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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 21:25:46 UTC

Update Date

2021-09-26 22:51:53 UTC

HMDB ID

HMDB0244258

Secondary Accession Numbers

None

Metabolite Identification

Common Name

N6-Etheno 2'-deoxyadenosine

Description

N6-Etheno 2'-deoxyadenosine, also known as 1,N(6)-deoxyethenoadenosine, 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. Based on a literature review very few articles have been published on N6-Etheno 2'-deoxyadenosine. This compound has been identified in human blood as reported by (PMID: 31557052 ). N6-etheno 2'-deoxyadenosine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically N6-Etheno 2'-deoxyadenosine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0244258
     RDKit          3D
N6-Etheno 2'-deoxyadenosine
 33 36  0  0  0  0  0  0  0  0999 V2000
   -3.4400    1.7487    0.5784 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6963    1.0770   -0.5899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8495   -0.1550   -0.7723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4883    0.1421   -0.7925 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9167   -1.1066   -0.6317 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4942   -1.0984   -0.5050 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2789   -2.1798   -0.6618 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5706   -1.8532   -0.4790 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6345   -0.5611   -0.2029 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3339   -0.1027   -0.2222 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1296    1.1960    0.0315 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1774    2.0336    0.2996 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4542    1.5906    0.3200 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6506    2.1568    0.5445 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6398    1.2032    0.4326 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0182    0.0537    0.1369 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6986    0.3041    0.0725 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6386   -1.6121    0.6103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0755   -1.1988    0.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7783   -0.7851    1.3669 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1978    1.7989    1.1978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7641    0.7995   -0.6143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5140    1.7581   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0887   -0.5902   -1.7658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2915   -1.7448   -1.4768 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9541   -3.1924   -0.9025 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0246    3.0834    0.5058 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8093    3.1963    0.7761 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7141    1.3786    0.5645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5391   -2.6839    0.7627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3689   -1.0184    1.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5541   -2.1278   -0.1494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3814   -1.5101    1.6919 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  0
  5 25  1  0
  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  0
 20 33  1  0
M  END


  Mrv1652309102123262D          

 20 23  0  0  0  0            999 V2000
    6.1592   -0.4376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5717   -1.1521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0196   -1.7652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2660   -1.4296    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3522   -0.6091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7391   -0.0571    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8253    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0717    1.0990    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5196    0.4859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9321   -0.2286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5196   -0.9431    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6946   -0.9431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2821   -0.2286    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6946    0.4859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1426    1.0990    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3889    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4752   -0.0571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1912   -2.5721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9758   -2.8271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3922   -1.2383    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 13 17  1  0  0  0  0
  3 18  1  0  0  0  0
 18 19  1  0  0  0  0
  2 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244258

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1OC(CC1O)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

> <INCHI_KEY>
XQQIMTUYVDUWKJ-UHFFFAOYSA-N

> <FORMULA>
C12H13N5O3

> <MOLECULAR_WEIGHT>
275.268

> <EXACT_MASS>
275.101839299

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
27.489638026299804

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
97.7

> <JCHEM_REFRACTIVITY>
68.0811

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.98e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0244258
     RDKit          3D
N6-Etheno 2'-deoxyadenosine
 33 36  0  0  0  0  0  0  0  0999 V2000
   -3.4400    1.7487    0.5784 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6963    1.0770   -0.5899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8495   -0.1550   -0.7723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4883    0.1421   -0.7925 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9167   -1.1066   -0.6317 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4942   -1.0984   -0.5050 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2789   -2.1798   -0.6618 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5706   -1.8532   -0.4790 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6345   -0.5611   -0.2029 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3339   -0.1027   -0.2222 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1296    1.1960    0.0315 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1774    2.0336    0.2996 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4542    1.5906    0.3200 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6506    2.1568    0.5445 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6398    1.2032    0.4326 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0182    0.0537    0.1369 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6986    0.3041    0.0725 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6386   -1.6121    0.6103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0755   -1.1988    0.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7783   -0.7851    1.3669 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1978    1.7989    1.1978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7641    0.7995   -0.6143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5140    1.7581   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0887   -0.5902   -1.7658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2915   -1.7448   -1.4768 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9541   -3.1924   -0.9025 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0246    3.0834    0.5058 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8093    3.1963    0.7761 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7141    1.3786    0.5645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5391   -2.6839    0.7627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3689   -1.0184    1.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5541   -2.1278   -0.1494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3814   -1.5101    1.6919 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  0
  5 25  1  0
  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  0
 20 33  1  0
M  END

HEADER    PROTEIN                                 10-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-21         0                                  
HETATM    1  C   UNK     0      11.497  -0.817   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.267  -2.151   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.237  -3.295   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       9.830  -2.669   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.991  -1.137   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       8.846  -0.107   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       9.007   1.425   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       7.600   2.051   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       6.570   0.907   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.340  -0.427   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       6.570  -1.760   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       5.030  -1.760   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       4.260  -0.427   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       5.030   0.907   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       4.000   2.051   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       2.593   1.425   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.754  -0.107   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.557  -4.801   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      13.021  -5.277   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      13.799  -2.311   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3   20                                                  
CONECT    3    2    4   18                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9    6   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13    9   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   13                                                       
CONECT   18    3   19                                                       
CONECT   19   18                                                            
CONECT   20    2                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   46    0
END

COMPND    HMDB0249728
HETATM    1  O1  UNL     1       4.947   1.252   1.254  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.640   1.566   0.909  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.782   0.300   0.964  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.483   0.596   0.623  1.00  0.00           O  
HETATM    5  C3  UNL     1       0.985  -0.611   0.156  1.00  0.00           C  
HETATM    6  N1  UNL     1      -0.313  -0.485  -0.466  1.00  0.00           N  
HETATM    7  C4  UNL     1      -0.593  -0.543  -1.780  1.00  0.00           C  
HETATM    8  N2  UNL     1      -1.934  -0.379  -1.956  1.00  0.00           N  
HETATM    9  C5  UNL     1      -2.503  -0.216  -0.750  1.00  0.00           C  
HETATM   10  C6  UNL     1      -1.467  -0.287   0.160  1.00  0.00           C  
HETATM   11  N3  UNL     1      -1.747  -0.153   1.489  1.00  0.00           N  
HETATM   12  C7  UNL     1      -3.019   0.045   1.906  1.00  0.00           C  
HETATM   13  N4  UNL     1      -4.055   0.119   1.034  1.00  0.00           N  
HETATM   14  C8  UNL     1      -5.375   0.308   1.238  1.00  0.00           C  
HETATM   15  C9  UNL     1      -5.948   0.293  -0.017  1.00  0.00           C  
HETATM   16  N5  UNL     1      -4.961   0.097  -0.915  1.00  0.00           N  
HETATM   17  C10 UNL     1      -3.777  -0.012  -0.264  1.00  0.00           C  
HETATM   18  C11 UNL     1       2.048  -1.013  -0.848  1.00  0.00           C  
HETATM   19  C12 UNL     1       3.313  -0.689  -0.042  1.00  0.00           C  
HETATM   20  O3  UNL     1       4.308  -0.164  -0.828  1.00  0.00           O  
HETATM   21  H1  UNL     1       5.553   1.541   0.530  1.00  0.00           H  
HETATM   22  H2  UNL     1       3.599   1.914  -0.136  1.00  0.00           H  
HETATM   23  H3  UNL     1       3.193   2.266   1.631  1.00  0.00           H  
HETATM   24  H4  UNL     1       2.852  -0.115   1.990  1.00  0.00           H  
HETATM   25  H5  UNL     1       1.012  -1.329   0.985  1.00  0.00           H  
HETATM   26  H6  UNL     1       0.110  -0.695  -2.589  1.00  0.00           H  
HETATM   27  H7  UNL     1      -3.262   0.154   2.959  1.00  0.00           H  
HETATM   28  H8  UNL     1      -5.890   0.445   2.183  1.00  0.00           H  
HETATM   29  H9  UNL     1      -7.002   0.417  -0.226  1.00  0.00           H  
HETATM   30  H10 UNL     1       2.006  -2.067  -1.132  1.00  0.00           H  
HETATM   31  H11 UNL     1       2.008  -0.324  -1.741  1.00  0.00           H  
HETATM   32  H12 UNL     1       3.600  -1.668   0.438  1.00  0.00           H  
HETATM   33  H13 UNL     1       4.405  -0.562  -1.712  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

HMDB0244258
     RDKit          3D
N6-Etheno 2'-deoxyadenosine
 33 36  0  0  0  0  0  0  0  0999 V2000
   -3.4400    1.7487    0.5784 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6963    1.0770   -0.5899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8495   -0.1550   -0.7723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4883    0.1421   -0.7925 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9167   -1.1066   -0.6317 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4942   -1.0984   -0.5050 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2789   -2.1798   -0.6618 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5706   -1.8532   -0.4790 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6345   -0.5611   -0.2029 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3339   -0.1027   -0.2222 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1296    1.1960    0.0315 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1774    2.0336    0.2996 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4542    1.5906    0.3200 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6506    2.1568    0.5445 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6398    1.2032    0.4326 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0182    0.0537    0.1369 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6986    0.3041    0.0725 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6386   -1.6121    0.6103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0755   -1.1988    0.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7783   -0.7851    1.3669 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1978    1.7989    1.1978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7641    0.7995   -0.6143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5140    1.7581   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0887   -0.5902   -1.7658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2915   -1.7448   -1.4768 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9541   -3.1924   -0.9025 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0246    3.0834    0.5058 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8093    3.1963    0.7761 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7141    1.3786    0.5645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5391   -2.6839    0.7627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3689   -1.0184    1.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5541   -2.1278   -0.1494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3814   -1.5101    1.6919 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  0
  5 25  1  0
  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  0
 20 33  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

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

Chemical Formula

C₁₂H₁₃N₅O₃

Average Molecular Weight

275.268

Monoisotopic Molecular Weight

275.101839299

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OCC1OC(CC1O)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

InChI Key

XQQIMTUYVDUWKJ-UHFFFAOYSA-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
Oxolane
Imidazole
Azole
Secondary alcohol
Oxacycle
Azacycle
Organic nitrogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

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
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	27.49 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
DeepCCS	[M-2H]-	185.656	30932474
DeepCCS	[M+Na]+	161.221	30932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
N6-Etheno 2'-deoxyadenosine,1TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O	2878.5	Semi standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,1TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O	2878.0	Standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,1TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O	4427.9	Standard polar	33892256
N6-Etheno 2'-deoxyadenosine,1TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=NC3=C2N=CN2C=CN=C32)OC1CO	2885.3	Semi standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,1TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=NC3=C2N=CN2C=CN=C32)OC1CO	2852.8	Standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,1TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=NC3=C2N=CN2C=CN=C32)OC1CO	4406.9	Standard polar	33892256
N6-Etheno 2'-deoxyadenosine,2TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O[Si](C)(C)C	2851.0	Semi standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,2TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O[Si](C)(C)C	2877.1	Standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,2TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O[Si](C)(C)C	3818.5	Standard polar	33892256
N6-Etheno 2'-deoxyadenosine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O	3092.4	Semi standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O	3125.0	Standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O	4433.2	Standard polar	33892256
N6-Etheno 2'-deoxyadenosine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=NC3=C2N=CN2C=CN=C32)OC1CO	3100.1	Semi standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=NC3=C2N=CN2C=CN=C32)OC1CO	3097.7	Standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=NC3=C2N=CN2C=CN=C32)OC1CO	4403.0	Standard polar	33892256
N6-Etheno 2'-deoxyadenosine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O[Si](C)(C)C(C)(C)C	3271.9	Semi standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O[Si](C)(C)C(C)(C)C	3359.5	Standard non polar	33892256
N6-Etheno 2'-deoxyadenosine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C2N=CN2C=CN=C32)CC1O[Si](C)(C)C(C)(C)C	3860.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Etheno 2'-deoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	splash10-054o-9170000000-59787ef95e13965a6f74	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Etheno 2'-deoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Etheno 2'-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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N6-Etheno 2'-deoxyadenosine 10V, Negative-QTOF	splash10-00di-0190000000-bf4918a4b52f776c05be	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N6-Etheno 2'-deoxyadenosine 20V, Negative-QTOF	splash10-0a4i-0900000000-9997b969fd66d57e3889	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N6-Etheno 2'-deoxyadenosine 40V, Negative-QTOF	splash10-0a4i-0900000000-4b150844edbbd4e15f69	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N6-Etheno 2'-deoxyadenosine 10V, Positive-QTOF	splash10-03di-0900000000-491bffd5eb2009008d64	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N6-Etheno 2'-deoxyadenosine 20V, Positive-QTOF	splash10-03di-0900000000-491bffd5eb2009008d64	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N6-Etheno 2'-deoxyadenosine 40V, Positive-QTOF	splash10-03di-0900000000-d0145665222b050d7b7c	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

3458967

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

4250940

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

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for N6-Etheno 2'-deoxyadenosine (HMDB0244258)

MOL for HMDB0244258 (N6-Etheno 2'-deoxyadenosine)

3D MOL for HMDB0244258 (N6-Etheno 2'-deoxyadenosine)

3D SDF for HMDB0244258 (N6-Etheno 2'-deoxyadenosine)

3D-SDF for HMDB0244258 (N6-Etheno 2'-deoxyadenosine)

PDB for HMDB0244258 (N6-Etheno 2'-deoxyadenosine)

3D PDB for HMDB0244258 (N6-Etheno 2'-deoxyadenosine)

SMILES for HMDB0244258 (N6-Etheno 2'-deoxyadenosine)

INCHI for HMDB0244258 (N6-Etheno 2'-deoxyadenosine)

Structure for HMDB0244258 (N6-Etheno 2'-deoxyadenosine)

3D Structure for HMDB0244258 (N6-Etheno 2'-deoxyadenosine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra