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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:07:23 UTC

Update Date

2021-09-26 22:54:56 UTC

HMDB ID

HMDB0246084

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3,N(4)-Ethenodeoxycytidine

Description

3,N(4)-Ethenodeoxycytidine belongs to the class of organic compounds known as imidazopyrimidines. These are organic polycyclic compounds containing an imidazole ring fused to a pyrimidine ring. Imidazole is 5-membered ring consisting of three carbon atoms, and two nitrogen centers at the 1- and 3-positions. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Based on a literature review a significant number of articles have been published on 3,N(4)-Ethenodeoxycytidine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3,n(4)-ethenodeoxycytidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3,N(4)-Ethenodeoxycytidine 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

HMDB0246084
     RDKit          3D
3,N(4)-Ethenodeoxycytidine
 31 33  0  0  0  0  0  0  0  0999 V2000
    1.2794    1.6767   -0.9838 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7169    0.6587   -0.3446 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8633   -0.3077    0.0512 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5152   -0.1345   -0.2746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3252   -1.4048   -0.2570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7325   -0.8074   -0.4098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9731   -0.7456   -1.7807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5226    0.6100    0.0767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4517    0.9296    1.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7731    0.8947    0.8286 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2220    0.6710    0.5877 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3521   -1.3657    0.7212 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7081   -1.4424    0.9894 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5324   -0.4250    0.5603 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8479   -0.2391    0.6756 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2036    0.9179    0.0909 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0499    1.4621   -0.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0368    0.6244   -0.1060 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6574    0.3033   -1.3060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3072   -1.8975    0.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0834   -2.1001   -1.0632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4817   -1.3617    0.1505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6187    0.1074   -2.1705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5846    1.3456   -0.7269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3147    0.2345    2.0749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1808    1.9483    1.5998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7991    0.5256   -0.0877 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6922   -2.1482    1.0468 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1454   -2.2802    1.5282 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2015    1.3578    0.0121 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9134    2.3924   -0.9441 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
  3 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18  2  1  0
 11  4  1  0
 18 14  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  0
 12 28  1  0
 13 29  1  0
 16 30  1  0
 17 31  1  0
M  END

  Mrv1652309112101072D          

 18 20  0  0  0  0            999 V2000
    4.1530    3.1684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9600    3.3400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3725    2.6255    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8204    2.0124    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1929    2.5392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6779    3.2067    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2955    4.0936    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
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
  9 13  1  0  0  0  0
 13 14  1  0  0  0  0
  6 14  1  0  0  0  0
 14 15  2  0  0  0  0
  3 16  1  0  0  0  0
 16 17  1  0  0  0  0
  2 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246084

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1OC(CC1O)N1C=CC2=NC=CN2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H13N3O4/c15-6-8-7(16)5-10(18-8)14-3-1-9-12-2-4-13(9)11(14)17/h1-4,7-8,10,15-16H,5-6H2

> <INCHI_KEY>
UFLBVEMEAYZXKY-UHFFFAOYSA-N

> <FORMULA>
C11H13N3O4

> <MOLECULAR_WEIGHT>
251.242

> <EXACT_MASS>
251.090605911

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
24.479478917673823

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5H,6H-imidazo[1,2-c]pyrimidin-5-one

> <ALOGPS_LOGP>
-1.11

> <JCHEM_LOGP>
-0.7307077566666667

> <ALOGPS_LOGS>
-1.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.787551901403909

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.894911536147799

> <JCHEM_PKA_STRONGEST_BASIC>
-0.03542453083463193

> <JCHEM_POLAR_SURFACE_AREA>
87.82000000000001

> <JCHEM_REFRACTIVITY>
59.746900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.46e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazo[1,2-c]pyrimidin-5-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0246084
     RDKit          3D
3,N(4)-Ethenodeoxycytidine
 31 33  0  0  0  0  0  0  0  0999 V2000
    1.2794    1.6767   -0.9838 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7169    0.6587   -0.3446 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8633   -0.3077    0.0512 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5152   -0.1345   -0.2746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3252   -1.4048   -0.2570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7325   -0.8074   -0.4098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9731   -0.7456   -1.7807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5226    0.6100    0.0767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4517    0.9296    1.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7731    0.8947    0.8286 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2220    0.6710    0.5877 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3521   -1.3657    0.7212 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7081   -1.4424    0.9894 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5324   -0.4250    0.5603 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8479   -0.2391    0.6756 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2036    0.9179    0.0909 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0499    1.4621   -0.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0368    0.6244   -0.1060 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6574    0.3033   -1.3060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3072   -1.8975    0.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0834   -2.1001   -1.0632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4817   -1.3617    0.1505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6187    0.1074   -2.1705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5846    1.3456   -0.7269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3147    0.2345    2.0749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1808    1.9483    1.5998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7991    0.5256   -0.0877 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6922   -2.1482    1.0468 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1454   -2.2802    1.5282 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2015    1.3578    0.0121 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9134    2.3924   -0.9441 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
  3 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18  2  1  0
 11  4  1  0
 18 14  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  0
 12 28  1  0
 13 29  1  0
 16 30  1  0
 17 31  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       7.752   5.914   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.259   6.235   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.029   4.901   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.998   3.756   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.591   4.383   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       6.258   3.613   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       3.590   3.613   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.924   5.923   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      11.560   4.740   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      12.465   5.986   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       9.885   7.641   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3   18                                                  
CONECT    3    2    4   16                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7   14                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    9   14                                                  
CONECT   14   13    6   15                                                  
CONECT   15   14                                                            
CONECT   16    3   17                                                       
CONECT   17   16                                                            
CONECT   18    2                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0246084
HETATM    1  O1  UNL     1       1.279   1.677  -0.984  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.717   0.659  -0.345  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.863  -0.308   0.051  1.00  0.00           N  
HETATM    4  C2  UNL     1      -0.515  -0.134  -0.275  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.325  -1.405  -0.257  1.00  0.00           C  
HETATM    6  C4  UNL     1      -2.733  -0.807  -0.410  1.00  0.00           C  
HETATM    7  O2  UNL     1      -2.973  -0.746  -1.781  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.523   0.610   0.077  1.00  0.00           C  
HETATM    9  C6  UNL     1      -3.452   0.930   1.233  1.00  0.00           C  
HETATM   10  O3  UNL     1      -4.773   0.895   0.829  1.00  0.00           O  
HETATM   11  O4  UNL     1      -1.222   0.671   0.588  1.00  0.00           O  
HETATM   12  C7  UNL     1       1.352  -1.366   0.721  1.00  0.00           C  
HETATM   13  C8  UNL     1       2.708  -1.442   0.989  1.00  0.00           C  
HETATM   14  C9  UNL     1       3.532  -0.425   0.560  1.00  0.00           C  
HETATM   15  N2  UNL     1       4.848  -0.239   0.676  1.00  0.00           N  
HETATM   16  C10 UNL     1       5.204   0.918   0.091  1.00  0.00           C  
HETATM   17  C11 UNL     1       4.050   1.462  -0.404  1.00  0.00           C  
HETATM   18  N3  UNL     1       3.037   0.624  -0.106  1.00  0.00           N  
HETATM   19  H1  UNL     1      -0.657   0.303  -1.306  1.00  0.00           H  
HETATM   20  H2  UNL     1      -1.307  -1.898   0.745  1.00  0.00           H  
HETATM   21  H3  UNL     1      -1.083  -2.100  -1.063  1.00  0.00           H  
HETATM   22  H4  UNL     1      -3.482  -1.362   0.150  1.00  0.00           H  
HETATM   23  H5  UNL     1      -2.619   0.107  -2.171  1.00  0.00           H  
HETATM   24  H6  UNL     1      -2.585   1.346  -0.727  1.00  0.00           H  
HETATM   25  H7  UNL     1      -3.315   0.235   2.075  1.00  0.00           H  
HETATM   26  H8  UNL     1      -3.181   1.948   1.600  1.00  0.00           H  
HETATM   27  H9  UNL     1      -4.799   0.526  -0.088  1.00  0.00           H  
HETATM   28  H10 UNL     1       0.692  -2.148   1.047  1.00  0.00           H  
HETATM   29  H11 UNL     1       3.145  -2.280   1.528  1.00  0.00           H  
HETATM   30  H12 UNL     1       6.202   1.358   0.012  1.00  0.00           H  
HETATM   31  H13 UNL     1       3.913   2.392  -0.944  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   18
CONECT    3    4   12
CONECT    4    5   11   19
CONECT    5    6   20   21
CONECT    6    7    8   22
CONECT    7   23
CONECT    8    9   11   24
CONECT    9   10   25   26
CONECT   10   27
CONECT   12   13   13   28
CONECT   13   14   29
CONECT   14   15   15   18
CONECT   15   16
CONECT   16   17   17   30
CONECT   17   18   31
END

HMDB0246084
     RDKit          3D
3,N(4)-Ethenodeoxycytidine
 31 33  0  0  0  0  0  0  0  0999 V2000
    1.2794    1.6767   -0.9838 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7169    0.6587   -0.3446 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8633   -0.3077    0.0512 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5152   -0.1345   -0.2746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3252   -1.4048   -0.2570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7325   -0.8074   -0.4098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9731   -0.7456   -1.7807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5226    0.6100    0.0767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4517    0.9296    1.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7731    0.8947    0.8286 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2220    0.6710    0.5877 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3521   -1.3657    0.7212 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7081   -1.4424    0.9894 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5324   -0.4250    0.5603 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8479   -0.2391    0.6756 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2036    0.9179    0.0909 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0499    1.4621   -0.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0368    0.6244   -0.1060 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6574    0.3033   -1.3060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3072   -1.8975    0.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0834   -2.1001   -1.0632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4817   -1.3617    0.1505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6187    0.1074   -2.1705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5846    1.3456   -0.7269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3147    0.2345    2.0749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1808    1.9483    1.5998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7991    0.5256   -0.0877 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6922   -2.1482    1.0468 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1454   -2.2802    1.5282 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2015    1.3578    0.0121 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9134    2.3924   -0.9441 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
  3 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18  2  1  0
 11  4  1  0
 18 14  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  0
 12 28  1  0
 13 29  1  0
 16 30  1  0
 17 31  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₁H₁₃N₃O₄

Average Molecular Weight

251.242

Monoisotopic Molecular Weight

251.090605911

IUPAC Name

6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5H,6H-imidazo[1,2-c]pyrimidin-5-one

Traditional Name

6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazo[1,2-c]pyrimidin-5-one

CAS Registry Number

Not Available

SMILES

OCC1OC(CC1O)N1C=CC2=NC=CN2C1=O

InChI Identifier

InChI=1S/C11H13N3O4/c15-6-8-7(16)5-10(18-8)14-3-1-9-12-2-4-13(9)11(14)17/h1-4,7-8,10,15-16H,5-6H2

InChI Key

UFLBVEMEAYZXKY-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as imidazopyrimidines. These are organic polycyclic compounds containing an imidazole ring fused to a pyrimidine ring. Imidazole is 5-membered ring consisting of three carbon atoms, and two nitrogen centers at the 1- and 3-positions. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyrimidines

Sub Class

Not Available

Direct Parent

Imidazopyrimidines

Alternative Parents

Substituents

Imidazopyrimidinone
Imidazopyrimidine
Pyrimidone
N-substituted imidazole
Pyrimidine
Heteroaromatic compound
Azole
Imidazole
Oxolane
Urea
Secondary alcohol
Oxacycle
Azacycle
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxygen compound
Organic nitrogen compound
Primary alcohol
Organic oxide
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)

Source

Exogenous

Exogenous (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	-0.73	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	-0.035	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	87.82 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	59.75 m³·mol⁻¹	ChemAxon
Polarizability	24.48 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
DeepCCS	[M+H]+	151.423	30932474
DeepCCS	[M-H]-	149.065	30932474
DeepCCS	[M-2H]-	182.998	30932474
DeepCCS	[M+Na]+	158.475	30932474
AllCCS	[M+H]+	156.7	32859911
AllCCS	[M+H-H2O]+	153.0	32859911
AllCCS	[M+NH4]+	160.2	32859911
AllCCS	[M+Na]+	161.2	32859911
AllCCS	[M-H]-	157.0	32859911
AllCCS	[M+Na-2H]-	156.7	32859911
AllCCS	[M+HCOO]-	156.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3,N(4)-Ethenodeoxycytidine	OCC1OC(CC1O)N1C=CC2=NC=CN2C1=O	3332.1	Standard polar	33892256
3,N(4)-Ethenodeoxycytidine	OCC1OC(CC1O)N1C=CC2=NC=CN2C1=O	2117.3	Standard non polar	33892256
3,N(4)-Ethenodeoxycytidine	OCC1OC(CC1O)N1C=CC2=NC=CN2C1=O	2542.6	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 - 3,N(4)-Ethenodeoxycytidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9130000000-9053fc5905e59a4a3b87	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,N(4)-Ethenodeoxycytidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,N(4)-Ethenodeoxycytidine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,N(4)-Ethenodeoxycytidine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,N(4)-Ethenodeoxycytidine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,N(4)-Ethenodeoxycytidine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,N(4)-Ethenodeoxycytidine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,N(4)-Ethenodeoxycytidine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	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 - 3,N(4)-Ethenodeoxycytidine 10V, Positive-QTOF	splash10-0udr-0890000000-4b1cf1d7811de2c3ee3d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,N(4)-Ethenodeoxycytidine 20V, Positive-QTOF	splash10-000i-0900000000-81bb6bbdb92fcd2ab0c7	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,N(4)-Ethenodeoxycytidine 40V, Positive-QTOF	splash10-053l-5900000000-2038bec5dee2a2ad2694	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,N(4)-Ethenodeoxycytidine 10V, Negative-QTOF	splash10-0f89-0690000000-a1ba8c24a39fb34ec95c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,N(4)-Ethenodeoxycytidine 20V, Negative-QTOF	splash10-06si-2910000000-d9a541a802984b3ac515	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,N(4)-Ethenodeoxycytidine 40V, Negative-QTOF	splash10-053r-4900000000-e101f77e409ad1e7d4b2	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14860098

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 3,N(4)-Ethenodeoxycytidine (HMDB0246084)

MOL for HMDB0246084 (3,N(4)-Ethenodeoxycytidine)

3D MOL for HMDB0246084 (3,N(4)-Ethenodeoxycytidine)

3D SDF for HMDB0246084 (3,N(4)-Ethenodeoxycytidine)

3D-SDF for HMDB0246084 (3,N(4)-Ethenodeoxycytidine)

PDB for HMDB0246084 (3,N(4)-Ethenodeoxycytidine)

3D PDB for HMDB0246084 (3,N(4)-Ethenodeoxycytidine)

SMILES for HMDB0246084 (3,N(4)-Ethenodeoxycytidine)

INCHI for HMDB0246084 (3,N(4)-Ethenodeoxycytidine)

Structure for HMDB0246084 (3,N(4)-Ethenodeoxycytidine)

3D Structure for HMDB0246084 (3,N(4)-Ethenodeoxycytidine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra