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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 07:49:42 UTC

Update Date

2021-09-26 23:02:21 UTC

HMDB ID

HMDB0250725

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Cytosine deoxyribonucleoside

Description

1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-ol belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. 1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-ol is an extremely weak basic (essentially neutral) compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). Cytosine deoxyribonucleoside is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Cytosine deoxyribonucleoside 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

HMDB0250725
     RDKit          3D
Cytosine deoxyribonucleoside
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.1635   -0.5693   -0.0557 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7876   -0.2268   -0.0172 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8550   -1.1359    0.4404 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5152   -0.7725    0.4666 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1425    0.4417    0.0531 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2336    0.8986    0.0484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8610    0.4206   -1.2619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9730   -0.4407   -0.7691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0578   -0.5297   -1.5864 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2748    0.2322    0.5679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1345   -0.6538    1.4277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4244   -0.7639    0.9120 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9793    0.3563    1.0659 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0852    1.2935   -0.3841 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7823    2.4662   -0.7904 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3878    0.9765   -0.4232 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8321   -0.0971    0.5891 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4606   -1.3023   -0.7488 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1246   -2.1159    0.7780 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7539   -1.4704    0.8235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2541    1.9923    0.1334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2588    1.3253   -1.8061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1275   -0.1219   -1.8914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5925   -1.4479   -0.5257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5090    0.3107   -1.7662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6797    1.2441    0.4476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7234   -1.6634    1.4947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1382   -0.2208    2.4588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6686   -0.0052    0.3190 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
  5 14  1  0
 14 15  2  0
 14 16  1  0
 16  2  2  0
 13  6  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  6 21  1  0
  7 22  1  0
  7 23  1  0
  8 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
M  END


  Mrv1533004201503102D          

 16 17  0  0  0  0            999 V2000
    0.7145    6.7661    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.5286    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.7036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.2911    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.2911    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.7036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    5.5286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    2.9812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    2.1965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119    1.5291    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830    1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526    0.7754    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
  9 16  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250725

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(=O)N(C=C1)C1CC(O)C(CO)O1

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)

> <INCHI_KEY>
CKTSBUTUHBMZGZ-UHFFFAOYSA-N

> <FORMULA>
C9H13N3O4

> <MOLECULAR_WEIGHT>
227.22

> <EXACT_MASS>
227.090605911

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.928854661129755

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.93

> <JCHEM_LOGP>
-1.8968792213333328

> <ALOGPS_LOGS>
-1.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.78753514288664

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.894899521324458

> <JCHEM_PKA_STRONGEST_BASIC>
0.3081753362314522

> <JCHEM_POLAR_SURFACE_AREA>
108.38000000000001

> <JCHEM_REFRACTIVITY>
53.0341

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.59e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
deoxycytidine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0250725
     RDKit          3D
Cytosine deoxyribonucleoside
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.1635   -0.5693   -0.0557 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7876   -0.2268   -0.0172 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8550   -1.1359    0.4404 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5152   -0.7725    0.4666 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1425    0.4417    0.0531 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2336    0.8986    0.0484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8610    0.4206   -1.2619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9730   -0.4407   -0.7691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0578   -0.5297   -1.5864 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2748    0.2322    0.5679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1345   -0.6538    1.4277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4244   -0.7639    0.9120 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9793    0.3563    1.0659 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0852    1.2935   -0.3841 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7823    2.4662   -0.7904 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3878    0.9765   -0.4232 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8321   -0.0971    0.5891 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4606   -1.3023   -0.7488 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1246   -2.1159    0.7780 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7539   -1.4704    0.8235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2541    1.9923    0.1334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2588    1.3253   -1.8061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1275   -0.1219   -1.8914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5925   -1.4479   -0.5257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5090    0.3107   -1.7662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6797    1.2441    0.4476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7234   -1.6634    1.4947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1382   -0.2208    2.4588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6686   -0.0052    0.3190 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
  5 14  1  0
 14 15  2  0
 14 16  1  0
 16  2  2  0
 13  6  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  6 21  1  0
  7 22  1  0
  7 23  1  0
  8 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
M  END

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  N   UNK     0       1.334  12.630   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.334  11.090   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.667  10.320   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       2.667   8.780   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001   8.010   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       1.334   8.010   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.000   8.780   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.000  10.320   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   6.470   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.580   5.565   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.104   4.100   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.009   2.854   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.564   4.100   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.342   2.854   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.285   1.447   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.088   5.565   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7    2                                                       
CONECT    9    6   10   16                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13    9                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

