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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (12) Show 12 proteins XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:48:16 UTC

HMDB ID

HMDB0000014

Secondary Accession Numbers

HMDB00014

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>
HMDB0000014

> <DATABASE_NAME>
hmdb

> <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

View in JSmol View Stereo Labels

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

Chemical Formula

C₉H₁₃N₃O₄

Average Molecular Weight

227.2172

Monoisotopic Molecular Weight

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

951-77-9

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 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	207 - 210 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	870 mg/mL	Not Available
LogP	-1.77	HANSCH,C ET AL. (1995)

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	MetCCS_train_neg	146.842	30932474
[M-H]-	Not Available	148.6	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000095

Predicted Molecular 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	149.431	31661259
DarkChem	[M-H]-	148.182	31661259
AllCCS	[M+H]+	151.032	32859911
AllCCS	[M-H]-	150.18	32859911
DeepCCS	[M+H]+	152.479	30932474
DeepCCS	[M-H]-	150.084	30932474
DeepCCS	[M-2H]-	183.619	30932474
DeepCCS	[M+Na]+	158.771	30932474
AllCCS	[M+H]+	151.0	32859911
AllCCS	[M+H-H2O]+	147.2	32859911
AllCCS	[M+NH4]+	154.6	32859911
AllCCS	[M+Na]+	155.6	32859911
AllCCS	[M-H]-	150.2	32859911
AllCCS	[M+Na-2H]-	150.3	32859911
AllCCS	[M+HCOO]-	150.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	1.71 minutes	32390414
Predicted by Siyang on May 30, 2022	8.961 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	5.07 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	129.5 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	463.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	236.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	66.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	156.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	57.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	285.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	249.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	649.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	572.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	45.9 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	735.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	162.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	184.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	553.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	364.7 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	176.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Deoxycytidine	NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1	3645.4	Standard polar	33892256
Deoxycytidine	NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1	2267.7	Standard non polar	33892256
Deoxycytidine	NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1	2531.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Deoxycytidine,1TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(N)=NC2=O)O[C@@H]1CO	2307.8	Semi standard non polar	33892256
Deoxycytidine,1TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C[C@@H]1O	2304.6	Semi standard non polar	33892256
Deoxycytidine,1TMS,isomer #3	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=C1	2373.7	Semi standard non polar	33892256
Deoxycytidine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C[C@@H]1O[Si](C)(C)C	2266.8	Semi standard non polar	33892256
Deoxycytidine,2TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO)O2)C=C1	2356.3	Semi standard non polar	33892256
Deoxycytidine,2TMS,isomer #3	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO[Si](C)(C)C)O2)C=C1	2348.1	Semi standard non polar	33892256
Deoxycytidine,2TMS,isomer #4	C[Si](C)(C)N(C1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=C1)[Si](C)(C)C	2328.2	Semi standard non polar	33892256
Deoxycytidine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C=C1	2347.2	Semi standard non polar	33892256
Deoxycytidine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C=C1	2462.3	Standard non polar	33892256
Deoxycytidine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C=C1	3051.1	Standard polar	33892256
Deoxycytidine,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O[C@@H]1CO	2310.2	Semi standard non polar	33892256
Deoxycytidine,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O[C@@H]1CO	2478.6	Standard non polar	33892256
Deoxycytidine,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O[C@@H]1CO	2913.3	Standard polar	33892256
Deoxycytidine,3TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O	2327.0	Semi standard non polar	33892256
Deoxycytidine,3TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O	2511.3	Standard non polar	33892256
Deoxycytidine,3TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O	2940.8	Standard polar	33892256
Deoxycytidine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C	2344.1	Semi standard non polar	33892256
Deoxycytidine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C	2511.0	Standard non polar	33892256
Deoxycytidine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C	2703.0	Standard polar	33892256
Deoxycytidine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(N)=NC2=O)O[C@@H]1CO	2565.3	Semi standard non polar	33892256
Deoxycytidine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C[C@@H]1O	2558.6	Semi standard non polar	33892256
Deoxycytidine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=C1	2637.0	Semi standard non polar	33892256
Deoxycytidine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C	2745.4	Semi standard non polar	33892256
Deoxycytidine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O2)C=C1	2813.5	Semi standard non polar	33892256
Deoxycytidine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C=C1	2804.8	Semi standard non polar	33892256
Deoxycytidine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=C1)[Si](C)(C)C(C)(C)C	2776.3	Semi standard non polar	33892256
Deoxycytidine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C=C1	3000.3	Semi standard non polar	33892256
Deoxycytidine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C=C1	3107.2	Standard non polar	33892256
Deoxycytidine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C=C1	3218.9	Standard polar	33892256
Deoxycytidine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O[C@@H]1CO	2978.2	Semi standard non polar	33892256
Deoxycytidine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O[C@@H]1CO	3117.6	Standard non polar	33892256
Deoxycytidine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O[C@@H]1CO	3103.6	Standard polar	33892256
Deoxycytidine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O	2968.3	Semi standard non polar	33892256
Deoxycytidine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O	3138.0	Standard non polar	33892256
Deoxycytidine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O	3138.2	Standard polar	33892256
Deoxycytidine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C	3181.9	Semi standard non polar	33892256
Deoxycytidine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C	3333.8	Standard non polar	33892256
Deoxycytidine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C	3050.0	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Extracellular
Mitochondria
Nucleus
Lysosome

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

All Tissues

Pathways

Name	SMPDB/PathBank	KEGG
Pyrimidine metabolism	Not Available
Beta Ureidopropionase Deficiency		Not Available
UMP Synthase Deficiency (Orotic Aciduria)		Not Available
Dihydropyrimidinase Deficiency		Not Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.2 (0.0-0.5) uM	Adult (>18 years old)	Both	Normal	3243806	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Normal	27609529	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Urine	Detected and Quantified	0.65 +/- 0.27 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	15116424	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Crohns disease	27609529	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Ulcerative colitis	27609529	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Unclassified IBD	27609529	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details

Associated Disorders and Diseases

Disease References

Crohn's disease
Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Ulcerative colitis
Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Colorectal cancer
Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]

Associated OMIM IDs

266600 (Crohn's disease)
114500 (Colorectal cancer)

External Links

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

VMH ID

DCYT

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Fox, Jack F.; Yung, Naishun; Wempen, Iris; Hoffer, Max. Pyrimidine nucleosides. XII. Direct synthesis of 2'-deoxycytidine and its a-anomer. Journal of the American Chemical Society (1961), 83 4066-50.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

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. [PubMed:15203276 ]
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. [PubMed:15116424 ]
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. [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 ]
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. [PubMed:3243806 ]
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 ]
(). Maley, F. et al., J. Biol. Chem., 1958, 233, 1538-1543, (5-diphosphate). .
(). Charubala, R. et al., Synthesis, 1984, 965-968, (5'-(4,4'-dimethoxytrityl) 4N-benzoyl). .
(). Schaller, H. et al., J.A.C.S., 1963, 85, 3821-3827, (5'-(4,4'-dimethoxytrityl) 4N-benzoyl). .
(). 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). .
(). Hruska, F.E. et al., Can. J. Chem., 1974, 52, 497-508, (pmr). .
(). Jones, A.J. et al., Proc. Natl. Acad. Sci. U.S.A., 1970, 65, 27-30, CA, 72, 96682j, (cmr). .
(). Miles, H.T., J.A.C.S., 1963, 85, 1007-1008, (ir, pmr). .
(). Young, D.W. et al., Acta Cryst. B, 1975, 31, 961-965, (cryst struct). .
(). Michelson, A.M. et al., J.C.S., 1954, 34-40, (phosphates, 3',4N-di-Ac, 5'-trityl, 5'-trityl 3',4N-di-Ac). .
(). Lewis, R.J., Sax's Dangerous Properties of Industrial Materials, 8th edn., Van Nostrand Reinhold, 1992, DAQ850. .
(). Aldrich Library of 13C and 1H FT NMR Spectra, 1992, 3, 396A, 396C, (nmr). .
(). Stawinski, J. et al., Chem. Comm., 1976, 243-244, (3',4N,5'-tribenzoyl). .
(). Ulbricht TL. Nucleosides. 3. Synthesis of 1-methyl-2'-deoxycytidine, and comments on the N.m.r. spectra of cytosine nucleosides. J Chem Soc Perkin 1. 1965 Sep:6134-5.. .
(). Wang Z, Prudhomme DR, Buck JR, Park M, Rizzo CJ. Stereocontrolled syntheses of deoxyribonucleosides via photoinduced electron-transfer deoxygenation of benzoyl-protected ribo- and arabinonucleosides. J Org Chem. 2000 Sep 22;65(19):5969-85. . .
(). Saneyoshi M, Tohyama J, Nakayama C, Takiya S, Iwabuchi M. Inhibitory effects of 3'deoxycytidine 5'-triphosphate and 3'-deoxyuridine 5'-triphosphate on DNA-dependent RNA polymerases I and II purified from Dictyostelium discoideum cells. Nucleic Acids Res. 1981 Jul 10;9(13):3129-38.. .
(). FOX JJ, WEMPEN I. Pyrimidine nucleosides. Adv Carbohydr Chem. 1959;14:283-380.. .
(). Raffaele Saladino, Enrico Mincione, Claudia Crestini, Maurizio Mezzetti. Transformations of thiopyrimidine and thiopurine nucleosides following oxidation with dimethyldioxirane. Tetrahedron, 1996, 52, 6759-6780. .
(). Aldrich Library of FT-IR Spectra, 1st edn., 1985, 2, 832B, 838D, 839C, (ir). .
(). Yang, J.T. et al., CA, 1966, 65, 12454, (ord). .

Only showing the first 10 proteins. There are 12 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details

1. 5'-nucleotidase

General function:: Involved in hydrolase activity
Specific function:: Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:: NT5E
Uniprot ID:: P21589
Molecular weight:: 57948.125

Reactions

dCMP + Water → Deoxycytidine + Phosphate	details

Enzyme Details

2. Cytosolic 5'-nucleotidase 1B

General function:: Involved in nucleotide binding
Specific function:: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:: NT5C1B
Uniprot ID:: Q96P26
Molecular weight:: 68803.055

Reactions

dCMP + Water → Deoxycytidine + Phosphate	details

Enzyme Details

3. Cytosolic 5'-nucleotidase 1A

General function:: Involved in nucleotide binding
Specific function:: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:: NT5C1A
Uniprot ID:: Q9BXI3
Molecular weight:: 41020.145

Reactions

dCMP + Water → Deoxycytidine + Phosphate	details

Enzyme Details

4. 5'(3')-deoxyribonucleotidase, cytosolic type

General function:: Involved in metal ion binding
Specific function:: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:: NT5C
Uniprot ID:: Q8TCD5
Molecular weight:: Not Available

Reactions

dCMP + Water → Deoxycytidine + Phosphate	details

Enzyme Details

5. Deoxycytidine kinase

General function:: Involved in ATP binding
Specific function:: Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.
Gene Name:: DCK
Uniprot ID:: P27707
Molecular weight:: 30518.315

Reactions

NTP + Deoxycytidine → NDP + dCMP	details
Adenosine triphosphate + Deoxycytidine → ADP + dCMP	details

References

Giovannetti E, Mey V, Loni L, Nannizzi S, Barsanti G, Savarino G, Ricciardi S, Del Tacca M, Danesi R: Cytotoxic activity of gemcitabine and correlation with expression profile of drug-related genes in human lymphoid cells. Pharmacol Res. 2007 Apr;55(4):343-9. Epub 2007 Jan 16. [PubMed:17296311 ]

Enzyme Details

6. 5'(3')-deoxyribonucleotidase, mitochondrial

General function:: Involved in phosphatase activity
Specific function:: Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:: NT5M
Uniprot ID:: Q9NPB1
Molecular weight:: Not Available

Reactions

dCMP + Water → Deoxycytidine + Phosphate	details

Enzyme Details

7. AID

General function:: Involved in zinc ion binding
Specific function:: Not Available
Gene Name:: AID
Uniprot ID:: Q546Y9
Molecular weight:: 23953.3

Enzyme Details

8. Cytosolic 5'-nucleotidase 3

General function:: Involved in magnesium ion binding
Specific function:: Can act both as nucleotidase and as phosphotransferase.
Gene Name:: NT5C3
Uniprot ID:: Q9H0P0
Molecular weight:: 33914.91

Reactions

dCMP + Water → Deoxycytidine + Phosphate	details

Enzyme Details

9. Cytosolic purine 5'-nucleotidase

General function:: Involved in 5'-nucleotidase activity
Specific function:: May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:: NT5C2
Uniprot ID:: P49902
Molecular weight:: 64969.2

Reactions

dCMP + Water → Deoxycytidine + Phosphate	details

Enzyme Details

10. Cytidine deaminase

General function:: Involved in zinc ion binding
Specific function:: This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
Gene Name:: CDA
Uniprot ID:: P32320
Molecular weight:: 16184.545

Reactions

Deoxycytidine + Water → Deoxyuridine + Ammonia	details

Only showing the first 10 proteins. There are 12 proteins in total.

Show all enzymes and transporters

Showing metabocard for Deoxycytidine (HMDB0000014)

MOL for HMDB0000014 (Deoxycytidine)

3D MOL for HMDB0000014 (Deoxycytidine)

3D SDF for HMDB0000014 (Deoxycytidine)

3D-SDF for HMDB0000014 (Deoxycytidine)

PDB for HMDB0000014 (Deoxycytidine)

3D PDB for HMDB0000014 (Deoxycytidine)

SMILES for HMDB0000014 (Deoxycytidine)

INCHI for HMDB0000014 (Deoxycytidine)

Structure for HMDB0000014 (Deoxycytidine)

3D Structure for HMDB0000014 (Deoxycytidine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

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References

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