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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:46:09 UTC

HMDB ID

HMDB0000982

Secondary Accession Numbers

HMDB00982

Metabolite Identification

Common Name

5-Methylcytidine

Description

5-Methylcytidine 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. 5-Methylcytidine has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 5-methylcytidine a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 5-Methylcytidine.

Structure

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

HMDB0000982
     RDKit          3D
5-Methylcytidine
 33 34  0  0  0  0  0  0  0  0999 V2000
    3.4820   -1.3202    1.1184 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7170   -0.2407    0.4343 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3382   -0.2589    0.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6923    0.7359   -0.1932 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7509    0.8197   -0.2554 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3511    0.2678    0.8769 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6222   -0.0054    0.4298 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4597   -0.7618    1.4288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5512    0.0259    2.5762 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3421   -0.8269   -0.8147 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4369   -0.9168   -1.6538 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2175   -0.0116   -1.4309 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8083    0.8304   -2.3789 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3983    1.7059   -0.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7802    2.6491   -1.3963 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7461    1.7226   -0.8006 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4567    0.7469   -0.1822 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8786    0.7536   -0.1771 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8248   -2.1809    1.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2391   -1.6762    0.3728 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0401   -0.9665    1.9925 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7729   -1.0445    0.9274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1074    1.8676   -0.3268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1374    0.9202    0.1258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0309   -1.7374    1.6671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4738   -0.8708    0.9914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9426    0.9078    2.3337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9108   -1.8165   -0.5542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5635   -1.8681   -1.9146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4247   -0.6441   -1.8509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0545    1.6827   -1.9530 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3931    0.2926    0.5840 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4261    1.2188   -0.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  7 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  4 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  2  0
 17 18  1  0
 17  2  1  0
 12  5  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  5 23  1  6
  7 24  1  6
  8 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  1
 11 29  1  0
 12 30  1  6
 13 31  1  0
 18 32  1  0
 18 33  1  0
M  END

  Mrv1652310241918272D          

 18 19  0  0  0  0            999 V2000
 9980.5524 9982.1968    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9982.3404 9982.1886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9982.8104 9980.3383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9983.5238 9980.7494    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9979.3307 9981.5742    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9977.9023 9979.1002    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9979.3307 9980.7507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9978.6161 9980.3381    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9978.6161 9979.5130    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.3307 9979.1006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9980.0453 9979.5130    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9980.0453 9980.3381    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9981.4295 9980.2555    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9980.7621 9980.7404    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9981.0170 9981.5251    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9981.8420 9981.5251    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9982.0969 9980.7404    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9979.3307 9978.2772    0.0000 C   0  0  0  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
 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
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  7 12  1  0  0  0  0
 11 12  1  0  0  0  0
  7  5  2  0  0  0  0
  9  6  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
 10 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000982

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N3O5/c1-4-2-13(10(17)12-8(4)11)9-7(16)6(15)5(3-14)18-9/h2,5-7,9,14-16H,3H2,1H3,(H2,11,12,17)/t5-,6-,7-,9-/m1/s1

> <INCHI_KEY>
ZAYHVCMSTBRABG-JXOAFFINSA-N

> <FORMULA>
C10H15N3O5

> <MOLECULAR_WEIGHT>
257.2432

> <EXACT_MASS>
257.101170605

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
24.537597480023877

> <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]-5-methyl-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-2.17

> <JCHEM_LOGP>
-2.4019667949999994

> <ALOGPS_LOGS>
-1.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.933684116802407

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.55323062400565

> <JCHEM_PKA_STRONGEST_BASIC>
0.13746485112525675

> <JCHEM_POLAR_SURFACE_AREA>
128.61

> <JCHEM_REFRACTIVITY>
58.9019

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-methylcytidine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000982
     RDKit          3D
5-Methylcytidine
 33 34  0  0  0  0  0  0  0  0999 V2000
    3.4820   -1.3202    1.1184 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7170   -0.2407    0.4343 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3382   -0.2589    0.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6923    0.7359   -0.1932 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7509    0.8197   -0.2554 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3511    0.2678    0.8769 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6222   -0.0054    0.4298 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4597   -0.7618    1.4288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5512    0.0259    2.5762 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3421   -0.8269   -0.8147 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4369   -0.9168   -1.6538 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2175   -0.0116   -1.4309 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8083    0.8304   -2.3789 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3983    1.7059   -0.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7802    2.6491   -1.3963 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7461    1.7226   -0.8006 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4567    0.7469   -0.1822 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8786    0.7536   -0.1771 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8248   -2.1809    1.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2391   -1.6762    0.3728 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0401   -0.9665    1.9925 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7729   -1.0445    0.9274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1074    1.8676   -0.3268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1374    0.9202    0.1258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0309   -1.7374    1.6671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4738   -0.8708    0.9914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9426    0.9078    2.3337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9108   -1.8165   -0.5542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5635   -1.8681   -1.9146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4247   -0.6441   -1.8509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0545    1.6827   -1.9530 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3931    0.2926    0.5840 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4261    1.2188   -0.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  7 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  4 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  2  0
 17 18  1  0
 17  2  1  0
 12  5  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  5 23  1  6
  7 24  1  6
  8 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  1
 11 29  1  0
 12 30  1  6
 13 31  1  0
 18 32  1  0
 18 33  1  0
M  END

HEADER    PROTEIN                                 24-OCT-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-OCT-19         0                                  
HETATM    1  O   UNK     0    8630.3648633.434   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8633.7028633.419   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8634.5798629.965   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8635.9118630.732   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8628.0848632.272   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0    8625.4188627.654   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8628.0848630.735   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0    8626.7508629.964   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0    8626.7508628.424   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8628.0848627.654   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8629.4188628.424   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0    8629.4188629.964   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0    8632.0028629.810   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0    8630.7568630.715   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8631.2328632.180   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8632.7728632.180   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8633.2488630.715   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8628.0848626.117   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   18                                                  
CONECT   11   10   12                                                       
CONECT   12    7   11   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                                                  
CONECT   18   10                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0000982
HETATM    1  C1  UNL     1       3.482  -1.320   1.118  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.717  -0.241   0.434  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.338  -0.259   0.437  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.692   0.736  -0.193  1.00  0.00           N  
HETATM    5  C4  UNL     1      -0.751   0.820  -0.255  1.00  0.00           C  
HETATM    6  O1  UNL     1      -1.351   0.268   0.877  1.00  0.00           O  
HETATM    7  C5  UNL     1      -2.622  -0.005   0.430  1.00  0.00           C  
HETATM    8  C6  UNL     1      -3.460  -0.762   1.429  1.00  0.00           C  
HETATM    9  O2  UNL     1      -3.551   0.026   2.576  1.00  0.00           O  
HETATM   10  C7  UNL     1      -2.342  -0.827  -0.815  1.00  0.00           C  
HETATM   11  O3  UNL     1      -3.437  -0.917  -1.654  1.00  0.00           O  
HETATM   12  C8  UNL     1      -1.218  -0.012  -1.431  1.00  0.00           C  
HETATM   13  O4  UNL     1      -1.808   0.830  -2.379  1.00  0.00           O  
HETATM   14  C9  UNL     1       1.398   1.706  -0.799  1.00  0.00           C  
HETATM   15  O5  UNL     1       0.780   2.649  -1.396  1.00  0.00           O  
HETATM   16  N2  UNL     1       2.746   1.723  -0.801  1.00  0.00           N  
HETATM   17  C10 UNL     1       3.457   0.747  -0.182  1.00  0.00           C  
HETATM   18  N3  UNL     1       4.879   0.754  -0.177  1.00  0.00           N  
HETATM   19  H1  UNL     1       2.825  -2.181   1.319  1.00  0.00           H  
HETATM   20  H2  UNL     1       4.239  -1.676   0.373  1.00  0.00           H  
HETATM   21  H3  UNL     1       4.040  -0.967   1.992  1.00  0.00           H  
HETATM   22  H4  UNL     1       0.773  -1.045   0.927  1.00  0.00           H  
HETATM   23  H5  UNL     1      -1.107   1.868  -0.327  1.00  0.00           H  
HETATM   24  H6  UNL     1      -3.137   0.920   0.126  1.00  0.00           H  
HETATM   25  H7  UNL     1      -3.031  -1.737   1.667  1.00  0.00           H  
HETATM   26  H8  UNL     1      -4.474  -0.871   0.991  1.00  0.00           H  
HETATM   27  H9  UNL     1      -3.943   0.908   2.334  1.00  0.00           H  
HETATM   28  H10 UNL     1      -1.911  -1.816  -0.554  1.00  0.00           H  
HETATM   29  H11 UNL     1      -3.564  -1.868  -1.915  1.00  0.00           H  
HETATM   30  H12 UNL     1      -0.425  -0.644  -1.851  1.00  0.00           H  
HETATM   31  H13 UNL     1      -2.054   1.683  -1.953  1.00  0.00           H  
HETATM   32  H14 UNL     1       5.393   0.293   0.584  1.00  0.00           H  
HETATM   33  H15 UNL     1       5.426   1.219  -0.933  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3    3   17
CONECT    3    4   22
CONECT    4    5   14
CONECT    5    6   12   23
CONECT    6    7
CONECT    7    8   10   24
CONECT    8    9   25   26
CONECT    9   27
CONECT   10   11   12   28
CONECT   11   29
CONECT   12   13   30
CONECT   13   31
CONECT   14   15   15   16
CONECT   16   17   17
CONECT   17   18
CONECT   18   32   33
END

HMDB0000982
     RDKit          3D
5-Methylcytidine
 33 34  0  0  0  0  0  0  0  0999 V2000
    3.4820   -1.3202    1.1184 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7170   -0.2407    0.4343 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3382   -0.2589    0.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6923    0.7359   -0.1932 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7509    0.8197   -0.2554 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3511    0.2678    0.8769 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6222   -0.0054    0.4298 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4597   -0.7618    1.4288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5512    0.0259    2.5762 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3421   -0.8269   -0.8147 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4369   -0.9168   -1.6538 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2175   -0.0116   -1.4309 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8083    0.8304   -2.3789 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3983    1.7059   -0.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7802    2.6491   -1.3963 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7461    1.7226   -0.8006 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4567    0.7469   -0.1822 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8786    0.7536   -0.1771 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8248   -2.1809    1.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2391   -1.6762    0.3728 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0401   -0.9665    1.9925 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7729   -1.0445    0.9274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1074    1.8676   -0.3268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1374    0.9202    0.1258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0309   -1.7374    1.6671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4738   -0.8708    0.9914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9426    0.9078    2.3337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9108   -1.8165   -0.5542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5635   -1.8681   -1.9146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4247   -0.6441   -1.8509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0545    1.6827   -1.9530 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3931    0.2926    0.5840 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4261    1.2188   -0.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  7 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  4 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  2  0
 17 18  1  0
 17  2  1  0
 12  5  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  5 23  1  6
  7 24  1  6
  8 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  1
 11 29  1  0
 12 30  1  6
 13 31  1  0
 18 32  1  0
 18 33  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
5-Methyl-cytidine	HMDB
5-Methylcytidine	HMDB

Chemical Formula

C₁₀H₁₅N₃O₅

Average Molecular Weight

257.2432

Monoisotopic Molecular Weight

257.101170605

IUPAC Name

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

Traditional Name

5-methylcytidine

CAS Registry Number

2140-61-6

SMILES

CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N

InChI Identifier

InChI=1S/C10H15N3O5/c1-4-2-13(10(17)12-8(4)11)9-7(16)6(15)5(3-14)18-9/h2,5-7,9,14-16H,3H2,1H3,(H2,11,12,17)/t5-,6-,7-,9-/m1/s1

InChI Key

ZAYHVCMSTBRABG-JXOAFFINSA-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
Hydroxypyrimidine
Hydropyrimidine
Monosaccharide
Pyrimidine
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organic nitrogen compound
Hydrocarbon derivative
Primary alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

methylcytidine (CHEBI:20607 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0000982)

Excreta

Biofluid or Excreta

Urine (PMID: 15116424)
Feces (PMID: 26848182)

Cellular substructure

Cytoplasm (HMDB: HMDB0000982)

Source

Endogenous

Endogenous (HMDB: HMDB0000982)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	213 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	-2.01	HANSCH,C ET AL. (1995)

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Baker	160.458	30932474
[M-H]-	MetCCS_train_neg	152.628	30932474
[M+H]+	Baker	157.509	30932474
[M+H]+	MetCCS_train_pos	157.391	30932474
[M-H]-	Not Available	156.5	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000111
[M+H]+	Not Available	157.8	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000111

Predicted Molecular Properties

Property	Value	Source
Water Solubility	20.8 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.4	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	0.14	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	58.9 m³·mol⁻¹	ChemAxon
Polarizability	24.54 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]+	157.877	31661259
DarkChem	[M-H]-	153.524	31661259
AllCCS	[M+H]+	158.234	32859911
AllCCS	[M-H]-	156.964	32859911
DeepCCS	[M+H]+	158.948	30932474
DeepCCS	[M-H]-	156.552	30932474
DeepCCS	[M-2H]-	191.013	30932474
DeepCCS	[M+Na]+	165.562	30932474
AllCCS	[M+H]+	158.2	32859911
AllCCS	[M+H-H2O]+	154.7	32859911
AllCCS	[M+NH4]+	161.5	32859911
AllCCS	[M+Na]+	162.5	32859911
AllCCS	[M-H]-	157.0	32859911
AllCCS	[M+Na-2H]-	157.0	32859911
AllCCS	[M+HCOO]-	157.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Methylcytidine	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N	3724.2	Standard polar	33892256
5-Methylcytidine	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N	2329.5	Standard non polar	33892256
5-Methylcytidine	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N	2673.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Methylcytidine,1TMS,isomer #1	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O)C(=O)N=C1N	2477.7	Semi standard non polar	33892256
5-Methylcytidine,1TMS,isomer #2	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)N=C1N	2481.8	Semi standard non polar	33892256
5-Methylcytidine,1TMS,isomer #3	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)N=C1N	2468.8	Semi standard non polar	33892256
5-Methylcytidine,1TMS,isomer #4	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N[Si](C)(C)C	2535.8	Semi standard non polar	33892256
5-Methylcytidine,2TMS,isomer #1	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)N=C1N	2467.9	Semi standard non polar	33892256
5-Methylcytidine,2TMS,isomer #2	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)N=C1N	2464.9	Semi standard non polar	33892256
5-Methylcytidine,2TMS,isomer #3	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O)C(=O)N=C1N[Si](C)(C)C	2492.8	Semi standard non polar	33892256
5-Methylcytidine,2TMS,isomer #4	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)N=C1N	2467.7	Semi standard non polar	33892256
5-Methylcytidine,2TMS,isomer #5	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)N=C1N[Si](C)(C)C	2507.1	Semi standard non polar	33892256
5-Methylcytidine,2TMS,isomer #6	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)N=C1N[Si](C)(C)C	2504.2	Semi standard non polar	33892256
5-Methylcytidine,2TMS,isomer #7	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2489.5	Semi standard non polar	33892256
5-Methylcytidine,3TMS,isomer #1	CC1=CN([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(=O)N=C1N	2454.3	Semi standard non polar	33892256
5-Methylcytidine,3TMS,isomer #2	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)N=C1N[Si](C)(C)C	2489.0	Semi standard non polar	33892256
5-Methylcytidine,3TMS,isomer #3	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)N=C1N[Si](C)(C)C	2492.9	Semi standard non polar	33892256
5-Methylcytidine,3TMS,isomer #4	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2464.8	Semi standard non polar	33892256
5-Methylcytidine,3TMS,isomer #5	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)N=C1N[Si](C)(C)C	2482.3	Semi standard non polar	33892256
5-Methylcytidine,3TMS,isomer #6	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2461.2	Semi standard non polar	33892256
5-Methylcytidine,3TMS,isomer #7	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2461.1	Semi standard non polar	33892256
5-Methylcytidine,4TMS,isomer #1	CC1=CN([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(=O)N=C1N[Si](C)(C)C	2507.5	Semi standard non polar	33892256
5-Methylcytidine,4TMS,isomer #1	CC1=CN([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(=O)N=C1N[Si](C)(C)C	2564.4	Standard non polar	33892256
5-Methylcytidine,4TMS,isomer #1	CC1=CN([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(=O)N=C1N[Si](C)(C)C	3016.6	Standard polar	33892256
5-Methylcytidine,4TMS,isomer #2	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2489.9	Semi standard non polar	33892256
5-Methylcytidine,4TMS,isomer #2	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2623.6	Standard non polar	33892256
5-Methylcytidine,4TMS,isomer #2	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2885.6	Standard polar	33892256
5-Methylcytidine,4TMS,isomer #3	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2498.3	Semi standard non polar	33892256
5-Methylcytidine,4TMS,isomer #3	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2634.6	Standard non polar	33892256
5-Methylcytidine,4TMS,isomer #3	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2929.0	Standard polar	33892256
5-Methylcytidine,4TMS,isomer #4	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2486.0	Semi standard non polar	33892256
5-Methylcytidine,4TMS,isomer #4	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2628.7	Standard non polar	33892256
5-Methylcytidine,4TMS,isomer #4	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2859.1	Standard polar	33892256
5-Methylcytidine,5TMS,isomer #1	CC1=CN([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(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2532.5	Semi standard non polar	33892256
5-Methylcytidine,5TMS,isomer #1	CC1=CN([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(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2617.3	Standard non polar	33892256
5-Methylcytidine,5TMS,isomer #1	CC1=CN([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(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2714.2	Standard polar	33892256
5-Methylcytidine,1TBDMS,isomer #1	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O)C(=O)N=C1N	2749.7	Semi standard non polar	33892256
5-Methylcytidine,1TBDMS,isomer #2	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C(=O)N=C1N	2737.5	Semi standard non polar	33892256
5-Methylcytidine,1TBDMS,isomer #3	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)N=C1N	2733.5	Semi standard non polar	33892256
5-Methylcytidine,1TBDMS,isomer #4	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N[Si](C)(C)C(C)(C)C	2787.2	Semi standard non polar	33892256
5-Methylcytidine,2TBDMS,isomer #1	CC1=CN([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(=O)N=C1N	2940.6	Semi standard non polar	33892256
5-Methylcytidine,2TBDMS,isomer #2	CC1=CN([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(=O)N=C1N	2940.4	Semi standard non polar	33892256
5-Methylcytidine,2TBDMS,isomer #3	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O)C(=O)N=C1N[Si](C)(C)C(C)(C)C	2973.0	Semi standard non polar	33892256
5-Methylcytidine,2TBDMS,isomer #4	CC1=CN([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(=O)N=C1N	2926.7	Semi standard non polar	33892256
5-Methylcytidine,2TBDMS,isomer #5	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C(=O)N=C1N[Si](C)(C)C(C)(C)C	2968.8	Semi standard non polar	33892256
5-Methylcytidine,2TBDMS,isomer #6	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)N=C1N[Si](C)(C)C(C)(C)C	2952.7	Semi standard non polar	33892256
5-Methylcytidine,2TBDMS,isomer #7	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2944.6	Semi standard non polar	33892256
5-Methylcytidine,3TBDMS,isomer #1	CC1=CN([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(=O)N=C1N	3151.1	Semi standard non polar	33892256
5-Methylcytidine,3TBDMS,isomer #2	CC1=CN([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(=O)N=C1N[Si](C)(C)C(C)(C)C	3171.0	Semi standard non polar	33892256
5-Methylcytidine,3TBDMS,isomer #3	CC1=CN([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(=O)N=C1N[Si](C)(C)C(C)(C)C	3176.7	Semi standard non polar	33892256
5-Methylcytidine,3TBDMS,isomer #4	CC1=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3144.6	Semi standard non polar	33892256
5-Methylcytidine,3TBDMS,isomer #5	CC1=CN([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(=O)N=C1N[Si](C)(C)C(C)(C)C	3161.3	Semi standard non polar	33892256
5-Methylcytidine,3TBDMS,isomer #6	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3158.0	Semi standard non polar	33892256
5-Methylcytidine,3TBDMS,isomer #7	CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3144.0	Semi standard non polar	33892256
5-Methylcytidine,4TBDMS,isomer #1	CC1=CN([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(=O)N=C1N[Si](C)(C)C(C)(C)C	3348.3	Semi standard non polar	33892256
5-Methylcytidine,4TBDMS,isomer #1	CC1=CN([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(=O)N=C1N[Si](C)(C)C(C)(C)C	3320.5	Standard non polar	33892256
5-Methylcytidine,4TBDMS,isomer #1	CC1=CN([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(=O)N=C1N[Si](C)(C)C(C)(C)C	3363.6	Standard polar	33892256
5-Methylcytidine,4TBDMS,isomer #2	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3349.1	Semi standard non polar	33892256
5-Methylcytidine,4TBDMS,isomer #2	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3375.0	Standard non polar	33892256
5-Methylcytidine,4TBDMS,isomer #2	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3222.2	Standard polar	33892256
5-Methylcytidine,4TBDMS,isomer #3	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3356.8	Semi standard non polar	33892256
5-Methylcytidine,4TBDMS,isomer #3	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3387.2	Standard non polar	33892256
5-Methylcytidine,4TBDMS,isomer #3	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3256.5	Standard polar	33892256
5-Methylcytidine,4TBDMS,isomer #4	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3344.4	Semi standard non polar	33892256
5-Methylcytidine,4TBDMS,isomer #4	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3374.1	Standard non polar	33892256
5-Methylcytidine,4TBDMS,isomer #4	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3204.0	Standard polar	33892256
5-Methylcytidine,5TBDMS,isomer #1	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3538.6	Semi standard non polar	33892256
5-Methylcytidine,5TBDMS,isomer #1	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3490.8	Standard non polar	33892256
5-Methylcytidine,5TBDMS,isomer #1	CC1=CN([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(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3189.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0adl-9420000000-0b05b3fff49a937e78cb	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (3 TMS) - 70eV, Positive	splash10-001i-6921100000-895058c6ba83f084d86e	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_3_5) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_3_6) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytidine GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-06	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-004i-0900000000-01346f227c58c4e64dd3	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-004i-0900000000-25d8b3fb44e47bc7f544	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-004i-1900000000-0ad90898ddb462fa200b	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine 40V, Positive-QTOF	splash10-004i-4900000000-ff34d9c361d96f5aa2de	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine 20V, Positive-QTOF	splash10-004i-0900000000-0366c638ef303f3731b3	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine 35V, Positive-QTOF	splash10-004i-0900000000-f936466105072c9b573c	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine 10V, Positive-QTOF	splash10-056r-0950000000-10971ba54196bbfdfc8d	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine 10V, Negative-QTOF	splash10-0a4i-0090000000-d8be738cdc4e54477227	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine 35V, Negative-QTOF	splash10-0gi0-1490000000-f34a1cb7ce97d538cb7a	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine 20V, Negative-QTOF	splash10-0avi-1960000000-da3e8a4eb805781bcbc6	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytidine 40V, Negative-QTOF	splash10-0002-9000000000-0a9ca0be7ac354db9478	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 10V, Positive-QTOF	splash10-004i-0910000000-960e39cedc554f014863	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 20V, Positive-QTOF	splash10-004i-2900000000-2ecbb224dc501d648886	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 40V, Positive-QTOF	splash10-056r-5900000000-55a400dd7cd5fcd9ea3d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 10V, Negative-QTOF	splash10-00di-0950000000-0275ab78e34a521999fb	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 20V, Negative-QTOF	splash10-00di-3920000000-50690663d91d4d14a39c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 40V, Negative-QTOF	splash10-007p-9200000000-978b587a0b7b22774839	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 10V, Negative-QTOF	splash10-0ab9-0890000000-24f0c238f60d3c00adbb	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 20V, Negative-QTOF	splash10-006y-9700000000-c0edbd46e86d76296c58	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 40V, Negative-QTOF	splash10-0005-9200000000-9358476776cf6eec42c1	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 10V, Positive-QTOF	splash10-004i-0900000000-a1c51dd1d9ae2dee6e38	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 20V, Positive-QTOF	splash10-004i-1910000000-f366741e71fc5efb780d	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytidine 40V, Positive-QTOF	splash10-0a7i-8900000000-f063ff1fc5cb2b980e9e	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	2012-12-04	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Detected and Quantified	2.2 (0.00-5.3) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	15116424	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Crohns disease	26848182	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Iron deficiency	26848182	details

Associated Disorders and Diseases

Disease References

Crohn's disease
Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Iron deficiency
Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]

Associated OMIM IDs

266600 (Crohn's disease)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022351

KNApSAcK ID

Not Available

Chemspider ID

83877

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

5-Methylcytidine

METLIN ID

5919

PubChem Compound

92918

PDB ID

Not Available

ChEBI ID

20607

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Mastronicolis S K; Kapoulas V M; Kroger H The isolation of antibodies specific for 5-methyl-cytidine-bovine serum albumin. Zeitschrift fur Naturforschung. Section C: Biosciences (1981), 36(5-6), 459-63.

Material Safety Data Sheet (MSDS)

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. [PubMed:15116424 ]
Reynaud C, Bruno C, Boullanger P, Grange J, Barbesti S, Niveleau A: Monitoring of urinary excretion of modified nucleosides in cancer patients using a set of six monoclonal antibodies. Cancer Lett. 1992 Jan 31;61(3):255-62. [PubMed:1739950 ]
Itoh K, Aida S, Ishiwata S, Yamaguchi T, Ishida N, Mizugaki M: Immunochemical detection of urinary 5-methyl-2'-deoxycytidine as a potential biologic marker for leukemia. Clin Chim Acta. 1995 Jan 31;234(1-2):37-45. [PubMed:7758221 ]
Strong LC: The nature of cancer and the mechanisms of its control: a review. Cytobios. 1980;28(111-112):187-208. [PubMed:6260434 ]

Showing metabocard for 5-Methylcytidine (HMDB0000982)

MOL for HMDB0000982 (5-Methylcytidine)

3D MOL for HMDB0000982 (5-Methylcytidine)

3D SDF for HMDB0000982 (5-Methylcytidine)

3D-SDF for HMDB0000982 (5-Methylcytidine)

PDB for HMDB0000982 (5-Methylcytidine)

3D PDB for HMDB0000982 (5-Methylcytidine)

SMILES for HMDB0000982 (5-Methylcytidine)

INCHI for HMDB0000982 (5-Methylcytidine)

Structure for HMDB0000982 (5-Methylcytidine)

3D Structure for HMDB0000982 (5-Methylcytidine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra