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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (22) Show 22 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 15:48:15 UTC

HMDB ID

HMDB0000089

Secondary Accession Numbers

HMDB00089

Metabolite Identification

Common Name

Cytidine

Description

Cytidine is a nucleoside that is composed of the base cytosine linked to the five-carbon sugar D-ribose. Cytidine is a pyrimidine that besides being incorporated into nucleic acids, can serve as a substrate for the salvage pathway of pyrimidine nucleotide synthesis. It is a precursor of cytidine triphosphate (CTP) needed in the phosphatidylcholine (PC) and phosphatidylethanolamine (PE) biosynthetic pathways. These variations probably reflect the species differences in cytidine deaminase, the enzyme that converts cytidine to uridine in the body. The transport of cytidine into the brain's extracellular fluid, and then into neurons and glia, are essential prerequisites for cytidine to be utilized in the brain. An efficient mechanism mediating the brain uptake of circulating cytidine has not yet been demonstrated. The biosynthesis of PC, the most abundant phosphatide in the brain, via the Kennedy pathway requires phosphocholine and cytidine triphosphate (CTP), a cytidine nucleotide involved in the rate-limiting step. The enzyme that converts CTP to endogenous CDP-choline (CTP:phosphocholine cytidylyltransferase) is unsaturated at physiological brain CTP levels. APOBEC is a family of enzymes that has been discovered with the ability to deaminate cytidines on RNA or DNA. The human apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G protein (APOBEC3G, or hA3G), provides cells with an intracellular antiretroviral activity that is associated with the hypermutation of viral DNA through cytidine deamination. Indeed, hA3G belongs to a family of vertebrate proteins that contains one or two copies of a signature sequence motif unique to cytidine deaminases (CTDAs) (PMID: 16769123 , 15780864 , 16720547 ).

Structure

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

HMDB0000089
     RDKit          3D
Cytidine
 30 31  0  0  0  0  0  0  0  0999 V2000
    5.1978    0.6246   -0.2072 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8005    0.4059   -0.0887 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2787   -0.7586   -0.5851 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -0.9812   -0.4771 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0904   -0.0790    0.1108 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2679   -0.4203    0.1625 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9377   -0.4091   -1.0625 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2769   -0.5996   -0.7784 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1069    0.4061   -1.5491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7614    1.7108   -1.2066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4905   -0.3544    0.6989 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4951   -1.5835    1.3652 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1797    0.3887    1.0053 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8959    0.3487    2.3596 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6152    1.0387    0.5834 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546    1.8762    1.1256 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9564    1.2668    0.4787 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8450    0.0758    0.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5941    1.3115   -0.8652 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9414   -1.4796   -1.0532 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5486   -1.9085   -0.8774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3521   -1.4868    0.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5697   -1.6285   -1.0734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9783    0.2807   -2.6508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1841    0.2988   -1.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2109    2.1478   -1.9007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3688    0.2575    0.9174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4873   -2.3421    0.7026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3689    1.4211    0.6382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7245    0.1713    2.8763 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
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  2  0
 13  6  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  6 22  1  1
  8 23  1  6
  9 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  6
 12 28  1  0
 13 29  1  6
 14 30  1  0
M  END


  Mrv1652309032023512D          

 17 18  0  0  0  0            999 V2000
10000.1808 9998.4527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.3932 9998.4609    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.925710000.3093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2110 9999.8986    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.3995 9999.0747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.828910001.5463    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10001.4009 9999.8967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.115310000.3092    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10002.115310001.1343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.400910001.5468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.686410001.1343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.686410000.3092    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.304010000.3929    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9714 9999.9079    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.7165 9999.1233    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.8915 9999.1233    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.6366 9999.9079    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  3  4  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
 11 12  1  0  0  0  0
 12  7  1  0  0  0  0
  7  5  2  0  0  0  0
  9  6  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 13 14  1  0  0  0  0
 13 17  1  0  0  0  0
 15  1  1  6  0  0  0
 14 12  1  1  0  0  0
 17  3  1  1  0  0  0
 16  2  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0000089

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
UHDGCWIWMRVCDJ-XVFCMESISA-N

> <FORMULA>
C9H13N3O5

> <MOLECULAR_WEIGHT>
243.2166

> <EXACT_MASS>
243.085520541

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
22.396851839019853

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-2.18

> <JCHEM_LOGP>
-2.7975172843333334

> <ALOGPS_LOGS>
-0.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.933688762534231

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.553240841265485

> <JCHEM_PKA_STRONGEST_BASIC>
-0.06234248538184939

> <JCHEM_POLAR_SURFACE_AREA>
128.60999999999999

> <JCHEM_REFRACTIVITY>
54.544799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.38e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cytidine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000089
     RDKit          3D
Cytidine
 30 31  0  0  0  0  0  0  0  0999 V2000
    5.1978    0.6246   -0.2072 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8005    0.4059   -0.0887 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2787   -0.7586   -0.5851 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -0.9812   -0.4771 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0904   -0.0790    0.1108 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2679   -0.4203    0.1625 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9377   -0.4091   -1.0625 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2769   -0.5996   -0.7784 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1069    0.4061   -1.5491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7614    1.7108   -1.2066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4905   -0.3544    0.6989 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4951   -1.5835    1.3652 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1797    0.3887    1.0053 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8959    0.3487    2.3596 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6152    1.0387    0.5834 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546    1.8762    1.1256 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9564    1.2668    0.4787 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8450    0.0758    0.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5941    1.3115   -0.8652 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9414   -1.4796   -1.0532 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5486   -1.9085   -0.8774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3521   -1.4868    0.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5697   -1.6285   -1.0734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9783    0.2807   -2.6508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1841    0.2988   -1.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2109    2.1478   -1.9007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3688    0.2575    0.9174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4873   -2.3421    0.7026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3689    1.4211    0.6382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7245    0.1713    2.8763 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
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  2  0
 13  6  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  6 22  1  1
  8 23  1  6
  9 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  6
 12 28  1  0
 13 29  1  6
 14 30  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  O   UNK     0    8667.0048663.778   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8663.6678663.794   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8662.7958667.244   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8661.4618666.477   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8669.2798664.939   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0    8671.9478669.553   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8669.2828666.474   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0    8670.6158667.244   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0    8670.6158668.784   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8669.2828669.554   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8667.9488668.784   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0    8667.9488667.244   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0    8665.3678667.400   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0    8666.6138666.495   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8666.1378665.030   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8664.5978665.030   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8664.1228666.495   0.000  0.00  0.00           C+0
CONECT    1   15                                                            
CONECT    2   16                                                            
CONECT    3    4   17                                                       
CONECT    4    3                                                            
CONECT    5    7                                                            
CONECT    6    9                                                            
CONECT    7    8   12    5                                                  
CONECT    8    7    9                                                       
CONECT    9   10    8    6                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    7   14                                                  
CONECT   13   14   17                                                       
CONECT   14   15   13   12                                                  
CONECT   15   14   16    1                                                  
CONECT   16   15   17    2                                                  
CONECT   17   16   13    3                                                  
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0000089
HETATM    1  N1  UNL     1       5.198   0.625  -0.207  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.800   0.406  -0.089  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.279  -0.759  -0.585  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.934  -0.981  -0.477  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.090  -0.079   0.111  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.268  -0.420   0.163  1.00  0.00           C  
HETATM    7  O1  UNL     1      -0.938  -0.409  -1.062  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.277  -0.600  -0.778  1.00  0.00           C  
HETATM    9  C6  UNL     1      -3.107   0.406  -1.549  1.00  0.00           C  
HETATM   10  O2  UNL     1      -2.761   1.711  -1.207  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.491  -0.354   0.699  1.00  0.00           C  
HETATM   12  O3  UNL     1      -2.495  -1.583   1.365  1.00  0.00           O  
HETATM   13  C8  UNL     1      -1.180   0.389   1.005  1.00  0.00           C  
HETATM   14  O4  UNL     1      -0.896   0.349   2.360  1.00  0.00           O  
HETATM   15  C9  UNL     1       1.615   1.039   0.583  1.00  0.00           C  
HETATM   16  O5  UNL     1       0.855   1.876   1.126  1.00  0.00           O  
HETATM   17  N3  UNL     1       2.956   1.267   0.479  1.00  0.00           N  
HETATM   18  H1  UNL     1       5.845   0.076   0.388  1.00  0.00           H  
HETATM   19  H2  UNL     1       5.594   1.312  -0.865  1.00  0.00           H  
HETATM   20  H3  UNL     1       3.941  -1.480  -1.053  1.00  0.00           H  
HETATM   21  H4  UNL     1       1.549  -1.909  -0.877  1.00  0.00           H  
HETATM   22  H5  UNL     1      -0.352  -1.487   0.524  1.00  0.00           H  
HETATM   23  H6  UNL     1      -2.570  -1.628  -1.073  1.00  0.00           H  
HETATM   24  H7  UNL     1      -2.978   0.281  -2.651  1.00  0.00           H  
HETATM   25  H8  UNL     1      -4.184   0.299  -1.354  1.00  0.00           H  
HETATM   26  H9  UNL     1      -2.211   2.148  -1.901  1.00  0.00           H  
HETATM   27  H10 UNL     1      -3.369   0.258   0.917  1.00  0.00           H  
HETATM   28  H11 UNL     1      -2.487  -2.342   0.703  1.00  0.00           H  
HETATM   29  H12 UNL     1      -1.369   1.421   0.638  1.00  0.00           H  
HETATM   30  H13 UNL     1      -1.724   0.171   2.876  1.00  0.00           H  
CONECT    1    2   18   19
CONECT    2    3   17   17
CONECT    3    4    4   20
CONECT    4    5   21
CONECT    5    6   15
CONECT    6    7   13   22
CONECT    7    8
CONECT    8    9   11   23
CONECT    9   10   24   25
CONECT   10   26
CONECT   11   12   13   27
CONECT   12   28
CONECT   13   14   29
CONECT   14   30
CONECT   15   16   16   17
END

HMDB0000089
     RDKit          3D
Cytidine
 30 31  0  0  0  0  0  0  0  0999 V2000
    5.1978    0.6246   -0.2072 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8005    0.4059   -0.0887 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2787   -0.7586   -0.5851 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -0.9812   -0.4771 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0904   -0.0790    0.1108 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2679   -0.4203    0.1625 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9377   -0.4091   -1.0625 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2769   -0.5996   -0.7784 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1069    0.4061   -1.5491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7614    1.7108   -1.2066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4905   -0.3544    0.6989 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4951   -1.5835    1.3652 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1797    0.3887    1.0053 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8959    0.3487    2.3596 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6152    1.0387    0.5834 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546    1.8762    1.1256 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9564    1.2668    0.4787 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8450    0.0758    0.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5941    1.3115   -0.8652 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9414   -1.4796   -1.0532 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5486   -1.9085   -0.8774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3521   -1.4868    0.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5697   -1.6285   -1.0734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9783    0.2807   -2.6508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1841    0.2988   -1.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2109    2.1478   -1.9007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3688    0.2575    0.9174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4873   -2.3421    0.7026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3689    1.4211    0.6382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7245    0.1713    2.8763 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
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  2  0
 13  6  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  6 22  1  1
  8 23  1  6
  9 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  6
 12 28  1  0
 13 29  1  6
 14 30  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1-beta-D-Ribofuranosylcytosine	ChEBI
1beta-D-Ribofuranosylcytosine	ChEBI
4-AMINO-1-BETA-D-ribofuranosyl-2(1H)-pyrimidinone	ChEBI
4-Amino-1-beta-D-ribofuranosylpyrimidin-2(1H)-one	ChEBI
4-Amino-1beta-D-ribofuranosyl-2(1H)-pyrimidinone	ChEBI
Cyd	ChEBI
Cytidin	ChEBI
Cytosine riboside	ChEBI
Cytosine-1beta-D-ribofuranoside	ChEBI
Zytidin	ChEBI
Posilent	Kegg
1-b-D-Ribofuranosylcytosine	Generator
1-Β-D-ribofuranosylcytosine	Generator
1b-D-Ribofuranosylcytosine	Generator
1Β-D-ribofuranosylcytosine	Generator
4-AMINO-1-b-D-ribofuranosyl-2(1H)-pyrimidinone	Generator
4-AMINO-1-β-D-ribofuranosyl-2(1H)-pyrimidinone	Generator
4-Amino-1-b-D-ribofuranosylpyrimidin-2(1H)-one	Generator
4-Amino-1-β-D-ribofuranosylpyrimidin-2(1H)-one	Generator
4-Amino-1b-D-ribofuranosyl-2(1H)-pyrimidinone	Generator
4-Amino-1β-D-ribofuranosyl-2(1H)-pyrimidinone	Generator
Cytosine-1b-D-ribofuranoside	Generator
Cytosine-1β-D-ribofuranoside	Generator
1-(b-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine	HMDB
1-(b-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine	HMDB
1-b-D-Ribosyl-cytosine	HMDB
1-beta-D-Ribofuranosyl-cytosine	HMDB
1-beta-delta-Ribofuranosyl-cytosine	HMDB
1-beta-delta-Ribofuranosylcytosine	HMDB
1-beta-delta-Ribosyl-cytosine	HMDB
1beta-delta-Ribofuranosylcytosine	HMDB
1beta-Ribofuranosylcytosine	HMDB
4-Amino-1-beta-delta-ribofuranosyl-2(1H)-pyrimidinone	HMDB
Cytosine-1b-delta-ribofuranoside	HMDB
Cytosine-1beta-delta-ribofuranoside	HMDB
Cytosine ribonucleoside	HMDB
Ribonucleoside, cytosine	HMDB
Riboside, cytosine	HMDB
1-(beta-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine	HMDB
1-(Β-D-ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine	HMDB

Chemical Formula

C₉H₁₃N₃O₅

Average Molecular Weight

243.2166

Monoisotopic Molecular Weight

243.085520541

IUPAC Name

4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

cytidine

CAS Registry Number

65-46-3

SMILES

NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1

InChI Key

UHDGCWIWMRVCDJ-XVFCMESISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Imidolactam
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Primary alcohol
Organic oxide
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organopnictogen compound
Organic oxygen compound
Primary amine
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

cytidines (CHEBI:17562 )
Ribonucleosides (C00475 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	230.5 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	-2.51	HANSCH,C ET AL. (1995)

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Astarita_neg	145.7	30932474
[M-H]-	MetCCS_test_neg	147.4	30932474
[M+H]+	Astarita_pos	148.0	30932474
[M-H]-	Not Available	149.3	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000147

Predicted Molecular Properties

Property	Value	Source
Water Solubility	43.8 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.8	ChemAxon
logS	-0.74	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	-0.062	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	128.61 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	54.54 m³·mol⁻¹	ChemAxon
Polarizability	22.4 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]+	154.289	31661259
DarkChem	[M-H]-	150.855	31661259
AllCCS	[M+H]+	154.648	32859911
AllCCS	[M-H]-	152.418	32859911
DeepCCS	[M+H]+	153.97	30932474
DeepCCS	[M-H]-	151.575	30932474
DeepCCS	[M-2H]-	185.966	30932474
DeepCCS	[M+Na]+	160.999	30932474
AllCCS	[M+H]+	154.6	32859911
AllCCS	[M+H-H2O]+	151.0	32859911
AllCCS	[M+NH4]+	158.1	32859911
AllCCS	[M+Na]+	159.1	32859911
AllCCS	[M-H]-	152.4	32859911
AllCCS	[M+Na-2H]-	152.4	32859911
AllCCS	[M+HCOO]-	152.5	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.	1.67 minutes	32390414
Predicted by Siyang on May 30, 2022	8.8002 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	6.49 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	218.4 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	419.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	241.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	50.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	157.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	50.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	298.5 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	236.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	731.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	540.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	40.3 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	684.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	166.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	201.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	630.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	444.4 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	270.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Cytidine	NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O	3802.7	Standard polar	33892256
Cytidine	NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O	2260.6	Standard non polar	33892256
Cytidine	NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O	2622.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cytidine,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@H](O)[C@@H]1O	2449.8	Semi standard non polar	33892256
Cytidine,1TMS,isomer #2	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N)=NC2=O)[C@@H]1O	2447.9	Semi standard non polar	33892256
Cytidine,1TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(N)=NC1=O	2442.5	Semi standard non polar	33892256
Cytidine,1TMS,isomer #4	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C=C1	2503.8	Semi standard non polar	33892256
Cytidine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2410.6	Semi standard non polar	33892256
Cytidine,2TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2406.7	Semi standard non polar	33892256
Cytidine,2TMS,isomer #3	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O)C=C1	2468.4	Semi standard non polar	33892256
Cytidine,2TMS,isomer #4	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N)=NC2=O)[C@@H]1O[Si](C)(C)C	2395.5	Semi standard non polar	33892256
Cytidine,2TMS,isomer #5	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O)C=C1	2475.9	Semi standard non polar	33892256
Cytidine,2TMS,isomer #6	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C)C=C1	2470.8	Semi standard non polar	33892256
Cytidine,2TMS,isomer #7	C[Si](C)(C)N(C1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C=C1)[Si](C)(C)C	2464.3	Semi standard non polar	33892256
Cytidine,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2357.3	Semi standard non polar	33892256
Cytidine,3TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C)C=C1	2457.8	Semi standard non polar	33892256
Cytidine,3TMS,isomer #3	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O)C=C1	2453.2	Semi standard non polar	33892256
Cytidine,3TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@H](O)[C@@H]1O	2420.4	Semi standard non polar	33892256
Cytidine,3TMS,isomer #5	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C=C1	2451.9	Semi standard non polar	33892256
Cytidine,3TMS,isomer #6	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H]1O	2405.7	Semi standard non polar	33892256
Cytidine,3TMS,isomer #7	C[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC1=O	2403.3	Semi standard non polar	33892256
Cytidine,4TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C=C1	2469.0	Semi standard non polar	33892256
Cytidine,4TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C=C1	2572.3	Standard non polar	33892256
Cytidine,4TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C=C1	2969.5	Standard polar	33892256
Cytidine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2441.6	Semi standard non polar	33892256
Cytidine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2581.5	Standard non polar	33892256
Cytidine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2890.7	Standard polar	33892256
Cytidine,4TMS,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@H](O)[C@@H]1O[Si](C)(C)C	2428.3	Semi standard non polar	33892256
Cytidine,4TMS,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@H](O)[C@@H]1O[Si](C)(C)C	2563.6	Standard non polar	33892256
Cytidine,4TMS,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@H](O)[C@@H]1O[Si](C)(C)C	2847.2	Standard polar	33892256
Cytidine,4TMS,isomer #4	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H]1O[Si](C)(C)C	2428.4	Semi standard non polar	33892256
Cytidine,4TMS,isomer #4	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H]1O[Si](C)(C)C	2576.3	Standard non polar	33892256
Cytidine,4TMS,isomer #4	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H]1O[Si](C)(C)C	2820.1	Standard polar	33892256
Cytidine,5TMS,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@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2477.5	Semi standard non polar	33892256
Cytidine,5TMS,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@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2558.6	Standard non polar	33892256
Cytidine,5TMS,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@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2669.6	Standard polar	33892256
Cytidine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@H](O)[C@@H]1O	2692.2	Semi standard non polar	33892256
Cytidine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N)=NC2=O)[C@@H]1O	2697.4	Semi standard non polar	33892256
Cytidine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(N)=NC1=O	2685.9	Semi standard non polar	33892256
Cytidine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C=C1	2782.1	Semi standard non polar	33892256
Cytidine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2869.2	Semi standard non polar	33892256
Cytidine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2870.8	Semi standard non polar	33892256
Cytidine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O)C=C1	2940.9	Semi standard non polar	33892256
Cytidine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N)=NC2=O)[C@@H]1O[Si](C)(C)C(C)(C)C	2854.9	Semi standard non polar	33892256
Cytidine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C=C1	2934.4	Semi standard non polar	33892256
Cytidine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1	2918.1	Semi standard non polar	33892256
Cytidine,2TBDMS,isomer #7	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C=C1)[Si](C)(C)C(C)(C)C	2911.3	Semi standard non polar	33892256
Cytidine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3063.3	Semi standard non polar	33892256
Cytidine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1	3137.1	Semi standard non polar	33892256
Cytidine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C=C1	3128.6	Semi standard non polar	33892256
Cytidine,3TBDMS,isomer #4	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@H](O)[C@@H]1O	3081.4	Semi standard non polar	33892256
Cytidine,3TBDMS,isomer #5	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1	3115.8	Semi standard non polar	33892256
Cytidine,3TBDMS,isomer #6	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H]1O	3096.2	Semi standard non polar	33892256
Cytidine,3TBDMS,isomer #7	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC1=O	3076.5	Semi standard non polar	33892256
Cytidine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1	3299.2	Semi standard non polar	33892256
Cytidine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1	3333.6	Standard non polar	33892256
Cytidine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1	3318.5	Standard polar	33892256
Cytidine,4TBDMS,isomer #2	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@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3281.9	Semi standard non polar	33892256
Cytidine,4TBDMS,isomer #2	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@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3368.3	Standard non polar	33892256
Cytidine,4TBDMS,isomer #2	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@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3209.7	Standard polar	33892256
Cytidine,4TBDMS,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@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3272.0	Semi standard non polar	33892256
Cytidine,4TBDMS,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@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3355.4	Standard non polar	33892256
Cytidine,4TBDMS,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@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3174.4	Standard polar	33892256
Cytidine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H]1O[Si](C)(C)C(C)(C)C	3274.3	Semi standard non polar	33892256
Cytidine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H]1O[Si](C)(C)C(C)(C)C	3358.3	Standard non polar	33892256
Cytidine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H]1O[Si](C)(C)C(C)(C)C	3156.0	Standard polar	33892256
Cytidine,5TBDMS,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@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3460.3	Semi standard non polar	33892256
Cytidine,5TBDMS,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@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3469.5	Standard non polar	33892256
Cytidine,5TBDMS,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@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3133.2	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Extracellular
Mitochondria
Nucleus
Lysosome

Biospecimen Locations

Blood
Breast Milk
Cerebrospinal Fluid (CSF)
Feces
Saliva
Urine

Tissue Locations

All Tissues
Placenta
Prostate

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	0.1 uM	Adult (>18 years old)	Both	Normal	6656991	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Blood	Detected and Quantified	0.25 +/- 0.19 uM	Adult (>18 years old)	Both	Normal	16139832	details
Blood	Detected and Quantified	<2 uM	Children (3 months - 6 years old)	Not Specified	Normal	12675874	details
Breast Milk	Detected and Quantified	5.14 +/- 3.49 uM	Adult (>18 years old)	Female	Normal	7702711	details
Breast Milk	Detected and Quantified	3.4 +/- 1.4 uM	Adult (>18 years old)	Female	Normal	24027187	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	0.44 +/- 0.32 uM	Infant (0-1 year old)	Both	Normal	3390913	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	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Normal	27609529	details
Saliva	Detected and Quantified	0.125 +/- 0.0812 uM	Adult (>18 years old)	Female	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	1.05 +/- 0.828 uM	Adult (>18 years old)	Male	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.237 +/- 0.184 uM	Adult (>18 years old)	Female	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.132 +/- 0.0808 uM	Adult (>18 years old)	Both	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.123 +/- 0.0900 uM	Adult (>18 years old)	Not Specified	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.0886 +/- 0.0760 uM	Adult (>18 years old)	Female	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.0787 +/- 0.0807 uM	Adult (>18 years old)	Female	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.0683 +/- 0.0749 uM	Adult (>18 years old)	Not Specified	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.0683 +/- 0.0749 uM	Adult (>18 years old)	Female	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.45 +/- 0.31 uM	Adult (>18 years old)	Female	Normal	23857558	details
Urine	Detected and Quantified	0.78 (0.00-1.6) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	15116424	details
Urine	Detected and Quantified	1.50 +/- 1.34 umol/mmol creatinine	Children (1-13 years old)	Both	Normal	16139832	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Urine	Detected and Quantified	0.07 +/- 0.05 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	9129323	details
Urine	Detected and Quantified	1.12 +/- 0.69 umol/mmol creatinine	Adolescent (13-18 years old)	Both	Normal	16139832	details
Urine	Detected and Quantified	0.33 +/- 0.17 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	16139832	details
Urine	Detected and Quantified	0.07 +/- 0.05 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	9129323	details
Urine	Detected and Quantified	0.08 +/- 0.06 umol/mmol creatinine	Adult (>18 years old)	Male	Normal	9129323	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.26 +/- 0.13 uM	Adult (>18 years old)	Both	Canavan disease	16139832	details
Blood	Detected and Quantified	2.920 +/- 1.230 uM	Children (3 months - 6 years old)	Not Specified	Uremia	12675874	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27015276	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	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
Saliva	Detected and Quantified	0.39 +/- 0.30 uM	Adult (>18 years old)	Male	Alzheimer's disease	23857558	details
Saliva	Detected and Quantified	0.48 +/- 0.23 uM	Adult (>18 years old)	Male	Frontotemporal lobe dementia	23857558	details
Saliva	Detected and Quantified	0.22 +/- 0.17 uM	Adult (>18 years old)	Both	Lewy body disease	23857558	details
Saliva	Detected and Quantified	0.0795 +/- 0.0643 uM	Adult (>18 years old)	Both	Tooth alignment disorders	Sugimoto et al. (...	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Attachment loss	31026179	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Missing teeth	31026179	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Periodontal Probing Depth	31026179	details
Urine	Detected and Quantified	4.03 +/- 1.77 umol/mmol creatinine	Adult (>18 years old)	Both	Canavan disease	16139832	details

Associated Disorders and Diseases

Disease References

Canavan disease
Tavazzi B, Lazzarino G, Leone P, Amorini AM, Bellia F, Janson CG, Di Pietro V, Ceccarelli L, Donzelli S, Francis JS, Giardina B: Simultaneous high performance liquid chromatographic separation of purines, pyrimidines, N-acetylated amino acids, and dicarboxylic acids for the chemical diagnosis of inborn errors of metabolism. Clin Biochem. 2005 Nov;38(11):997-1008. Epub 2005 Sep 1. [PubMed:16139832 ]
Uremia
Vanholder R, De Smet R, Glorieux G, Argiles A, Baurmeister U, Brunet P, Clark W, Cohen G, De Deyn PP, Deppisch R, Descamps-Latscha B, Henle T, Jorres A, Lemke HD, Massy ZA, Passlick-Deetjen J, Rodriguez M, Stegmayr B, Stenvinkel P, Tetta C, Wanner C, Zidek W: Review on uremic toxins: classification, concentration, and interindividual variability. Kidney Int. 2003 May;63(5):1934-43. doi: 10.1046/j.1523-1755.2003.00924.x. [PubMed:12675874 ]
Colorectal cancer
Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ] Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ] 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 ]
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 ]
Alzheimer's disease
Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Frontotemporal dementia
Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Lewy body disease
Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Attachment loss
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Missing teeth
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Periodontal Probing Depth
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]

Associated OMIM IDs

271900 (Canavan disease)
114500 (Colorectal cancer)
266600 (Crohn's disease)
104300 (Alzheimer's disease)
600274 (Frontotemporal dementia)

External Links

DrugBank ID

DB02097

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17562

Food Biomarker Ontology

Not Available

VMH ID

CYTD

MarkerDB ID

MDB00000047

Good Scents ID

Not Available

References

Synthesis Reference

Qu, Guirong; Yang, Xining; Shen, Yanhong; Dong, Chunhong; Guo, Haiming; Wang, Xiuqiang; Wang, Dongchao. Synthesis of cytidine. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 11pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. [PubMed:6656991 ]
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 ]
Mahieux R, Suspene R, Delebecque F, Henry M, Schwartz O, Wain-Hobson S, Vartanian JP: Extensive editing of a small fraction of human T-cell leukemia virus type 1 genomes by four APOBEC3 cytidine deaminases. J Gen Virol. 2005 Sep;86(Pt 9):2489-94. [PubMed:16099907 ]
Schrofelbauer B, Yu Q, Zeitlin SG, Landau NR: Human immunodeficiency virus type 1 Vpr induces the degradation of the UNG and SMUG uracil-DNA glycosylases. J Virol. 2005 Sep;79(17):10978-87. [PubMed:16103149 ]
Min IM, Selsing E: Antibody class switch recombination: roles for switch sequences and mismatch repair proteins. Adv Immunol. 2005;87:297-328. [PubMed:16102577 ]
Zhong SQ, Sun LJ, Yan YZ, Sun YQ, Zhong YY: Effect of Xuesaitong soft capsule on hemorrheology and in auxiliarily treating patients with acute cerebral infarction. Chin J Integr Med. 2005 Jun;11(2):128-31. [PubMed:16150200 ]
Barbour JD, Grant RM: The role of viral fitness in HIV pathogenesis. Curr HIV/AIDS Rep. 2005 Feb;2(1):29-34. [PubMed:16091246 ]
Cansev M: Uridine and cytidine in the brain: their transport and utilization. Brain Res Rev. 2006 Sep;52(2):389-97. [PubMed:16769123 ]
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Only showing the first 10 proteins. There are 22 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

Cytidine monophosphate + Water → Cytidine + 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

Cytidine monophosphate + Water → Cytidine + 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

Cytidine monophosphate + Water → Cytidine + 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

Cytidine monophosphate + Water → Cytidine + Phosphate	details

Enzyme Details

5. 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

Cytidine monophosphate + Water → Cytidine + Phosphate	details

Enzyme Details

6. Uridine-cytidine kinase 1

General function:: Involved in ATP binding
Specific function:: Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:: UCK1
Uniprot ID:: Q9HA47
Molecular weight:: 22760.43

Reactions

Adenosine triphosphate + Cytidine → ADP + Cytidine monophosphate	details
Uridine triphosphate + Cytidine → Uridine 5'-diphosphate + Cytidine monophosphate	details
Guanosine triphosphate + Cytidine → Guanosine diphosphate + Cytidine monophosphate	details
Inosine triphosphate + Cytidine → IDP + Cytidine monophosphate	details
Deoxyadenosine triphosphate + Cytidine → dADP + Cytidine monophosphate	details
dGTP + Cytidine → dGDP + Cytidine monophosphate	details
Thymidine 5'-triphosphate + Cytidine → dTDP + Cytidine monophosphate	details
dCTP + Cytidine → dCDP + Cytidine monophosphate	details
Deoxyuridine triphosphate + Cytidine → dUDP + Cytidine monophosphate	details

Enzyme Details

7. Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase

General function:: Involved in ATP binding
Specific function:: Regulates and initiates biosynthesis of N-acetylneuraminic acid (NeuAc), a precursor of sialic acids. Plays an essential role in early development (By similarity). Required for normal sialylation in hematopoietic cells. Sialylation is implicated in cell adhesion, signal transduction, tumorigenicity and metastatic behavior of malignant cells.
Gene Name:: GNE
Uniprot ID:: Q9Y223
Molecular weight:: 83065.25

Enzyme Details

8. Uridine-cytidine kinase 2

General function:: Involved in ATP binding
Specific function:: Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:: UCK2
Uniprot ID:: Q9BZX2
Molecular weight:: 29298.92

Reactions

Adenosine triphosphate + Cytidine → ADP + Cytidine monophosphate	details
Uridine triphosphate + Cytidine → Uridine 5'-diphosphate + Cytidine monophosphate	details
Guanosine triphosphate + Cytidine → Guanosine diphosphate + Cytidine monophosphate	details
Inosine triphosphate + Cytidine → IDP + Cytidine monophosphate	details
Deoxyadenosine triphosphate + Cytidine → dADP + Cytidine monophosphate	details
dGTP + Cytidine → dGDP + Cytidine monophosphate	details
Thymidine 5'-triphosphate + Cytidine → dTDP + Cytidine monophosphate	details
dCTP + Cytidine → dCDP + Cytidine monophosphate	details
Deoxyuridine triphosphate + Cytidine → dUDP + Cytidine monophosphate	details

Enzyme Details

9. AID

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

Enzyme Details

10. 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

Cytidine monophosphate + Water → Cytidine + Phosphate	details

Only showing the first 10 proteins. There are 22 proteins in total.

Show all enzymes and transporters

Showing metabocard for Cytidine (HMDB0000089)

MOL for HMDB0000089 (Cytidine)

3D MOL for HMDB0000089 (Cytidine)

3D SDF for HMDB0000089 (Cytidine)

3D-SDF for HMDB0000089 (Cytidine)

PDB for HMDB0000089 (Cytidine)

3D PDB for HMDB0000089 (Cytidine)

SMILES for HMDB0000089 (Cytidine)

INCHI for HMDB0000089 (Cytidine)

Structure for HMDB0000089 (Cytidine)

3D Structure for HMDB0000089 (Cytidine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

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