MiMeDB: Showing metabocard for Deoxycytidine (MMDBc0000490)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:38:57 UTC

Update Date

2024-10-11 01:00:24 UTC

Metabolite ID

MMDBc0000490

Metabolite Identification

Common Name

Deoxycytidine

Description

Deoxycytidine, also known as dC, 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. Deoxycytidine is also classified as a deoxyribonucleoside, a component of deoxyribonucleic acid (DNA). Deoxycytidine is similar to the ribonucleoside cytidine, but with one hydroxyl group removed from the 2' position. Deoxycytidine exists in all living species, ranging from bacteria to plants to humans. Degradation of DNA through apoptosis or cell death produces deoxycytidine. Within humans, deoxycytidine participates in a number of enzymatic reactions. In particular, deoxycytidine can be biosynthesized from dCMP through the action of the enzyme cytosolic purine 5'-nucleotidase. In addition, deoxycytidine can be converted into dCMP; which is mediated by the enzyme uridine-cytidine kinase-like 1. Deoxycytidine can be phosphorylated at the C-5 position by the enzyme deoxycytidine kinase to produce deoxycytidine monophosphate (dCMP), and to a lesser extent, deoxycytidine diphosphate (dCDP), and deoxycytidine triphosphate (dCTP). Deoxycytidine can also be phosphorylated by thymidine kinase 2 (TK2). Deoxycytidine can potentially be used for the treatment of the metabolic disorder known as thymidine kinase 2 deficiency (TK2 deficiency). TK2 deficiency has three disease subtypes: i) infantile-onset myopathy with rapid progression to early death ii) childhood-onset myopathy, which resembles spinal muscular atrophy (SMA) type III, begins between ages 1 and 12 years with progression to loss of ambulation within few years and iii) late-onset myopathy starting at age 12 year or later with moderate to severe myopathy manifesting as either isolated chronic progressive external ophthalmoplegia (CPEO) or a generalized myopathy with CPEO plus facial and limb weakness, gradual progression, and, in some cases, respiratory failure and loss of ability to walk in adulthood (PMID: 28318037 ). In mouse models of TK2, dC was shown to delay disease onset, prolong life span and restore mtDNA copy number as well as respiratory chain enzyme activities (PMID: 28318037 ).

Structure

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

HMDB0000014
     RDKit          3D
Deoxycytidine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.1845    0.2113    0.4449 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7824    0.1243    0.1569 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9756    1.2408    0.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6301    1.1095   -0.1699 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0719   -0.1096   -0.4066 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3190   -0.2009   -0.6928 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9723   -1.4702   -0.2454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4122   -0.9988    0.0063 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1889   -1.5075   -1.0595 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3006    0.4668   -0.1828 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1762    1.2915    0.7090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0114    1.0519    2.0446 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9768    0.7418    0.1327 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8799   -1.1666   -0.3547 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3490   -2.3063   -0.5777 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2050   -1.0670   -0.0807 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7828    0.5930   -0.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5769   -0.0970    1.3693 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3794    2.2252    0.2931 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9650    1.9831   -0.2123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5975    0.0476   -1.7217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9454   -2.2541   -1.0214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5380   -1.8160    0.7165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7686   -1.3318    0.9784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7464   -1.1944   -1.8992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4450    0.7540   -1.2407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2403    1.1763    0.3658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9279    2.3613    0.5188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2159    0.1420    2.3236 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  6
  7 22  1  0
  7 23  1  0
  8 24  1  1
  9 25  1  0
 10 26  1  6
 11 27  1  0
 11 28  1  0
 12 29  1  0
M  END


  Mrv1652309032023492D          

 16 17  0  0  1  0            999 V2000
   -0.2649   -0.0103    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5196    0.2409    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9396    0.4989    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5092   -0.7745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1186   -0.3200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7057    1.0359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6037    0.0034    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3457   -0.7745    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9102   -0.0860    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9362   -1.1288    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4936    1.2803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3920    0.2546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6003   -1.5796    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0891    0.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0009   -0.2993    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8874    0.9465    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  2  0  0  0  0
  7 12  1  1  0  0  0
  8 13  1  6  0  0  0
  9 14  2  0  0  0  0
 12 15  1  0  0  0  0
 14 16  1  0  0  0  0
  7  8  1  0  0  0  0
 11 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000490

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](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)/t5-,6+,8+/m0/s1

> <INCHI_KEY>
CKTSBUTUHBMZGZ-SHYZEUOFSA-N

> <FORMULA>
C9H13N3O4

> <MOLECULAR_WEIGHT>
227.2172

> <EXACT_MASS>
227.090605919

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.64578911898849

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[(2R,4S,5R)-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>
108.38

> <JCHEM_REFRACTIVITY>
53.0341

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.59e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2'-deoxycytidine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000014
     RDKit          3D
Deoxycytidine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.1845    0.2113    0.4449 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7824    0.1243    0.1569 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9756    1.2408    0.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6301    1.1095   -0.1699 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0719   -0.1096   -0.4066 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3190   -0.2009   -0.6928 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9723   -1.4702   -0.2454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4122   -0.9988    0.0063 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1889   -1.5075   -1.0595 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3006    0.4668   -0.1828 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1762    1.2915    0.7090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0114    1.0519    2.0446 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9768    0.7418    0.1327 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8799   -1.1666   -0.3547 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3490   -2.3063   -0.5777 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2050   -1.0670   -0.0807 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7828    0.5930   -0.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5769   -0.0970    1.3693 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3794    2.2252    0.2931 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9650    1.9831   -0.2123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5975    0.0476   -1.7217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9454   -2.2541   -1.0214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5380   -1.8160    0.7165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7686   -1.3318    0.9784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7464   -1.1944   -1.8992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4450    0.7540   -1.2407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2403    1.1763    0.3658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9279    2.3613    0.5188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2159    0.1420    2.3236 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  6
  7 22  1  0
  7 23  1  0
  8 24  1  1
  9 25  1  0
 10 26  1  6
 11 27  1  0
 11 28  1  0
 12 29  1  0
M  END

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0      -0.495  -0.019   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       0.970   0.450   0.000  0.00  0.00           N+0
HETATM    3  O   UNK     0      -1.754   0.931   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.951  -1.446   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.088  -0.597   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.317   1.934   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.994   0.006   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.512  -1.446   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.566  -0.161   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       1.748  -2.107   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.788   2.390   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.465   0.475   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -2.987  -2.949   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.900   1.330   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -5.602  -0.559   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0       5.390   1.767   0.000  0.00  0.00           N+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8                                                       
CONECT    5    2    9   10                                                  
CONECT    6    2   11                                                       
CONECT    7    3   12    8                                                  
CONECT    8    4   13    7                                                  
CONECT    9    5   14                                                       
CONECT   10    5                                                            
CONECT   11    6   14                                                       
CONECT   12    7   15                                                       
CONECT   13    8                                                            
CONECT   14    9   16   11                                                  
CONECT   15   12                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

COMPND    HMDB0000014
HETATM    1  N1  UNL     1       5.185   0.211   0.445  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.782   0.124   0.157  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.976   1.241   0.111  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.630   1.109  -0.170  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.072  -0.110  -0.407  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.319  -0.201  -0.693  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.972  -1.470  -0.245  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.412  -0.999   0.006  1.00  0.00           C  
HETATM    9  O1  UNL     1      -3.189  -1.507  -1.059  1.00  0.00           O  
HETATM   10  C7  UNL     1      -2.301   0.467  -0.183  1.00  0.00           C  
HETATM   11  C8  UNL     1      -3.176   1.291   0.709  1.00  0.00           C  
HETATM   12  O2  UNL     1      -3.011   1.052   2.045  1.00  0.00           O  
HETATM   13  O3  UNL     1      -0.977   0.742   0.133  1.00  0.00           O  
HETATM   14  C9  UNL     1       1.880  -1.167  -0.355  1.00  0.00           C  
HETATM   15  O4  UNL     1       1.349  -2.306  -0.578  1.00  0.00           O  
HETATM   16  N3  UNL     1       3.205  -1.067  -0.081  1.00  0.00           N  
HETATM   17  H1  UNL     1       5.783   0.593  -0.306  1.00  0.00           H  
HETATM   18  H2  UNL     1       5.577  -0.097   1.369  1.00  0.00           H  
HETATM   19  H3  UNL     1       3.379   2.225   0.293  1.00  0.00           H  
HETATM   20  H4  UNL     1       0.965   1.983  -0.212  1.00  0.00           H  
HETATM   21  H5  UNL     1      -0.598   0.048  -1.722  1.00  0.00           H  
HETATM   22  H6  UNL     1      -0.945  -2.254  -1.021  1.00  0.00           H  
HETATM   23  H7  UNL     1      -0.538  -1.816   0.716  1.00  0.00           H  
HETATM   24  H8  UNL     1      -2.769  -1.332   0.978  1.00  0.00           H  
HETATM   25  H9  UNL     1      -2.746  -1.194  -1.899  1.00  0.00           H  
HETATM   26  H10 UNL     1      -2.445   0.754  -1.241  1.00  0.00           H  
HETATM   27  H11 UNL     1      -4.240   1.176   0.366  1.00  0.00           H  
HETATM   28  H12 UNL     1      -2.928   2.361   0.519  1.00  0.00           H  
HETATM   29  H13 UNL     1      -3.216   0.142   2.324  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

HMDB0000014
     RDKit          3D
Deoxycytidine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.1845    0.2113    0.4449 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7824    0.1243    0.1569 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9756    1.2408    0.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6301    1.1095   -0.1699 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0719   -0.1096   -0.4066 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3190   -0.2009   -0.6928 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9723   -1.4702   -0.2454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4122   -0.9988    0.0063 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1889   -1.5075   -1.0595 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3006    0.4668   -0.1828 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1762    1.2915    0.7090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0114    1.0519    2.0446 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9768    0.7418    0.1327 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8799   -1.1666   -0.3547 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3490   -2.3063   -0.5777 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2050   -1.0670   -0.0807 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7828    0.5930   -0.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5769   -0.0970    1.3693 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3794    2.2252    0.2931 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9650    1.9831   -0.2123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5975    0.0476   -1.7217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9454   -2.2541   -1.0214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5380   -1.8160    0.7165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7686   -1.3318    0.9784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7464   -1.1944   -1.8992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4450    0.7540   -1.2407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2403    1.1763    0.3658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9279    2.3613    0.5188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2159    0.1420    2.3236 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  6
  7 22  1  0
  7 23  1  0
  8 24  1  1
  9 25  1  0
 10 26  1  6
 11 27  1  0
 11 28  1  0
 12 29  1  0
M  END

Synonyms

Value	Source
4-Amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2(1H)-one	ChEBI
dC	ChEBI
DCYD	ChEBI
2'-Deoxycytidine	Kegg
1-(2-Deoxy-b-D-ribofuranosyl)cytosine	HMDB
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-cytosine	HMDB
1-(2-Deoxy-beta-D-ribofuranosyl)cytosine	HMDB
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-cytosine	HMDB
1-(2-Deoxy-beta-delta-ribofuranosyl)cytosine	HMDB
2-Deoxy-cytidine	HMDB
4-Amino-1-(2-deoxy-b-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone	HMDB
4-Amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone	HMDB
4-Amino-1-(2-deoxy-beta-delta-erythro-pentofuranosyl)-2(1H)-pyrimidinone	HMDB
Cytosine deoxyribonucleoside	HMDB
Cytosine deoxyriboside	HMDB
Deoxy-cytidine	HMDB
Deoxyribose cytidine	HMDB
Desoxycytidine	HMDB
Deoxyribonucleoside, cytosine	HMDB
Deoxyriboside, cytosine	HMDB
Deoxycytidine	ChEBI

Molecular Formula

C₉H₁₃N₃O₄

Average Mass

227.2172

Monoisotopic Mass

227.090605919

IUPAC Name

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

Traditional Name

2'-deoxycytidine

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](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)/t5-,6+,8+/m0/s1

InChI Key

CKTSBUTUHBMZGZ-SHYZEUOFSA-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

pyrimidine 2'-deoxyribonucleoside (CHEBI:15698 )
Deoxyribonucleosides (C00881 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	15.9 g/L	ALOGPS
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	21.65 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9510000000-43f83823bd8a63669514	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0gb9-4912000000-fef878d78b0000e850bb	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-0900000000-27431bdd2327f6f2b886	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-1900000000-0ea85f3f3940843e385b	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-03dl-9500000000-569e473eba0b700f5b6e	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-004i-0090000000-5c8c0fde4f2163fbc335	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0006-9420000000-28279714b575d59761ce	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0006-9200000000-df7c76b755c9fac5267b	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0006-9100000000-acbd1d7557be6d716a19	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-00kf-9100000000-056ef35d3aa743e0d5cf	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-03di-0910000000-52e9d173bb94576f7d9e	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-03di-0900000000-e06e5a9f19c4162aa24f	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-03di-0900000000-551d8ee9679ef3fb65fa	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-03di-3900000000-4c62633283ba566dbee0	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-03di-0900000000-bac3656523b118a2c1bc	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-03dj-6900000000-dfa8435d3dd8b8981621	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-01t9-0690000000-72302b09c51553dde169	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positive	splash10-03fr-0930000000-f5c80400a73719f6211f	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0006-9130000000-c7f95a478d22e3cc83f4	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-0090000000-af75883dba546c82e7bc	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9420000000-562a675c6278a4ae2bc4	2017-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-e9d4ffd1148d792f5132	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-b2a5f419f882d45f6ae7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-8900000000-0bbcfd7be44c4f38c4fc	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-1890000000-395ff33971fbc8368eca	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0016-4910000000-2dc8aa3aad2b1c83316f	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9200000000-cc82bf3d145faf0a6ca3	2016-09-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, experimental)		2021-10-10	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-04	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Lysosome
Mitochondria
Nucleus

Biospecimen Locations

All Tissues
Blood
Feces
Urine

Tissue Locations

All Tissues

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191677	5'-nucleotidase	Unknown	P21589	Homo sapiens
MMDBp0191680	Cytosolic 5'-nucleotidase 1B	Unknown	Q96P26	Homo sapiens
MMDBp0191681	Cytosolic 5'-nucleotidase 1A	Unknown	Q9BXI3	Homo sapiens
MMDBp0191682	5'(3')-deoxyribonucleotidase, cytosolic type	Unknown	Q8TCD5	Homo sapiens
MMDBp0191683	Deoxycytidine kinase	Enzyme	P27707	Homo sapiens
MMDBp0191684	5'(3')-deoxyribonucleotidase, mitochondrial	Unknown	Q9NPB1	Homo sapiens
MMDBp0193783	AID	Enzyme	Q546Y9	Homo sapiens
MMDBp0193860	Cytosolic 5'-nucleotidase 3	Enzyme	Q9H0P0	Homo sapiens
MMDBp0193932	Cytosolic purine 5'-nucleotidase	Unknown	P49902	Homo sapiens
MMDBp0194012	Cytidine deaminase	Unknown	P32320	Homo sapiens
MMDBp0194185	Uridine-cytidine kinase-like 1	Enzyme	Q9NWZ5	Homo sapiens
MMDBp0196672	DNA dC->dU-editing enzyme APOBEC-3G	Unknown	Q9HC16

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0000628	Deoxycytidine	dCMP	Not Available	VMH; KEGG	265735
MMDBr0000629	Deoxycytidine	dCMP	deoxycytidine kinase	VMH; KEGG	10387103 12535661 9342341
MMDBr0000630	Deoxycytidine	dCMP	deoxycytidine kinase	VMH	10387103 12535661 9342341
MMDBr0000638	Deoxycytidine	Deoxyuridine	Not Available	VMH; KEGG	14744791 15087440 7923172 8001985 8422236
MMDBr0000639	Deoxycytidine	Deoxyuridine	activation-induced cytidine deaminase	VMH; KEGG	15087440
MMDBr0001789	dCMP	Deoxycytidine	acid phosphatase 2, lysosomal	VMH	30371894
MMDBr0002524	Deoxycytidine	dCMP	Not Available	VMH	12036920 1657002 213049 8399394 9342341 9593124
MMDBr0007922	dCMP	Deoxycytidine	Not Available	VMH; KEGG	30371894
MMDBr0008426	Deoxycytidine	dCMP	Not Available	VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	571	Human feces; Human stool; Human ; Human urine; Human mucosa; Human supragingival plaque; Human saliva; Human subgingival plaque; Human pleural fluid plaque; Pig ; Human sputum; Cattle	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Bacteroidetes	242	Human ; Human feces; Human appendix biopsy; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	358	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Chicken	Metabolic reconstruction
Bacteria	Actinobacteria	169	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Synergistetes	6	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	15	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	3		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	2	Human feces	Metabolic reconstruction
Bacteria	Tenericutes	11	Human feces; Human	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	3	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference
Animal		Haliotis	FooDB	31437929
Animal		Strombidae	FooDB	31437929
Animal		Clupea harengus harengus	FooDB	31437929
Animal		Undaria pinnatifida	FooDB	31437929
Animal		Peprilus triacanthus	FooDB	31437929
Animal		Rhodophyta	FooDB	31437929
Animal		Myoxocephalus	FooDB	31437929
Animal		Eucheuma	FooDB	31437929
Animal		Saccharina japonica	FooDB	31437929
Animal		Spirulina	FooDB	31437929
Animal		Lota lota	FooDB	31437929
Animal		Porphyra umbilicalis	FooDB	31437929
Animal		Chondrus crispus	FooDB	31437929
Animal	Milk	Bos taurus	FooDB	31437929
Animal		Laminaria	FooDB	31437929
Plant		Capsicum baccatum var. baccatum	FooDB	31437929
Plant		Citrus latifolia	FooDB	31437929
Plant			FooDB	31437929
Plant		Byrsonima crassifolia	FooDB	31437929
Plant		Capsicum pubescens	FooDB	31437929
Plant		Carya illinoinensis	FooDB	31437929
Plant		Crateva religiosa	FooDB	31437929
Plant		Vitis aestivalis	FooDB	31437929
Plant		Eugenia javanica	FooDB	31437929
Plant		Mentha arvensis	FooDB	31437929
Plant		Cucumis sativus	FooDB	31437929
Plant			FooDB	31437929
Plant		Vaccinium stamineum	FooDB	31437929
Plant		Brassica rapa var. chinensis	FooDB	31437929
Plant		Cinnamomum aromaticum	FooDB	31437929
Plant		Ribes rubrum	FooDB	31437929
Plant		Psophocarpus tetragonolobus	FooDB	31437929
Plant		Ipomoea batatas	FooDB	31437929
Plant		Solanum lycopersicum var. cerasiforme	FooDB	31437929
Plant		Portulaca oleracea	FooDB	31437929
Plant		Chenopodium album	FooDB	31437929
Plant		Pastinaca sativa	FooDB	31437929
Plant		Allium ampeloprasum	FooDB	31437929
Plant		Cucurbita maxima	FooDB	31437929
Plant		Grataegosorbus mitschurinii	FooDB	31437929
Plant		Sechium edule	FooDB	31437929
Plant		Brassica oleracea	FooDB	31437929
Plant		Diospyros virginiana	FooDB	31437929
Plant		Origanum x majoricum	FooDB	31437929
Plant		Lactuca sativa l. var. longifolia	FooDB	31437929
Plant		Rumex	FooDB	31437929
Plant		Rubus x loganobaccus	FooDB	31437929
Plant		Tragopogon porrifolius	FooDB	31437929
Plant		Allium ascalonicum	FooDB	31437929
Plant		Citrullus lanatus var. fistulosus	FooDB	31437929
Plant		Taraxacum officinale	FooDB	31437929
Plant		Rubus chamaemorus	FooDB	31437929
Plant		Amelanchier alnifolia	FooDB	31437929
Plant		Eugenia uniflora	FooDB	31437929
Plant		Curcuma longa	FooDB	31437929
Plant		Annona reticulata	FooDB	31437929
Plant		Sesbania bispinosa	FooDB	31437929
Plant		Elettaria cardamomum	FooDB	31437929
Plant		Ananas comosus	FooDB	31437929
Plant		Persea americana	FooDB	31437929
Plant		Ribes x nidigrolaria	FooDB	31437929
Plant		Garcinia mangostana	FooDB	31437929
Plant		Lathyrus sativus	FooDB	31437929
Plant		Dioscorea pentaphylla	FooDB	31437929
Plant		Allium tuberosum	FooDB	31437929
Plant		Brassica oleracea var. botrytis	FooDB	31437929
Plant		Chenopodium quinoa	FooDB	31437929
Plant		Cichorium intybus	FooDB	31437929
Plant		Corchorus olitorius	FooDB	31437929
Plant		Cucumis melo	FooDB	31437929
Plant		Juglans nigra	FooDB	31437929
Plant		Gaylussacia baccata	FooDB	31437929
Plant		Petasites japonicus	FooDB	31437929
Plant		Prunus tomentosa	FooDB	31437929
Plant		Maranta arundinacea	FooDB	31437929
Plant		Mentha x piperita	FooDB	31437929
Plant		Cinnamomum verum	FooDB	31437929
Plant		Matteuccia struthiopteris	FooDB	31437929
Plant		Cucurbita moschata	FooDB	31437929
Plant		Glycine max	FooDB	31437929
Plant		Vaccinium myrtilloides	FooDB	31437929
Plant		Ocimum basilicum	FooDB	31437929
Plant		Macadamia	FooDB	31437929
Plant		Tilia	FooDB	31437929
Plant		Nelumbo	FooDB	31437929
Plant		Papaver	FooDB	31437929
Plant		Rosa	FooDB	31437929
Plant		Brassica oleracea var. conica	FooDB	31437929
Plant		Citrus limon	FooDB	31437929
Plant		Apium graveolens var. rapaceum	FooDB	31437929
Plant		Capsicum annuum var. annuum	FooDB	31437929
Plant		Lippia graveolens	FooDB	31437929
Plant		Annona cherimola	FooDB	31437929
Plant		Sesamum orientale	FooDB	31437929
Plant		Brassica rapa var. pekinensis	FooDB	31437929
Plant		Brassica rapa	FooDB	31437929
Plant		Prunus	FooDB	31437929
Plant		Capparis spinosa	FooDB	31437929
Plant		Vaccinium deliciosum	FooDB	31437929
Plant		Citrus sinensis	FooDB	31437929
Plant		Lens culinaris	FooDB	31437929
Plant		Phaseolus lunatus	FooDB	31437929
Plant		Artocarpus heterophyllus	FooDB	31437929
Plant		Prunus virginiana	FooDB	31437929
Plant		Musa acuminata	FooDB	31437929
Plant		Macadamia tetraphylla	FooDB	31437929
Plant		Vigna unguiculata ssp. unguiculata	FooDB	31437929
Plant		Citrullus lanatus	FooDB	31437929
Plant		Lagenaria siceraria	FooDB	31437929
Plant		Linum usitatissimum	FooDB	31437929
Plant		Carissa macrocarpa	FooDB	31437929
Plant		Phyllostachys edulis	FooDB	31437929
Plant		Satureja hortensis	FooDB	31437929
Plant		Averrhoa carambola	FooDB	31437929
Plant		Prunus domestica	FooDB	31437929
Plant		Prunus armeniaca	FooDB	31437929
Plant		Sorbus aucuparia	FooDB	31437929
Plant		Carum carvi	FooDB	31437929
Plant		Allium schoenoprasum	FooDB	31437929
Plant		Citrus reticulata	FooDB	31437929
Plant		Brassica oleracea var. costata	FooDB	31437929
Plant		Panax	FooDB	31437929
Plant		Nelumbo nucifera	FooDB	31437929
Plant		Brassica rapa var. rapa	FooDB	31437929
Plant		Bertholletia excelsa	FooDB	31437929
Plant		Cymbopogon citratus	FooDB	31437929
Plant		Ceratonia siliqua	FooDB	31437929
Plant		Anethum graveolens	FooDB	31437929
Plant		Coriandrum sativum	FooDB	31437929
Plant		Luffa aegyptiaca	FooDB	31437929
Plant		Vigna umbellata	FooDB	31437929
Plant		Rubus occidentalis	FooDB	31437929
Plant		Allium fistulosum	FooDB	31437929
Plant		Capsicum	FooDB	31437929
Plant		Carthamus tinctorius	FooDB	31437929
Plant		Cicer arietinum	FooDB	31437929
Plant		Tilia cordata	FooDB	31437929
Plant		Vaccinium alaskaense	FooDB	31437929
Plant		Lupinus	FooDB	31437929
Plant		Anacardium occidentale	FooDB	31437929
Plant		Durio zibethinus	FooDB	31437929
Plant		Prunus persica var. nucipersica	FooDB	31437929
Plant		Eriobotrya japonica	FooDB	31437929
Plant		Ribes glandulosum	FooDB	31437929
Plant		Brassica napus var. pabularia	FooDB	31437929
Plant		Verbena officinalis	FooDB	31437929
Plant		Diospyros kaki	FooDB	31437929
Plant		Oenothera biennis	FooDB	31437929
Plant		Vaccinium oxycoccos	FooDB	31437929
Plant		Virola surinamensis	FooDB	31437929
Plant		Camellia sinensis	FooDB	31437929
Plant		Rumex acetosa	FooDB	31437929
Plant		Theobroma cacao	FooDB	31437929
Plant		Solanum lycopersicum var. lycopersicum	FooDB	31437929
Plant		Aloysia triphylla	FooDB	31437929
Plant		Vaccinium parvifolium	FooDB	31437929
Plant		Capsicum chinense	FooDB	31437929
Plant		Pyrus pyrifolia	FooDB	31437929
Plant		Phaseolus vulgaris	FooDB	31437929
Plant		Brassica oleracea var. capitata	FooDB	31437929
Plant		Vaccinium reticulatum	FooDB	31437929
Plant		Solanum quitoense	FooDB	31437929
Plant		Vaccinium myrtillus	FooDB	31437929
Plant		Daucus carota ssp. sativus	FooDB	31437929
Plant		Theobroma grandiflorum	FooDB	31437929
Plant		Syzygium aromaticum	FooDB	31437929
Plant		Ginkgo biloba	FooDB	31437929
Plant		Vigna unguiculata ssp. cylindrica	FooDB	31437929
Plant			FooDB	31437929
Plant		Flammulina velutipes	FooDB	31437929
Plant		Vicia faba	FooDB	31437929
Plant		Satureja montana	FooDB	31437929
Plant		Perideridia oregana	FooDB	31437929
Plant		Citrus japonica	FooDB	31437929
Plant		Vaccinium arboreum	FooDB	31437929
Plant		Wasabia japonica	FooDB	31437929
Plant		Origanum onites	FooDB	31437929
Plant		Prunus avium	FooDB	31437929
Plant		Pouteria sapota	FooDB	31437929
Plant		Piper nigrum	FooDB	31437929
Plant		Viburnum edule	FooDB	31437929
Plant		Vitis vinifera	FooDB	31437929
Plant		Origanum vulgare	FooDB	31437929
Plant		Capsicum annuum	FooDB	31437929
Plant		Dioscorea	FooDB	31437929
Plant		Vaccinium uliginosum	FooDB	31437929
Plant		Momordica charantia	FooDB	31437929
Plant		Rubus ursinus x idaeus	FooDB	31437929
Plant		Castanea	FooDB	31437929
Plant		Cirsium	FooDB	31437929
Plant		Raphanus sativus var. sativus	FooDB	31437929
Plant		Pleurotus ostreatus	FooDB	31437929
Plant		Opuntia	FooDB	31437929
Plant		Brassica oleracea var. italica	FooDB	31437929
Plant		Colocasia esculenta	FooDB	31437929
Plant		Prunus persica var. persica	FooDB	31437929
Plant		Anthriscus cerefolium	FooDB	31437929
Plant		Solanum melongena	FooDB	31437929
Plant		Nuphar lutea	FooDB	31437929
Plant		Pachyrhizus erosus	FooDB	31437929
Plant		Lupinus albus	FooDB	31437929
Plant		Cichorium endivia	FooDB	31437929
Plant		Myristica fragrans	FooDB	31437929
Plant		Elaeis	FooDB	31437929
Plant		Dysphania ambrosioides	FooDB	31437929
Plant		Raphanus sativus var. niger	FooDB	31437929
Plant		Cinnamomum	FooDB	31437929
Plant		Photinia melanocarpa	FooDB	31437929
Plant		Ribes uva-crispa	FooDB	31437929
Plant		Feijoa sellowiana	FooDB	31437929
Plant		Vaccinium	FooDB	31437929
Plant		Lablab purpureus	FooDB	31437929
Plant		Apium graveolens	FooDB	31437929
Plant		Rheum rhabarbarum	FooDB	31437929
Plant		Crocus sativus	FooDB	31437929
Plant		Syzygium jambos	FooDB	31437929
Plant		Salix pulchra	FooDB	31437929
Plant		Citrus maxima	FooDB	31437929
Plant		Fagus	FooDB	31437929
Plant		Salvia officinalis	FooDB	31437929
Plant		Castanea sativa	FooDB	31437929
Plant		Cydonia oblonga	FooDB	31437929
Plant		Opuntia cochenillifera	FooDB	31437929
Plant		Annona muricata	FooDB	31437929
Plant		Vaccinium ovatum	FooDB	31437929
Plant		Thymus pulegioides	FooDB	31437929
Plant		Phaseolus coccineus	FooDB	31437929
Plant		Cucurbita	FooDB	31437929
Plant		Mespilus germanica	FooDB	31437929
Plant		Cocos nucifera	FooDB	31437929
Plant		Tamarindus indica	FooDB	31437929
Plant		Brassica rapa var. perviridis	FooDB	31437929
Plant		Mentha aquatica	FooDB	31437929
Plant		Salvia elegans	FooDB	31437929
Plant		Mentha	FooDB	31437929
Plant		Cucurbita pepo var. cylindrica	FooDB	31437929
Plant		Sagittaria latifolia	FooDB	31437929
Plant		Sambucus	FooDB	31437929
Plant		Syzygium cumini	FooDB	31437929
Plant		Psidium guajava	FooDB	31437929
Plant		Typha angustifolia	FooDB	31437929
Plant		Pinus	FooDB	31437929
Plant		Tilia tomentosa	FooDB	31437929
Plant		Empetrum nigrum	FooDB	31437929
Plant		Olea europaea	FooDB	31437929
Plant		Myrica rubra	FooDB	31437929
Plant		Valerianella locusta	FooDB	31437929
Plant		Vaccinium angustifolium x vaccinium corymbosum	FooDB	31437929
Plant		Sisymbrium	FooDB	31437929
Plant		Vaccinium vitis-idaea	FooDB	31437929
Plant		Solanum tuberosum	FooDB	31437929
Plant		Vanilla	FooDB	31437929
Plant		Daucus carota	FooDB	31437929
Plant		Carya	FooDB	31437929
Plant		Physalis philadelphica var. immaculata	FooDB	31437929
Plant		Borago officinalis	FooDB	31437929
Plant		Hyssopus officinalis	FooDB	31437929
Plant		Manihot esculenta	FooDB	31437929
Plant		Raphanus sativus	FooDB	31437929
Plant		Scorzonera hispanica	FooDB	31437929
Plant		Vigna unguiculata ssp. sesquipedalis	FooDB	31437929
Plant		Angelica keiskei	FooDB	31437929
Plant		Brassica oleracea l. var. capitata l. f. alba dc.	FooDB	31437929
Plant		Vigna radiata	FooDB	31437929
Plant		Prunus dulcis	FooDB	31437929
Plant		Beta vulgaris ssp. cicla	FooDB	31437929
Plant		Ipomoea aquatica	FooDB	31437929
Plant		Rubus spectabilis	FooDB	31437929
Plant		Musa x paradisiaca	FooDB	31437929
Plant		Cuminum cyminum	FooDB	31437929
Plant		Allium sativum	FooDB	31437929
Plant		Sinapis alba	FooDB	31437929
Plant		Cantharellus cibarius	FooDB	31437929
Plant		Fragaria x ananassa	FooDB	31437929
Plant		Brassica ruvo	FooDB	31437929
Plant		Arachis hypogaea	FooDB	31437929
Plant		Pyrus communis	FooDB	31437929
Plant		Rubus idaeus	FooDB	31437929
Plant		Morus nigra	FooDB	31437929
Plant		Apium graveolens var. secalinum	FooDB	31437929
Plant		Pinus edulis	FooDB	31437929
Plant		Abelmoschus esculentus	FooDB	31437929
Plant		Solanum lycopersicum	FooDB	31437929
Plant		Opuntia macrorhiza	FooDB	31437929
Plant		Moringa oleifera	FooDB	31437929
Plant		Passiflora edulis	FooDB	31437929
Plant		Vigna angularis	FooDB	31437929
Plant		Manilkara zapota	FooDB	31437929
Plant		Allium cepa	FooDB	31437929
Plant		Mentha spicata	FooDB	31437929
Plant		Malus	FooDB	31437929
Plant		Cucurbita pepo var. clypeata	FooDB	31437929
Plant		Corylus	FooDB	31437929
Plant		Juglans	FooDB	31437929
Plant		Sambucus nigra	FooDB	31437929
Plant		Helianthus annuus	FooDB	31437929
Plant		Mangifera indica	FooDB	31437929
Plant			FooDB	31437929
Plant		Ribes nigrum	FooDB	31437929
Plant		Illicium verum	FooDB	31437929
Plant		Zingiber officinale	FooDB	31437929
Plant		Chamaemelum nobile	FooDB	31437929
Plant		Auricularia auricula-judae	FooDB	31437929
Plant		Petroselinum crispum	FooDB	31437929
Plant		Pisum sativum	FooDB	31437929
Plant		Laurus nobilis	FooDB	31437929
Plant		Attalea speciosa	FooDB	31437929
Plant		Juglans ailanthifolia	FooDB	31437929
Plant		Polygonum alpinum	FooDB	31437929
Plant		Melissa officinalis	FooDB	31437929
Plant		Hippophae rhamnoides	FooDB	31437929
Plant		Pediomelum esculentum	FooDB	31437929
Plant		Brassica juncea	FooDB	31437929
Plant		Auricularia polytricha	FooDB	31437929
Plant		Camellia oleifera	FooDB	31437929
Plant		Vaccinium corymbosum	FooDB	31437929
Plant		Chrysanthemum coronarium	FooDB	31437929
Plant		Eleocharis dulcis	FooDB	31437929
Plant		Actinidia chinensis	FooDB	31437929
Plant		Spinacia oleracea	FooDB	31437929
Plant		Carica papaya	FooDB	31437929
Plant		Thymus vulgaris	FooDB	31437929
Plant		Rubus arcticus	FooDB	31437929
Plant		Medicago sativa	FooDB	31437929
Plant		Pimenta dioica	FooDB	31437929
Plant		Rumex articus	FooDB	31437929
Plant		Vigna mungo	FooDB	31437929
Plant		Agaricus bisporus	FooDB	31437929
Plant		Cajanus cajan	FooDB	31437929
Plant		Hibiscus sabdariffa	FooDB	31437929
Plant		Canarium ovatum	FooDB	31437929
Plant		Benincasa hispida	FooDB	31437929
Plant		Ribes aureum var. villosum	FooDB	31437929
Plant		Origanum majorana	FooDB	31437929
Plant		Armoracia rusticana	FooDB	31437929
Plant		Prunus persica	FooDB	31437929
Plant		Cucurbita pepo var. cylindrica	FooDB	31437929
Plant		Brassica oleracea var. gemmifera	FooDB	31437929
Plant		Vaccinium macrocarpon	FooDB	31437929
Plant		Brassica oleracea var. gongylodes	FooDB	31437929
Plant		Eruca vesicaria ssp. sativa	FooDB	31437929
Plant		Foeniculum vulgare	FooDB	31437929
Plant		Arctium lappa	FooDB	31437929
Plant		Juglans cinerea	FooDB	31437929
Plant		Phoenix dactylifera	FooDB	31437929
Plant		Artocarpus altilis	FooDB	31437929
Plant		Metroxylon sagu	FooDB	31437929
Plant		Vitis rotundifolia	FooDB	31437929
Plant		Prunus cerasus	FooDB	31437929
Plant		Vigna unguiculata	FooDB	31437929
Plant		Cynara scolymus	FooDB	31437929
Plant		Psidium cattleianum	FooDB	31437929
Plant		Cyathea	FooDB	31437929
Plant			FooDB	31437929
Plant		Brosimum alicastrum	FooDB	31437929
Plant		Citrus x paradisi	FooDB	31437929
Plant		Rosmarinus officinalis	FooDB	31437929
Plant		Castanea mollissima	FooDB	31437929
Plant		Lentinus edodes	FooDB	31437929
Plant		Ficus carica	FooDB	31437929
Plant		Morus	FooDB	31437929
Plant		Vitis labrusca	FooDB	31437929
Plant		Lepidium sativum	FooDB	31437929
Plant		Phytolacca americana	FooDB	31437929
Plant		Helianthus tuberosus	FooDB	31437929
Plant		Grifola frondosa	FooDB	31437929
Plant		Beta vulgaris var. rubra	FooDB	31437929
Plant		Tetragonia tetragonioides	FooDB	31437929
Plant		Cucumis metuliferus	FooDB	31437929
Plant		Myrica	FooDB	31437929
Plant		Nephelium lappaceum	FooDB	31437929
Plant		Artemisia vulgaris	FooDB	31437929
Plant		Castanea crenata	FooDB	31437929
Plant		Litchi chinensis	FooDB	31437929
Plant		Quercus	FooDB	31437929
Plant		Corylus avellana	FooDB	31437929
Plant		Vaccinium angustifolium	FooDB	31437929
Plant		Malpighia emarginata	FooDB	31437929
Plant		Juglans regia	FooDB	31437929
Plant		Trigonella foenum-graecum	FooDB	31437929
Plant		Physalis	FooDB	31437929
Plant		Thelesperma	FooDB	31437929
Plant			FooDB	31437929
Plant		Brassica oleracea var. sabauda	FooDB	31437929
Plant		Chamerion angustifolium	FooDB	31437929
Plant		Brassica napus	FooDB	31437929
Plant		Vaccinium elliottii	FooDB	31437929
Plant		Asparagus officinalis	FooDB	31437929
Plant		Levisticum officinale	FooDB	31437929
Plant		Ziziphus zizyphus	FooDB	31437929
Plant		Dimocarpus longan	FooDB	31437929
Plant		Citrus aurantiifolia	FooDB	31437929
Plant		Salvia hispanica	FooDB	31437929
Plant		Matricaria recutita	FooDB	31437929
Plant		Cynara cardunculus	FooDB	31437929
Plant		Pangium edule	FooDB	31437929
Plant		Lactuca sativa	FooDB	31437929
Plant		Pimpinella anisum	FooDB	31437929
Plant		Artemisia dracunculus	FooDB	31437929
Plant		Vitellaria paradoxa	FooDB	31437929
Plant		Allium	FooDB	31437929
Plant		Brassica oleracea var. viridis	FooDB	31437929
Plant		Eragrostis tef	FooDB	31437929
Plant		Agave	FooDB	31437929
Plant		Pistacia vera	FooDB	31437929
Plant		Hedysarum alpinum	FooDB	31437929
Plant		Vigna aconitifolia	FooDB	31437929
Plant		Malus pumila	FooDB	31437929
Plant		Diospyros	FooDB	31437929
Plant		Amaranthus	FooDB	31437929
Plant		Punica granatum	FooDB	31437929
Plant		Mammea americana	FooDB	31437929
Plant		Gossypium	FooDB	31437929
Plant		Brassica alboglabra	FooDB	31437929
Plant		Apium graveolens var. dulce	FooDB	31437929
Plant		Beta vulgaris	FooDB	31437929
Plant		Annona squamosa	FooDB	31437929
Plant		Xanthosoma sagittifolium	FooDB	31437929
Plant		Basella alba	FooDB	31437929
Plant		Vitis	FooDB	31437929

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Blood	Detected and Quantified	0.2		0.0	0.5	uM	Adult (>18 years old)	Both	Normal	HMDB	3243806
Human Urine	Detected and Quantified	0.65	0.27			umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	15116424
Human All tissues	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified						Children (6 - 18 years old)	Not Specified	Normal	HMDB	27609529
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0000014

DrugBank ID

DB02594

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021871

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

15698

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Olivares J, Verdys M: Isocratic high-performance liquid chromatographic method for studying the metabolism of blood plasma pyrimidine nucleosides and bases: concentration and radioactivity measurements. J Chromatogr. 1988 Dec 29;434(1):111-21. doi: 10.1016/0378-4347(88)80066-5. [PubMed:3243806 ]
Wepierre J, Marty JP, Chanal JL, Sincholle D: Percutaneous absorption of 5-iodo-2' deoxycytidine in the hairless rat and in man. Eur J Drug Metab Pharmacokinet. 1984 Jan-Mar;9(1):79-83. doi: 10.1007/BF03189608. [PubMed:6714272 ]
Coral S, Sigalotti L, Altomonte M, Engelsberg A, Colizzi F, Cattarossi I, Maraskovsky E, Jager E, Seliger B, Maio M: 5-aza-2'-deoxycytidine-induced expression of functional cancer testis antigens in human renal cell carcinoma: immunotherapeutic implications. Clin Cancer Res. 2002 Aug;8(8):2690-5. [PubMed:12171902 ]
Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. doi: 10.1002/rcm.1400. [PubMed:15116424 ]
van den Bosch J, Lubbert M, Verhoef G, Wijermans PW: The effects of 5-aza-2'-deoxycytidine (Decitabine) on the platelet count in patients with intermediate and high-risk myelodysplastic syndromes. Leuk Res. 2004 Aug;28(8):785-90. doi: 10.1016/j.leukres.2003.11.016. [PubMed:15203276 ]
Lopez-Gomez C, Levy RJ, Sanchez-Quintero MJ, Juanola-Falgarona M, Barca E, Garcia-Diaz B, Tadesse S, Garone C, Hirano M: Deoxycytidine and Deoxythymidine Treatment for Thymidine Kinase 2 Deficiency. Ann Neurol. 2017 May;81(5):641-652. doi: 10.1002/ana.24922. Epub 2017 May 4. [PubMed:28318037 ]
Charles J. Pouchert (1992). Aldrich Library of 13C and 1H FT NMR Spectra, 1992, 3, 396A, 396C, (nmr). Aldrich Chemical.
Charles J. Pouchert (1985). Aldrich Library of FT-IR Spectra, 1st edn., 1985, 2, 832B, 838D, 839C, (ir). Aldrich Chemical Company.
Benz, E. et al. (1965). Benz, E. et al., J.O.C., 1965, 30, 3067-3071, (4N-benzoyl, 5'-tosyl, 3',4N-dibenzoyl, 4N,5'-dibenzoyl, 5'-tosyl 4N-benzoyl, 5'-trityl 3',4N-dibenzoyl). J.O.C..
Charubala, R. et al. (1984). Charubala, R. et al., Synthesis, 1984, 965-968, (5'-(4,4'-dimethoxytrityl) 4N-benzoyl). Synthesis.
FOX JJ, WEMPEN I. (1959). FOX JJ, WEMPEN I. Pyrimidine nucleosides. Adv Carbohydr Chem. 1959;14:283-380.. Adv Carbohydr Chem..
Hruska, F.E. et al. (1974). Hruska, F.E. et al., Can. J. Chem., 1974, 52, 497-508, (pmr). Can. J. Chem..
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Showing metabocard for Deoxycytidine (MMDBc0000490)

MOL for #<Metabolite:0x00007f4660b526f8>

3D MOL for #<Metabolite:0x00007f4660b526f8>

3D SDF for #<Metabolite:0x00007f4660b526f8>

3D-SDF for #<Metabolite:0x00007f4660b526f8>

PDB for #<Metabolite:0x00007f4660b526f8>

3D PDB for #<Metabolite:0x00007f4660b526f8>

SMILES for #<Metabolite:0x00007f4660b526f8>

INCHI for #<Metabolite:0x00007f4660b526f8>

Structure for #<Metabolite:0x00007f4660b526f8>

3D Structure for #<Metabolite:0x00007f4660b526f8>