MiMeDB: Showing metabocard for Cytidine (MMDBc0000023)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:27:33 UTC

Update Date

2024-04-30 19:30:52 UTC

Metabolite ID

MMDBc0000023

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>
MMDBc0000023

> <DATABASE_NAME>
MIME

> <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

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

Molecular Formula

C₉H₁₃N₃O₅

Average Mass

243.2166

Monoisotopic Mass

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-0g4j-2980000000-9337623aef7fec22dd97	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0g4j-2980000000-9337623aef7fec22dd97	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-05dl-9420000000-f2b3f5707444409e125d	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0083-6964300000-64e7e138ddd30a0aec2c	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-0900000000-177050786fcbfaf2d270	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-0900000000-1251248af66dca3401e2	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-03di-6900000000-c6b010a1d3e65a0942ee	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0006-0590100000-94eb2baae24aa405b1ba	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0006-9000000000-8155621584c25975ffa1	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-03di-0900000000-5065bc83a32bee37d07c	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0006-0590200000-4d5dc5376c40d083efbe	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-001i-0900000000-6ea86f62a48910b456a0	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-03di-0900000000-5c93b66b8899a4d3ce06	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0006-0090000000-f0e6ac0bacdbef1206b0	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-000f-0090010000-1cf915fa4dfb86b5861b	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0a4i-0900000000-6bb7990f165932decea7	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0006-0090000000-0b7dc368d61ee31afb78	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-000l-0090020000-fa04fb11f98259c403b6	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0006-0190172001-0671df3c315b8af9e13f	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0a4i-0900000000-8aa3fec051a7d9807888	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0006-0090000000-0563823e8f3a9def519a	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-004i-0028900000-f4b6c319a7e9fb17df2e	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-01ox-0590000000-d5d20f84ab30e96c30f6	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positive	splash10-03di-0930000000-c4d3377790616b8b7869	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0a4i-1930000000-faec28788ea577988b82	2012-08-31	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0910000000-9575881412c4c94a7eae	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-5900000000-2cb5f7e3dbd7baa35b56	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dj-9600000000-7d281b2b2d57c8786e11	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01ox-0960000000-db9207082a1fabf42dae	2016-09-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)		2012-12-04	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-04	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Lysosome
Mitochondria
Nucleus

Biospecimen Locations

All Tissues
Blood
Breast Milk
Cerebrospinal Fluid (CSF)
Feces
Placenta
Prostate
Saliva
Urine

Tissue Locations

All Tissues
Placenta
Prostate

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191677	5'-nucleotidase	Unknown	P21589	Homo sapiens
MMDBp0191680	Cytosolic 5'-nucleotidase 1B	Unknown	Q96P26	Homo sapiens
MMDBp0191681	Cytosolic 5'-nucleotidase 1A	Unknown	Q9BXI3	Homo sapiens
MMDBp0191682	5'(3')-deoxyribonucleotidase, cytosolic type	Unknown	Q8TCD5	Homo sapiens
MMDBp0191684	5'(3')-deoxyribonucleotidase, mitochondrial	Unknown	Q9NPB1	Homo sapiens
MMDBp0191778	Uridine-cytidine kinase 1	Unknown	Q9HA47	Homo sapiens
MMDBp0192001	Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase	Enzyme	Q9Y223	Homo sapiens
MMDBp0193590	Uridine-cytidine kinase 2	Unknown	Q9BZX2	Homo sapiens
MMDBp0193783	AID	Enzyme	Q546Y9	Homo sapiens
MMDBp0193860	Cytosolic 5'-nucleotidase 3	Enzyme	Q9H0P0	Homo sapiens
MMDBp0193932	Cytosolic purine 5'-nucleotidase	Unknown	P49902	Homo sapiens
MMDBp0194012	Cytidine deaminase	Unknown	P32320	Homo sapiens
MMDBp0194185	Uridine-cytidine kinase-like 1	Enzyme	Q9NWZ5	Homo sapiens
MMDBp0196270	DNA dC->dU-editing enzyme APOBEC-3H	Enzyme	Q6NTF7	Homo sapiens
MMDBp0196330	Zinc finger protein 638	Unknown	Q14966	Homo sapiens
MMDBp0196331	CUGBP Elav-like family member 2	Unknown	O95319	Homo sapiens
MMDBp0196667	Probable DNA dC->dU-editing enzyme APOBEC-3A	Unknown	P31941
MMDBp0196668	Probable DNA dC->dU-editing enzyme APOBEC-3B	Unknown	Q9UH17
MMDBp0196669	Probable DNA dC->dU-editing enzyme APOBEC-3C	Unknown	Q9NRW3
MMDBp0196670	Probable DNA dC->dU-editing enzyme APOBEC-3D	Unknown	Q96AK3
MMDBp0196671	DNA dC->dU-editing enzyme APOBEC-3F	Unknown	Q8IUX4
MMDBp0196681	Activation-induced cytidine deaminase	Unknown	Q9GZX7

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0000574	Cytidine	Ammonia	Not Available	Cytidine Deaminase	VMH; KEGG	14744791 15087440 7923172 8001985 8422236
MMDBr0000575	Adenosine triphosphate	ADP	Not Available	ATPcytidine 5-Phosphotransferase	VMH; KEGG	30371894
MMDBr0000576	Adenosine triphosphate	ADP	Not Available	Cytidine Kinase (ATP), Mitochondrial	VMH; KEGG	30371894
MMDBr0000577	Cytidine	Ammonia	Activation-induced cytidine deaminase	Cytidine Deaminase, Nuclear	VMH; KEGG	15087440
MMDBr0000578	Cytidine	Cytidine	Solute carrier family 29 (equilibrative nucleoside transporter), member 1	Cytidine Faciliated Transport in Cytosol	VMH	10722669 12838422
MMDBr0000579	Cytidine	Cytidine	Not Available	Cytidine Transport in via Sodium Symport	VMH	12856181
MMDBr0000580	Cytidine	Cytidine	Solute carrier family 29 (equilibrative nucleoside transporter), member 3	Cytidine Faciliated Transport from Lysosome	VMH	12838422 15701636 2925670
MMDBr0000581	Cytidine	Cytidine	Solute carrier family 29 (equilibrative nucleoside transporter), member 1	Cytidine Faciliated Transport in Mitochondria	VMH	10722669 12838422 14607828
MMDBr0000582	Cytidine	Cytidine	Not Available	Cytidine Transport in Nucleus	VMH	30371894
MMDBr0001790	Cytidine monophosphate	Cytidine	5', 3'-nucleotidase, cytosolic	5'-Nucleotidase (CMP), Extracellular	VMH; KEGG	30371894
MMDBr0001791	Cytidine monophosphate	Cytidine	Acid phosphatase 2, lysosomal	5'-Nucleotidase (CMP), Lysosomal	VMH; KEGG	30371894
MMDBr0002585	Cytidine	Cytidine monophosphate	Uridine-cytidine kinase 1	DUTP:Cytidine 5-Phosphotransferase	VMH	11306702 9923963
MMDBr0005436	Cytidine	Cytidine	Solute carrier family 28 (concentrative nucleoside transporter), member 3	Cytidine Transport (1:2 Na/Cytd Symport)	VMH	30371894
MMDBr0006922	Cytidine	Cytidine monophosphate	Not Available	ITPcytidine 5-phosphotransferase	VMH	30371894
MMDBr0007295	Cytidine	Cytidine	Not Available	Cytidine Transport in via Proton Symport, Reversible	VMH	30371894
MMDBr0007638	Cytidine monophosphate	Cytidine	Not Available	5'-Nucleotidase (CMP)	VMH; KEGG	30371894
MMDBr0007742	Cytidine	Cytidine monophosphate	Not Available	Cytidine kinase (GTP)	VMH; KEGG	30371894
MMDBr0007743	Cytidine	Cytidine monophosphate	Not Available	UTPcytidine 5-phosphotransferase	VMH	30371894
MMDBr0007997	Cytidine	Cytidine monophosphate	Not Available	Cytidine kinase (dCTP:Cytidine)	VMH	30371894
MMDBr0007998	Cytidine	Cytidine monophosphate	Not Available	Cytidine kinase (dUTP:Cytidine)	VMH	30371894
MMDBr0007999	Cytidine	Cytidine monophosphate	Not Available	Cytidine kinase (dATP:Cytidine)	VMH	30371894
MMDBr0008000	Cytidine	Cytidine monophosphate	Not Available	Cytidine kinase (dGTP:Cytidine)	VMH	30371894
MMDBr0008001	Cytidine	Cytidine monophosphate	Not Available	Cytidine kinase (dTTP:Cytidine)	VMH	30371894
MMDBr0008073	Cytosine	Cytidine	Not Available	Pyrimidine nucleoside phosphorylase cytosine	VMH	30371894
MMDBr0008452	Cytidine	Cytosine	Not Available	Cytidine hydrolase	VMH	30371894
MMDBr0008513	Cytidine	Cytidine	Not Available	Cytidine transport in via proton symport	VMH	30371894
MMDBr0010274	Cytidine	Cytidine monophosphate	Family with sequence similarity 20 member b	HMR_4182	VMH	30371894
MMDBr0013493	Cytidine	Ammonium	Cytidine deaminase	Deamination	RHEA	34755880
MMDBr0014472	Adenosine triphosphate	ADP	Cytidine kinase	Phosphorylation	RHEA	34755880
MMDBr0014473	Adenosine triphosphate	ADP	Uridine kinase	Phosphorylation	RHEA	34755880
MMDBr0014748	3'-CMP	Cytidine	5'/3'-nucleotidase SurE	Hydrolysis of nucleotide	RHEA	34755880
MMDBr0016600	Cytidine	Ribose-1-phosphate	Pyrimidine/purine nucleoside phosphorylase	Phosphorylation	RHEA	34755880
MMDBr0017322	Water	Acetic acid	N(4)-acetylcytidine amidohydrolase	Hydrolysis of bond	RHEA	34755880
MMDBr0019167	Cytidine	Uridine	Cytidine deaminase		PathBank	31602464
MMDBr0026010	Cytidine 3'-monophosphate	Cytidine	5'/3'-nucleotidase SurE	Hydrolysis of nucleotide	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Alzheimer's disease	Slight Decrease	Association	Human Saliva	HMDB	23857558
Canavan disease	Increased	Association	Human Blood	HMDB	16139832
Canavan disease	Increased	Association	Human Urine	HMDB	16139832
Frontotemporal dementia		Association	Human Saliva	HMDB	23857558
Uremia	Slight Increase	Association	Human Blood	HMDB	12675874

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota	Parabasalia	1		Microbial culture
Bacteria	Bacteroidetes	242	Human ; Human urine; Human feces; Human appendix biopsy; Human stool; Human saliva; Human gastric fluid; Human subgingival plaque; Human supragingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Firmicutes	667	Human stool; Human ; Human feces; Human urine; Human saliva; Human sputum; Human subgingival plaque; Human vaginal fluid; Human supragingival plaque; Human mucosa; Human pleural fluid plaque; Pig ; Cattle ; Catfish	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	486	Human feces; Human stool; Human ; Human mucosa; Human supragingival plaque; Human saliva; Human subgingival plaque; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Chicken	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Actinobacteria	190	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Verrucomicrobia	2	Human ; Human feces	Metabolic reconstruction
Bacteria	Synergistetes	5	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	13	Human feces; Human ; Relapsing fever tick	Metabolic reconstruction
Archaea	Thaumarchaeota	2		Metabolic reconstruction
Bacteria	Fusobacteria	29	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	7		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	2	Human feces	Metabolic reconstruction
Bacteria	Tenericutes	12	Human feces; Human	Metabolic reconstruction
Bacteria	Planctomycetes	3	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	2		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	3	Human feces; Human saliva	Unknown
Archaea/Archaea	Euryarchaeota	4		Metabolic reconstruction
Bacteria	Chloroflexi	3
Bacteria	Chlamydiae	1	Human
Bacteria	Deinococcus-thermus	4
Bacteria	Chlorobi	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Saliva	Detected and Quantified	0.39	0.30			uM	Adult (>18 years old)	Male	Alzheimer's disease	HMDB	23857558
Human Blood	Detected and Quantified	0.26	0.13			uM	Adult (>18 years old)	Both	Canavan disease	HMDB	16139832
Human Urine	Detected and Quantified	4.03	1.77			umol/mmol creatinine	Adult (>18 years old)	Both	Canavan disease	HMDB	16139832
Human Saliva	Detected and Quantified	0.48	0.23			uM	Adult (>18 years old)	Male	Frontotemporal lobe dementia	HMDB	23857558
Human Saliva	Detected and Quantified	0.22	0.17			uM	Adult (>18 years old)	Both	Lewy body disease	HMDB	23857558
Human Blood	Detected and Quantified	2.920	1.230			uM	Children (3 months - 6 years old)	Not Specified	Uremia	HMDB	12675874
Human Blood	Detected and Quantified	0.1				uM	Adult (>18 years old)	Both	Normal	HMDB	6656991
Human Blood	Detected and Quantified	<2				uM	Children (3 months - 6 years old)	Not Specified	Normal	HMDB	12675874
Human Urine	Detected and Quantified	0.07	0.05			umol/mmol creatinine	Adult (>18 years old)	Female	Normal	HMDB	9129323
Human Urine	Detected and Quantified	0.07	0.05			umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	9129323
Human Urine	Detected and Quantified	0.08	0.06			umol/mmol creatinine	Adult (>18 years old)	Male	Normal	HMDB	9129323
Human Blood	Detected and Quantified	0.25	0.19			uM	Adult (>18 years old)	Both	Normal	HMDB	16139832
Human Urine	Detected and Quantified	0.33	0.17			umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	16139832
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.44	0.32			uM	Infant (0-1 year old)	Both	Normal	HMDB	3390913
Human Saliva	Detected and Quantified	0.45	0.31			uM	Adult (>18 years old)	Female	Normal	HMDB	23857558
Human Urine	Detected and Quantified	0.78		0.00	1.6	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	15116424
Human Urine	Detected and Quantified	1.12	0.69			umol/mmol creatinine	Adolescent (13-18 years old)	Both	Normal	HMDB	16139832
Human Urine	Detected and Quantified	1.50	1.34			umol/mmol creatinine	Children (1-13 years old)	Both	Normal	HMDB	16139832
Human Breast milk	Detected and Quantified	3.4	1.4			uM	Adult (>18 years old)	Female	Normal	HMDB	24027187
Human Breast milk	Detected and Quantified	5.14	3.49			uM	Adult (>18 years old)	Female	Normal	HMDB	7702711
Human Saliva	Detected and Quantified	0.0683	0.0749			uM	Adult (>18 years old)	Female	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	0.0683	0.0749			uM	Adult (>18 years old)	Not Specified	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	0.0787	0.0807			uM	Adult (>18 years old)	Female	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	0.0886	0.0760			uM	Adult (>18 years old)	Female	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	0.123	0.0900			uM	Adult (>18 years old)	Not Specified	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	0.125	0.0812			uM	Adult (>18 years old)	Female	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	0.132	0.0808			uM	Adult (>18 years old)	Both	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	0.237	0.184			uM	Adult (>18 years old)	Female	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	1.05	0.828			uM	Adult (>18 years old)	Male	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human All tissues	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Prostate	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified						Children (6 - 18 years old)	Not Specified	Normal	HMDB	27609529
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

HMDB0000089

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

References

Synthesis Reference

Not Available

General References

Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. doi: 10.1002/rcm.1400. [PubMed:15116424 ]
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):2489-2494. doi: 10.1099/vir.0.80973-0. [PubMed:16099907 ]
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. doi: 10.1007/BF00965000. [PubMed:6656991 ]
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. doi: 10.1128/JVI.79.17.10978-10987.2005. [PubMed:16103149 ]
Min IM, Selsing E: Antibody class switch recombination: roles for switch sequences and mismatch repair proteins. Adv Immunol. 2005;87:297-328. doi: 10.1016/S0065-2776(05)87008-7. [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. doi: 10.1007/BF02836469. [PubMed:16150200 ]
Barbour JD, Grant RM: The role of viral fitness in HIV pathogenesis. Curr HIV/AIDS Rep. 2005 Feb;2(1):29-34. doi: 10.1007/s11904-996-0006-1. [PubMed:16091246 ]
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 ]
Cansev M: Uridine and cytidine in the brain: their transport and utilization. Brain Res Rev. 2006 Sep;52(2):389-97. doi: 10.1016/j.brainresrev.2006.05.001. [PubMed:16769123 ]
Huthoff H, Malim MH: Cytidine deamination and resistance to retroviral infection: towards a structural understanding of the APOBEC proteins. Virology. 2005 Apr 10;334(2):147-53. doi: 10.1016/j.virol.2005.01.038. [PubMed:15780864 ]
Navaratnam N, Sarwar R: An overview of cytidine deaminases. Int J Hematol. 2006 Apr;83(3):195-200. doi: 10.1532/IJH97.06032. [PubMed:16720547 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for Cytidine (MMDBc0000023)

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