COMPND    HMDB0250725
HETATM    1  N1  UNL     1       5.164  -0.569  -0.056  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.788  -0.227  -0.017  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.855  -1.136   0.440  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.515  -0.772   0.467  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.142   0.442   0.053  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.234   0.899   0.048  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.861   0.421  -1.262  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.973  -0.441  -0.769  1.00  0.00           C  
HETATM    9  O1  UNL     1      -3.058  -0.530  -1.586  1.00  0.00           O  
HETATM   10  C7  UNL     1      -2.275   0.232   0.568  1.00  0.00           C  
HETATM   11  C8  UNL     1      -3.135  -0.654   1.428  1.00  0.00           C  
HETATM   12  O2  UNL     1      -4.424  -0.764   0.912  1.00  0.00           O  
HETATM   13  O3  UNL     1      -0.979   0.356   1.066  1.00  0.00           O  
HETATM   14  C9  UNL     1       2.085   1.294  -0.384  1.00  0.00           C  
HETATM   15  O4  UNL     1       1.782   2.466  -0.790  1.00  0.00           O  
HETATM   16  N3  UNL     1       3.388   0.976  -0.423  1.00  0.00           N  
HETATM   17  H1  UNL     1       5.832  -0.097   0.589  1.00  0.00           H  
HETATM   18  H2  UNL     1       5.461  -1.302  -0.749  1.00  0.00           H  
HETATM   19  H3  UNL     1       3.125  -2.116   0.778  1.00  0.00           H  
HETATM   20  H4  UNL     1       0.754  -1.470   0.823  1.00  0.00           H  
HETATM   21  H5  UNL     1      -0.254   1.992   0.133  1.00  0.00           H  
HETATM   22  H6  UNL     1      -1.259   1.325  -1.806  1.00  0.00           H  
HETATM   23  H7  UNL     1      -0.127  -0.122  -1.891  1.00  0.00           H  
HETATM   24  H8  UNL     1      -1.593  -1.448  -0.526  1.00  0.00           H  
HETATM   25  H9  UNL     1      -3.509   0.311  -1.766  1.00  0.00           H  
HETATM   26  H10 UNL     1      -2.680   1.244   0.448  1.00  0.00           H  
HETATM   27  H11 UNL     1      -2.723  -1.663   1.495  1.00  0.00           H  
HETATM   28  H12 UNL     1      -3.138  -0.221   2.459  1.00  0.00           H  
HETATM   29  H13 UNL     1      -4.669  -0.005   0.319  1.00  0.00           H  
CONECT    1    2   17   18
CONECT    2    3   16   16
CONECT    3    4    4   19
CONECT    4    5   20
CONECT    5    6   14
CONECT    6    7   13   21
CONECT    7    8   22   23
CONECT    8    9   10   24
CONECT    9   25
CONECT   10   11   13   26
CONECT   11   12   27   28
CONECT   12   29
CONECT   14   15   15   16
END

HMDB0250725
     RDKit          3D
Cytosine deoxyribonucleoside
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.1635   -0.5693   -0.0557 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7876   -0.2268   -0.0172 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8550   -1.1359    0.4404 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5152   -0.7725    0.4666 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1425    0.4417    0.0531 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2336    0.8986    0.0484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8610    0.4206   -1.2619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9730   -0.4407   -0.7691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0578   -0.5297   -1.5864 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2748    0.2322    0.5679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1345   -0.6538    1.4277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4244   -0.7639    0.9120 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9793    0.3563    1.0659 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0852    1.2935   -0.3841 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7823    2.4662   -0.7904 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3878    0.9765   -0.4232 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8321   -0.0971    0.5891 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4606   -1.3023   -0.7488 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1246   -2.1159    0.7780 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7539   -1.4704    0.8235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2541    1.9923    0.1334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2588    1.3253   -1.8061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1275   -0.1219   -1.8914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5925   -1.4479   -0.5257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5090    0.3107   -1.7662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6797    1.2441    0.4476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7234   -1.6634    1.4947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1382   -0.2208    2.4588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6686   -0.0052    0.3190 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
  5 14  1  0
 14 15  2  0
 14 16  1  0
 16  2  2  0
 13  6  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  6 21  1  0
  7 22  1  0
  7 23  1  0
  8 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Cytosine deoxyriboside	MeSH
Deoxyriboside, cytosine	MeSH
Deoxyribonucleoside, cytosine	MeSH
Deoxycytidine	MeSH

Chemical Formula

C₉H₁₃N₃O₄

Average Molecular Weight

227.22

Monoisotopic Molecular Weight

227.090605911

IUPAC Name

4-amino-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

deoxycytidine

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)C1CC(O)C(CO)O1

InChI Identifier

InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)

InChI Key

CKTSBUTUHBMZGZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a pyrimidine-related compound (DEOXYCYTIDINE )
a deoxynucleoside (DEOXYCYTIDINE )

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	-1.9	ALOGPS
logP	-1.9	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	0.31	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	108.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	53.03 m³·mol⁻¹	ChemAxon
Polarizability	21.93 Å³	ChemAxon
Number of Rings	2	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]+	153.021	30932474
DeepCCS	[M-H]-	150.663	30932474
DeepCCS	[M-2H]-	184.723	30932474
DeepCCS	[M+Na]+	159.678	30932474
AllCCS	[M+H]+	151.7	32859911
AllCCS	[M+H-H2O]+	147.8	32859911
AllCCS	[M+NH4]+	155.3	32859911
AllCCS	[M+Na]+	156.4	32859911
AllCCS	[M-H]-	150.3	32859911
AllCCS	[M+Na-2H]-	150.4	32859911
AllCCS	[M+HCOO]-	150.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Cytosine deoxyribonucleoside	NC1=NC(=O)N(C=C1)C1CC(O)C(CO)O1	3796.1	Standard polar	33892256
Cytosine deoxyribonucleoside	NC1=NC(=O)N(C=C1)C1CC(O)C(CO)O1	1940.5	Standard non polar	33892256
Cytosine deoxyribonucleoside	NC1=NC(=O)N(C=C1)C1CC(O)C(CO)O1	2441.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cytosine deoxyribonucleoside,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O2)C=C1	2369.5	Semi standard non polar	33892256
Cytosine deoxyribonucleoside,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O2)C=C1	2421.4	Standard non polar	33892256
Cytosine deoxyribonucleoside,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O2)C=C1	2958.4	Standard polar	33892256
Cytosine deoxyribonucleoside,3TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)OC1CO	2361.2	Semi standard non polar	33892256
Cytosine deoxyribonucleoside,3TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)OC1CO	2539.8	Standard non polar	33892256
Cytosine deoxyribonucleoside,3TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)OC1CO	2963.3	Standard polar	33892256
Cytosine deoxyribonucleoside,3TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CC1O	2369.5	Semi standard non polar	33892256
Cytosine deoxyribonucleoside,3TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CC1O	2569.3	Standard non polar	33892256
Cytosine deoxyribonucleoside,3TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CC1O	3003.2	Standard polar	33892256
Cytosine deoxyribonucleoside,4TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CC1O[Si](C)(C)C	2369.2	Semi standard non polar	33892256
Cytosine deoxyribonucleoside,4TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CC1O[Si](C)(C)C	2532.5	Standard non polar	33892256
Cytosine deoxyribonucleoside,4TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CC1O[Si](C)(C)C	2650.4	Standard polar	33892256
Cytosine deoxyribonucleoside,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O2)C=C1	3036.8	Semi standard non polar	33892256
Cytosine deoxyribonucleoside,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O2)C=C1	3079.5	Standard non polar	33892256
Cytosine deoxyribonucleoside,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O2)C=C1	3158.5	Standard polar	33892256
Cytosine deoxyribonucleoside,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)OC1CO	3026.5	Semi standard non polar	33892256
Cytosine deoxyribonucleoside,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)OC1CO	3167.1	Standard non polar	33892256
Cytosine deoxyribonucleoside,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)OC1CO	3126.6	Standard polar	33892256
Cytosine deoxyribonucleoside,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CC1O	3024.6	Semi standard non polar	33892256
Cytosine deoxyribonucleoside,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CC1O	3204.7	Standard non polar	33892256
Cytosine deoxyribonucleoside,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CC1O	3167.0	Standard polar	33892256
Cytosine deoxyribonucleoside,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CC1O[Si](C)(C)C(C)(C)C	3212.7	Semi standard non polar	33892256
Cytosine deoxyribonucleoside,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CC1O[Si](C)(C)C(C)(C)C	3346.6	Standard non polar	33892256
Cytosine deoxyribonucleoside,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CC1O[Si](C)(C)C(C)(C)C	3000.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9510000000-0d341d698aaedbfca406	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytosine deoxyribonucleoside GC-MS (TBDMS_2_4) - 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 - Cytosine deoxyribonucleoside 10V, Positive-QTOF	splash10-03di-0900000000-61fe3ac4032a2baf1b89	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytosine deoxyribonucleoside 20V, Positive-QTOF	splash10-03di-2900000000-87e7bfde0f536c442cf8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytosine deoxyribonucleoside 40V, Positive-QTOF	splash10-02t9-9500000000-2864b2716412070da939	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytosine deoxyribonucleoside 10V, Negative-QTOF	splash10-01ti-0940000000-2837e623295e850bde13	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytosine deoxyribonucleoside 20V, Negative-QTOF	splash10-0006-7900000000-9a01b6cdc7efff3c4bb0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytosine deoxyribonucleoside 40V, Negative-QTOF	splash10-0006-9500000000-6db2e60bf227251f1ff4	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View

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

637

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 Cytosine deoxyribonucleoside (HMDB0250725)

MOL for HMDB0250725 (Cytosine deoxyribonucleoside)

3D MOL for HMDB0250725 (Cytosine deoxyribonucleoside)

3D SDF for HMDB0250725 (Cytosine deoxyribonucleoside)

3D-SDF for HMDB0250725 (Cytosine deoxyribonucleoside)

PDB for HMDB0250725 (Cytosine deoxyribonucleoside)

3D PDB for HMDB0250725 (Cytosine deoxyribonucleoside)

SMILES for HMDB0250725 (Cytosine deoxyribonucleoside)

INCHI for HMDB0250725 (Cytosine deoxyribonucleoside)

Structure for HMDB0250725 (Cytosine deoxyribonucleoside)

3D Structure for HMDB0250725 (Cytosine deoxyribonucleoside)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra