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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2005-11-20 22:13:26 UTC

Update Date

2021-09-14 15:44:42 UTC

HMDB ID

HMDB0001786

Secondary Accession Numbers

HMDB01786

Metabolite Identification

Common Name

Ethenodeoxyadenosine

Description

Etheno nucleosides are a new class of chemically modified components of nucleic acids. These base-modified nucleosides demonstrate significant biological properties, acting, among others, as antiviral or antitumor agents. One of the possible modifications of the nucleoside is their transformation into ethenonucleosides. Thus, nucleosides or their respective heterocyclic bases, possessing an exocyclic amino group, as well as a neighboring endocyclic nitrogen, can react with some bifunctional reagents (e.g., α-halocarbonyl compounds) to form products with an additional five-membered ring of the imidazole type. The ethenonucleosides basically do not occur in nature; some of the only exceptions are Y-nucleosides. Etheno modified DNA bases are generated from the carcinogens vinyl chloride and urethane, but also by reactions of DNA with products derived from lipid peroxidation (LPO) and oxidative stress via endogenous pathways. Highly variable background levels of epsilon-adducts were detected in DNA from different organs of unexposed humans and rodents. Several known cancer risk factors increased the level of these DNA lesions in target organs: elevated epsilon-adducts were found in hepatic DNA from patients with metal storage diseases, after overproduction of nitric oxide (NO) by inducible NO synthase (iNOS) in a mouse model, and in colonic polyps of familial adenomatous polyposis patients. A high omega-6-polyunsaturated fatty acid diet increased epsilon-DNA adducts in white blood cells of female subjects. (PMID:10882861 ).

Structure

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

HMDB0001786
     RDKit          3D
Ethenodeoxyadenosine
 33 36  0  0  0  0  0  0  0  0999 V2000
   -3.6925    1.1587   -1.6983 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9862   -0.1365   -1.3473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0923   -0.6877   -0.2740 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7673   -0.6787   -0.6854 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9743   -0.7708    0.4309 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2023    0.0994    0.3626 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2676    1.4083    0.6347 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5403    1.8537    0.4524 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2957    0.8233    0.0608 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4460   -0.2709    0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9666   -1.4648   -0.3676 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2715   -1.5719   -0.6780 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0818   -0.4989   -0.6213 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4113   -0.3628   -0.8839 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7966    0.9473   -0.6819 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6581    1.5909   -0.2907 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6358    0.7168   -0.2572 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7887   -0.3348    1.6215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0584    0.1604    0.9594 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1712   -0.0268    1.7734 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5323    1.6896   -1.8768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0518   -0.2794   -1.0619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8328   -0.7848   -2.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4563   -1.7032   -0.0261 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6856   -1.8259    0.5651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5376    2.0465    0.9514 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7156   -2.5262   -0.9845 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0708   -1.1524   -1.2017 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7855    1.3572   -0.8096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0616   -1.2195    2.2472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2817    0.4491    2.2107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9508    1.2348    0.6687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2239    0.7600    2.3743 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  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
  5 18  1  0
 18 19  1  0
 19 20  1  0
 19  3  1  0
 10  6  1  0
 17 13  1  0
 17  9  1  0
  1 21  1  0
  2 22  1  0
  2 23  1  0
  3 24  1  1
  5 25  1  1
  7 26  1  0
 12 27  1  0
 14 28  1  0
 15 29  1  0
 18 30  1  0
 18 31  1  0
 19 32  1  6
 20 33  1  0
M  END


  Mrv1652305271900112D          

 20 23  0  0  1  0            999 V2000
   16.4580   -7.9769    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.7225   -7.7383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7225   -6.9382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4580   -6.6947    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.9252   -7.3408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0119   -6.5307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0119   -8.1409    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.3409   -6.9382    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.3409   -7.7383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0119   -5.7454    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.4580   -9.2590    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.1113   -9.2590    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.7971   -8.7769    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3796  -10.0542    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.2046  -10.0542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8827  -10.7152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3261   -9.0056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7049   -9.5622    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.6871   -6.3410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0990   -5.4969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  5  1  1  0  0  0  0
 11  1  1  1  0  0  0
  3  2  2  0  0  0  0
  7  2  1  0  0  0  0
  6  3  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  2  0  0  0  0
 10  6  2  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
  9  8  1  0  0  0  0
 13 11  1  0  0  0  0
 15 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14 12  1  0  0  0  0
 12 17  1  1  0  0  0
 15 14  1  0  0  0  0
 14 16  1  6  0  0  0
 18 17  1  0  0  0  0
 19  8  1  0  0  0  0
 20 10  1  0  0  0  0
 20 19  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001786

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN1C=CN=C21

> <INCHI_IDENTIFIER>
InChI=1S/C12H13N5O3/c18-4-8-7(19)3-9(20-8)17-6-14-10-11-13-1-2-16(11)5-15-12(10)17/h1-2,5-9,18-19H,3-4H2/t7-,8+,9+/m0/s1

> <INCHI_KEY>
XQQIMTUYVDUWKJ-DJLDLDEBSA-N

> <FORMULA>
C12H13N5O3

> <MOLECULAR_WEIGHT>
275.2633

> <EXACT_MASS>
275.101839307

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
27.098075913275682

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,5R)-2-(hydroxymethyl)-5-{3H-imidazo[2,1-f]purin-3-yl}oxolan-3-ol

> <ALOGPS_LOGP>
-1.07

> <JCHEM_LOGP>
-1.4443975519999996

> <ALOGPS_LOGS>
-1.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.785104069805804

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.8867434595094

> <JCHEM_PKA_STRONGEST_BASIC>
4.959729910909882

> <JCHEM_POLAR_SURFACE_AREA>
97.70000000000002

> <JCHEM_REFRACTIVITY>
68.08109999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.98e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ethenodeoxyadenosine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001786
     RDKit          3D
Ethenodeoxyadenosine
 33 36  0  0  0  0  0  0  0  0999 V2000
   -3.6925    1.1587   -1.6983 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9862   -0.1365   -1.3473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0923   -0.6877   -0.2740 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7673   -0.6787   -0.6854 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9743   -0.7708    0.4309 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2023    0.0994    0.3626 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2676    1.4083    0.6347 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5403    1.8537    0.4524 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2957    0.8233    0.0608 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4460   -0.2709    0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9666   -1.4648   -0.3676 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2715   -1.5719   -0.6780 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0818   -0.4989   -0.6213 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4113   -0.3628   -0.8839 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7966    0.9473   -0.6819 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6581    1.5909   -0.2907 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6358    0.7168   -0.2572 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7887   -0.3348    1.6215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0584    0.1604    0.9594 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1712   -0.0268    1.7734 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5323    1.6896   -1.8768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0518   -0.2794   -1.0619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8328   -0.7848   -2.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4563   -1.7032   -0.0261 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6856   -1.8259    0.5651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5376    2.0465    0.9514 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7156   -2.5262   -0.9845 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0708   -1.1524   -1.2017 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7855    1.3572   -0.8096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0616   -1.2195    2.2472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2817    0.4491    2.2107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9508    1.2348    0.6687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2239    0.7600    2.3743 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  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
  5 18  1  0
 18 19  1  0
 19 20  1  0
 19  3  1  0
 10  6  1  0
 17 13  1  0
 17  9  1  0
  1 21  1  0
  2 22  1  0
  2 23  1  0
  3 24  1  1
  5 25  1  1
  7 26  1  0
 12 27  1  0
 14 28  1  0
 15 29  1  0
 18 30  1  0
 18 31  1  0
 19 32  1  6
 20 33  1  0
M  END

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  N   UNK     0      30.722 -14.890   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      29.349 -14.445   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      29.349 -12.951   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      30.722 -12.497   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      31.594 -13.703   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      28.022 -12.191   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      28.022 -15.196   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      26.770 -12.951   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      26.770 -14.445   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      28.022 -10.725   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      30.722 -17.283   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      28.208 -17.283   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      29.488 -16.384   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      28.709 -18.768   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      30.249 -18.768   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      27.781 -20.002   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      26.742 -16.810   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      25.582 -17.849   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      25.549 -11.837   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      26.318 -10.261   0.000  0.00  0.00           C+0
CONECT    1    2    5   11                                                  
CONECT    2    1    3    7                                                  
CONECT    3    2    6    4                                                  
CONECT    4    3    5                                                       
CONECT    5    1    4                                                       
CONECT    6    3   10    8                                                  
CONECT    7    2    9                                                       
CONECT    8    6    9   19                                                  
CONECT    9    7    8                                                       
CONECT   10    6   20                                                       
CONECT   11    1   13   15                                                  
CONECT   12   13   14   17                                                  
CONECT   13   11   12                                                       
CONECT   14   12   15   16                                                  
CONECT   15   11   14                                                       
CONECT   16   14                                                            
CONECT   17   12   18                                                       
CONECT   18   17                                                            
CONECT   19    8   20                                                       
CONECT   20   10   19                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   46    0
END

COMPND    HMDB0001786
HETATM    1  O1  UNL     1      -3.693   1.159  -1.698  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.986  -0.136  -1.347  1.00  0.00           C  
HETATM    3  C2  UNL     1      -3.092  -0.688  -0.274  1.00  0.00           C  
HETATM    4  O2  UNL     1      -1.767  -0.679  -0.685  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.974  -0.771   0.431  1.00  0.00           C  
HETATM    6  N1  UNL     1       0.202   0.099   0.363  1.00  0.00           N  
HETATM    7  C4  UNL     1       0.268   1.408   0.635  1.00  0.00           C  
HETATM    8  N2  UNL     1       1.540   1.854   0.452  1.00  0.00           N  
HETATM    9  C5  UNL     1       2.296   0.823   0.061  1.00  0.00           C  
HETATM   10  C6  UNL     1       1.446  -0.271   0.008  1.00  0.00           C  
HETATM   11  N3  UNL     1       1.967  -1.465  -0.368  1.00  0.00           N  
HETATM   12  C7  UNL     1       3.271  -1.572  -0.678  1.00  0.00           C  
HETATM   13  N4  UNL     1       4.082  -0.499  -0.621  1.00  0.00           N  
HETATM   14  C8  UNL     1       5.411  -0.363  -0.884  1.00  0.00           C  
HETATM   15  C9  UNL     1       5.797   0.947  -0.682  1.00  0.00           C  
HETATM   16  N5  UNL     1       4.658   1.591  -0.291  1.00  0.00           N  
HETATM   17  C10 UNL     1       3.636   0.717  -0.257  1.00  0.00           C  
HETATM   18  C11 UNL     1      -1.789  -0.335   1.621  1.00  0.00           C  
HETATM   19  C12 UNL     1      -3.058   0.160   0.959  1.00  0.00           C  
HETATM   20  O3  UNL     1      -4.171  -0.027   1.773  1.00  0.00           O  
HETATM   21  H1  UNL     1      -4.532   1.690  -1.877  1.00  0.00           H  
HETATM   22  H2  UNL     1      -5.052  -0.279  -1.062  1.00  0.00           H  
HETATM   23  H3  UNL     1      -3.833  -0.785  -2.255  1.00  0.00           H  
HETATM   24  H4  UNL     1      -3.456  -1.703  -0.026  1.00  0.00           H  
HETATM   25  H5  UNL     1      -0.686  -1.826   0.565  1.00  0.00           H  
HETATM   26  H6  UNL     1      -0.538   2.046   0.951  1.00  0.00           H  
HETATM   27  H7  UNL     1       3.716  -2.526  -0.984  1.00  0.00           H  
HETATM   28  H8  UNL     1       6.071  -1.152  -1.202  1.00  0.00           H  
HETATM   29  H9  UNL     1       6.785   1.357  -0.810  1.00  0.00           H  
HETATM   30  H10 UNL     1      -2.062  -1.219   2.247  1.00  0.00           H  
HETATM   31  H11 UNL     1      -1.282   0.449   2.211  1.00  0.00           H  
HETATM   32  H12 UNL     1      -2.951   1.235   0.669  1.00  0.00           H  
HETATM   33  H13 UNL     1      -4.224   0.760   2.374  1.00  0.00           H  
CONECT    1    2   21
CONECT    2    3   22   23
CONECT    3    4   19   24
CONECT    4    5
CONECT    5    6   18   25
CONECT    6    7   10
CONECT    7    8    8   26
CONECT    8    9
CONECT    9   10   10   17
CONECT   10   11
CONECT   11   12   12
CONECT   12   13   27
CONECT   13   14   17
CONECT   14   15   15   28
CONECT   15   16   29
CONECT   16   17   17
CONECT   18   19   30   31
CONECT   19   20   32
CONECT   20   33
END

HMDB0001786
     RDKit          3D
Ethenodeoxyadenosine
 33 36  0  0  0  0  0  0  0  0999 V2000
   -3.6925    1.1587   -1.6983 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9862   -0.1365   -1.3473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0923   -0.6877   -0.2740 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7673   -0.6787   -0.6854 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9743   -0.7708    0.4309 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2023    0.0994    0.3626 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2676    1.4083    0.6347 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5403    1.8537    0.4524 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2957    0.8233    0.0608 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4460   -0.2709    0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9666   -1.4648   -0.3676 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2715   -1.5719   -0.6780 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0818   -0.4989   -0.6213 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4113   -0.3628   -0.8839 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7966    0.9473   -0.6819 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6581    1.5909   -0.2907 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6358    0.7168   -0.2572 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7887   -0.3348    1.6215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0584    0.1604    0.9594 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1712   -0.0268    1.7734 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5323    1.6896   -1.8768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0518   -0.2794   -1.0619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8328   -0.7848   -2.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4563   -1.7032   -0.0261 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6856   -1.8259    0.5651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5376    2.0465    0.9514 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7156   -2.5262   -0.9845 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0708   -1.1524   -1.2017 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7855    1.3572   -0.8096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0616   -1.2195    2.2472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2817    0.4491    2.2107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9508    1.2348    0.6687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2239    0.7600    2.3743 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  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
  5 18  1  0
 18 19  1  0
 19 20  1  0
 19  3  1  0
 10  6  1  0
 17 13  1  0
 17  9  1  0
  1 21  1  0
  2 22  1  0
  2 23  1  0
  3 24  1  1
  5 25  1  1
  7 26  1  0
 12 27  1  0
 14 28  1  0
 15 29  1  0
 18 30  1  0
 18 31  1  0
 19 32  1  6
 20 33  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1,N(6)-Deoxyethenoadenosine	MeSH
1,N(6)-Ethenodeoxyadenosine	MeSH
1,N2-Etheno-2'-deoxyguanosine	MeSH
1,N6-Etheno-2'-deoxyadenosine	MeSH
2'-Deoxy-2-deuteroethenoadenosine	MeSH
1,N6-etheno-DA	HMDB
1,N6-Ethenodeoxyadenosine	HMDB
N1,N6-etheno-2'-Deoxyadenosine	HMDB

Chemical Formula

C₁₂H₁₃N₅O₃

Average Molecular Weight

275.2633

Monoisotopic Molecular Weight

275.101839307

IUPAC Name

(2R,3S,5R)-2-(hydroxymethyl)-5-{3H-imidazo[2,1-f]purin-3-yl}oxolan-3-ol

Traditional Name

ethenodeoxyadenosine

CAS Registry Number

68498-25-9

SMILES

OC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN1C=CN=C21

InChI Identifier

InChI=1S/C12H13N5O3/c18-4-8-7(19)3-9(20-8)17-6-14-10-11-13-1-2-16(11)5-15-12(10)17/h1-2,5-9,18-19H,3-4H2/t7-,8+,9+/m0/s1

InChI Key

XQQIMTUYVDUWKJ-DJLDLDEBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purines and purine derivatives. These are aromatic heterocyclic compounds containing a purine moiety, which is formed a pyrimidine-ring ring fused to an imidazole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyrimidines

Sub Class

Purines and purine derivatives

Direct Parent

Purines and purine derivatives

Alternative Parents

Substituents

Purine
N-substituted imidazole
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Imidazole
Azole
Secondary alcohol
Oxacycle
Azacycle
Hydrocarbon derivative
Organic nitrogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Organopnictogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	5.98 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-1.4	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	4.96	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	97.7 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	68.08 m³·mol⁻¹	ChemAxon
Polarizability	27.1 Å³	ChemAxon
Number of Rings	4	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]+	160.503	31661259
DarkChem	[M-H]-	160.609	31661259
AllCCS	[M+H]+	163.113	32859911
AllCCS	[M-H]-	164.291	32859911
DeepCCS	[M-2H]-	187.323	30932474
DeepCCS	[M+Na]+	162.532	30932474
AllCCS	[M+H]+	163.1	32859911
AllCCS	[M+H-H2O]+	159.6	32859911
AllCCS	[M+NH4]+	166.4	32859911
AllCCS	[M+Na]+	167.4	32859911
AllCCS	[M-H]-	164.3	32859911
AllCCS	[M+Na-2H]-	163.6	32859911
AllCCS	[M+HCOO]-	162.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Ethenodeoxyadenosine	OC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN1C=CN=C21	3268.0	Standard polar	33892256
Ethenodeoxyadenosine	OC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN1C=CN=C21	2433.1	Standard non polar	33892256
Ethenodeoxyadenosine	OC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN1C=CN=C21	2913.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Ethenodeoxyadenosine,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C2N=CN2C=CN=C32)C[C@@H]1O	2871.0	Semi standard non polar	33892256
Ethenodeoxyadenosine,1TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=NC3=C2N=CN2C=CN=C32)O[C@@H]1CO	2870.0	Semi standard non polar	33892256
Ethenodeoxyadenosine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C2N=CN2C=CN=C32)C[C@@H]1O[Si](C)(C)C	2871.5	Semi standard non polar	33892256
Ethenodeoxyadenosine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C2N=CN2C=CN=C32)C[C@@H]1O	3086.1	Semi standard non polar	33892256
Ethenodeoxyadenosine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=NC3=C2N=CN2C=CN=C32)O[C@@H]1CO	3087.4	Semi standard non polar	33892256
Ethenodeoxyadenosine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C2N=CN2C=CN=C32)C[C@@H]1O[Si](C)(C)C(C)(C)C	3292.3	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Ethenodeoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	splash10-054o-9170000000-59787ef95e13965a6f74	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ethenodeoxyadenosine GC-MS (2 TMS) - 70eV, Positive	splash10-0v4i-9855100000-1aa19e03cd5abf43bec2	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ethenodeoxyadenosine 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 - Ethenodeoxyadenosine Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-004i-0090000000-1cbcf897b8d539f74c9d	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ethenodeoxyadenosine Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-03di-0900000000-7351b3ecaf69532e4ae9	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ethenodeoxyadenosine Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-03di-1900000000-cea99433c51ea3b57b8c	2012-07-24	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 10V, Positive-QTOF	splash10-03di-0920000000-4723a3e7bccfd3fb82a3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 20V, Positive-QTOF	splash10-03di-0900000000-319e0450fd20aa8b295f	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 40V, Positive-QTOF	splash10-03di-0900000000-123c329a87834ac8c719	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 10V, Negative-QTOF	splash10-00di-0290000000-8d53e894625170dfa26f	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 20V, Negative-QTOF	splash10-0a4i-0910000000-c8a7d5a2ae45462ace75	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 40V, Negative-QTOF	splash10-0a4i-0900000000-944674f1809414d8aa98	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 10V, Positive-QTOF	splash10-03di-0900000000-491bffd5eb2009008d64	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 20V, Positive-QTOF	splash10-03di-0900000000-491bffd5eb2009008d64	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 40V, Positive-QTOF	splash10-03di-0900000000-d0145665222b050d7b7c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 10V, Negative-QTOF	splash10-00di-0190000000-bf4918a4b52f776c05be	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 20V, Negative-QTOF	splash10-0a4i-0900000000-9997b969fd66d57e3889	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 40V, Negative-QTOF	splash10-0a4i-0900000000-614f89543dcac00da239	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, 5%_DMSO, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

FDB022701

KNApSAcK ID

Not Available

Chemspider ID

9120894

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6339

PubChem Compound

10945668

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Schmid K; Nair J; Winde G; Velic I; Bartsch H Increased levels of promutagenic etheno-DNA adducts in colonic polyps of FAP patients. International journal of cancer. Journal international du cancer (2000), 87(1), 1-4.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Hanaoka T, Nair J, Takahashi Y, Sasaki S, Bartsch H, Tsugane S: Urinary level of 1,N(6) -ethenodeoxyadenosine, a marker of oxidative stress, is associated with salt excretion and omega 6-polyunsaturated fatty acid intake in postmenopausal Japanese women. Int J Cancer. 2002 Jul 1;100(1):71-5. [PubMed:12115589 ]
Hillestrom PR, Nyssonen K, Tuomainen TP, Pukkala E, Salonen JT, Poulsen HE: Urinary excretion of epsilondA is not predictive of cancer development: a prospective nested case-control study. Free Radic Res. 2005 Jan;39(1):51-3. [PubMed:15875811 ]
Bartsch H, Nair J: New DNA-based biomarkers for oxidative stress and cancer chemoprevention studies. Eur J Cancer. 2000 Jun;36(10):1229-34. [PubMed:10882861 ]

Showing metabocard for Ethenodeoxyadenosine (HMDB0001786)

MOL for HMDB0001786 (Ethenodeoxyadenosine)

3D MOL for HMDB0001786 (Ethenodeoxyadenosine)

3D SDF for HMDB0001786 (Ethenodeoxyadenosine)

3D-SDF for HMDB0001786 (Ethenodeoxyadenosine)

PDB for HMDB0001786 (Ethenodeoxyadenosine)

3D PDB for HMDB0001786 (Ethenodeoxyadenosine)

SMILES for HMDB0001786 (Ethenodeoxyadenosine)

INCHI for HMDB0001786 (Ethenodeoxyadenosine)

Structure for HMDB0001786 (Ethenodeoxyadenosine)

3D Structure for HMDB0001786 (Ethenodeoxyadenosine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra