deoxyadenosine,4TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3464.5	Standard non polar	33892256
5'-Deoxyadenosine,4TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3321.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Deoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	splash10-05dl-9640000000-ee63a0f0a804463c5d3b	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Deoxyadenosine GC-MS (2 TMS) - 70eV, Positive	splash10-00wi-9757000000-b8ba57885a813934cb02	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Deoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Deoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine , negative-QTOF	splash10-001i-0910000000-e2fb3e0d3b85b88eaf9f	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine LC-ESI-QQ , positive-QTOF	splash10-0udi-0490000000-2d56a55a6dcc84b79cbb	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine LC-ESI-QQ , positive-QTOF	splash10-000i-0900000000-bc60a46e6751486debe1	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine LC-ESI-QQ , positive-QTOF	splash10-000i-1900000000-aa5e98075bbd2c17e6e9	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine LC-ESI-QQ , positive-QTOF	splash10-000i-3900000000-97cb5373efd784d8bc46	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine LC-ESI-QQ , positive-QTOF	splash10-000i-5900000000-fc447cfd2476fd6fc248	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine LC-ESI-IT , positive-QTOF	splash10-000i-0900000000-decd8c6638992a36e5c1	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine , positive-QTOF	splash10-000i-0900000000-bcb75d9aef2d7b125ff7	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 20V, Positive-QTOF	splash10-000i-0900000000-7753a248c8f9e8bd3c17	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 10V, Positive-QTOF	splash10-000i-0910000000-89ee982504aa7d7e8d86	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 35V, Positive-QTOF	splash10-000i-0900000000-88f38e28bec54de698eb	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 40V, Positive-QTOF	splash10-00kr-2900000000-7f30e8fa287a8c04426f	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 10V, Positive-QTOF	splash10-000i-0900000000-0b1ad0521a9e5b4f4e69	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 20V, Positive-QTOF	splash10-000i-0900000000-33ce25ce3b126b922477	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 40V, Positive-QTOF	splash10-000i-1900000000-5ffeb1c5e0b4ba70a9a0	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 35V, Positive-QTOF	splash10-000i-0900000000-94d5e457c8b194127db1	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 35V, Negative-QTOF	splash10-001i-0910000000-5ef9ec3078fd4597497f	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 10V, Positive-QTOF	splash10-000i-0910000000-896c15b06d2fe2a894be	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5'-Deoxyadenosine 20V, Negative-QTOF	splash10-001i-0900000000-0364ac4f65cbde9247ab	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxyadenosine 10V, Positive-QTOF	splash10-000i-0940000000-20bada9b7c3914ebd835	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxyadenosine 20V, Positive-QTOF	splash10-000i-0900000000-e218ae45a376f2d35bff	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxyadenosine 40V, Positive-QTOF	splash10-014r-3900000000-4803d4734d389249e54b	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxyadenosine 10V, Negative-QTOF	splash10-0ue9-0790000000-e9f6fee027d381974116	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxyadenosine 20V, Negative-QTOF	splash10-001i-0900000000-f8cfbe38fa6d8b9a9b3e	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxyadenosine 40V, Negative-QTOF	splash10-05o0-4900000000-b861ad521faa95835ac1	2015-09-15	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Detected and Quantified	0.078 (0.054-0.102) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	15116424	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022781

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439182

PDB ID

Not Available

ChEBI ID

17319

Food Biomarker Ontology

Not Available

VMH ID

DAD_5

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Lerner, Leon M. An improved preparation of 5'-deoxyadenosine by coupling methods. Carbohydrate Research (1988), 184 250-3.

Material Safety Data Sheet (MSDS)

Not Available

General References

Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. [PubMed:15116424 ]

Enzymes

Enzyme Details

1. Lipoyl synthase, mitochondrial

General function:: Involved in catalytic activity
Specific function:: Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives (By similarity).
Gene Name:: LIAS
Uniprot ID:: O43766
Molecular weight:: 41910.695

Reactions

Protein N(6)-(octanoyl)lysine + Hydrogen sulfide + S-Adenosylmethionine → protein N(6)-(lipoyl)lysine + Methionine + 5'-Deoxyadenosine	details
Protein N6-(octanoyl)lysine + Sulfur donor + S-Adenosylmethionine → Protein N6-(lipoyl)lysine + Methionine + 5'-Deoxyadenosine	details
Octanoyl-[acp] + Sulfur donor + S-Adenosylmethionine → Lipoyl-[acp] + Methionine + 5'-Deoxyadenosine	details

Showing metabocard for 5'-Deoxyadenosine (HMDB0001983)

MOL for HMDB0001983 (5'-Deoxyadenosine)

3D MOL for HMDB0001983 (5'-Deoxyadenosine)

3D SDF for HMDB0001983 (5'-Deoxyadenosine)

3D-SDF for HMDB0001983 (5'-Deoxyadenosine)

PDB for HMDB0001983 (5'-Deoxyadenosine)

3D PDB for HMDB0001983 (5'-Deoxyadenosine)

SMILES for HMDB0001983 (5'-Deoxyadenosine)

INCHI for HMDB0001983 (5'-Deoxyadenosine)

Structure for HMDB0001983 (5'-Deoxyadenosine)

3D Structure for HMDB0001983 (5'-Deoxyadenosine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions