Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2019-10-24 15:55:51 UTC

Update Date

2022-09-22 18:34:32 UTC

HMDB ID

HMDB0240577

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3-Methylcytidine

Description

3-Methylcytidine belongs to the class of organic compounds known as pyrimidine nucleosides. These are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. 3-Methylcytidine is a potential urinary biomarker of whole grain intake (PMID: 27805021 ). 3-Methylcytidine has been identified in the human placenta (PMID: 32033212 ).

Structure

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

HMDB0240577
     RDKit          3D
3-Methylcytidine
 33 34  0  0  0  0  0  0  0  0999 V2000
    3.6987    1.9070   -0.2177 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9150    0.6889   -0.1111 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5387   -0.4443    0.2590 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8160   -0.4711    0.5207 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7694   -1.5858    0.3519 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4135   -1.5436    0.0711 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8127   -0.3882   -0.2992 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5897   -0.3175   -0.5955 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1249    0.8655   -0.0589 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4828    0.6955   -0.3223 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3291    1.6779    0.4708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1182    1.4840    1.8279 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7913   -0.7378    0.0982 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5965   -1.2930   -0.8735 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3995   -1.3831    0.1029 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4612   -2.5150   -0.6855 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5912    0.7035   -0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0515    1.7897   -0.7227 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2882    1.8330   -1.1494 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9914    2.7716   -0.3716 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3002    2.1144    0.6791 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3680    0.3923    0.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2246   -2.5215    0.6456 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7791   -2.4208    0.1339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7826   -0.2984   -1.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6234    0.8534   -1.4007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3779    1.4928    0.2056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0481    2.6904    0.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9866    1.5938    2.2918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2424   -0.7509    1.0990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1589   -1.9758   -1.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0272   -1.5512    1.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4178   -3.3558   -0.1675 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17  2  1  0
 15  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  8 25  1  6
 10 26  1  6
 11 27  1  0
 11 28  1  0
 12 29  1  0
 13 30  1  1
 14 31  1  0
 15 32  1  1
 16 33  1  0
M  END


  Mrv1652310241917592D          

 18 19  0  0  0  0            999 V2000
 9999.908810001.5532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.696810001.5450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.1668 9999.6948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.880210000.1059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.687210000.9306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.119710000.1863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2589 9998.4567    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.687210000.1071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9727 9999.6946    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9727 9998.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6872 9998.4571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4017 9998.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4017 9999.6946    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10000.7859 9999.6119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.118510000.0969    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.373410000.8815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.198410000.8815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.453310000.0969    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  3  4  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 14 15  1  0  0  0  0
 14 18  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  8 13  1  0  0  0  0
 12 13  1  0  0  0  0
  8  5  2  0  0  0  0
  9  6  1  0  0  0  0
 10  7  2  0  0  0  0
 16  1  1  6  0  0  0
 15 13  1  1  0  0  0
 18  3  1  1  0  0  0
 17  2  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0240577

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O

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

> <INCHI_KEY>
RDPUKVRQKWBSPK-ZOQUXTDFSA-N

> <FORMULA>
C10H15N3O5

> <MOLECULAR_WEIGHT>
257.246

> <EXACT_MASS>
257.101170595

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
24.42945309479645

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.71

> <JCHEM_LOGP>
-1.817037896

> <ALOGPS_LOGS>
-1.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.933965309537061

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.55383331073508

> <JCHEM_PKA_STRONGEST_BASIC>
-0.017893755025645386

> <JCHEM_POLAR_SURFACE_AREA>
117.31999999999998

> <JCHEM_REFRACTIVITY>
69.93430000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.43e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methylcytidine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0240577
     RDKit          3D
3-Methylcytidine
 33 34  0  0  0  0  0  0  0  0999 V2000
    3.6987    1.9070   -0.2177 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9150    0.6889   -0.1111 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5387   -0.4443    0.2590 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8160   -0.4711    0.5207 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7694   -1.5858    0.3519 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4135   -1.5436    0.0711 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8127   -0.3882   -0.2992 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5897   -0.3175   -0.5955 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1249    0.8655   -0.0589 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4828    0.6955   -0.3223 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3291    1.6779    0.4708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1182    1.4840    1.8279 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7913   -0.7378    0.0982 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5965   -1.2930   -0.8735 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3995   -1.3831    0.1029 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4612   -2.5150   -0.6855 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5912    0.7035   -0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0515    1.7897   -0.7227 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2882    1.8330   -1.1494 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9914    2.7716   -0.3716 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3002    2.1144    0.6791 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3680    0.3923    0.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2246   -2.5215    0.6456 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7791   -2.4208    0.1339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7826   -0.2984   -1.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6234    0.8534   -1.4007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3779    1.4928    0.2056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0481    2.6904    0.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9866    1.5938    2.2918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2424   -0.7509    1.0990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1589   -1.9758   -1.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0272   -1.5512    1.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4178   -3.3558   -0.1675 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17  2  1  0
 15  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  8 25  1  6
 10 26  1  6
 11 27  1  0
 11 28  1  0
 12 29  1  0
 13 30  1  1
 14 31  1  0
 15 32  1  1
 16 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    8666.4968669.566   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8669.8348669.551   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8670.7118666.097   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8672.0438666.864   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8664.2168668.404   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0    8661.2908667.014   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0    8661.5508663.786   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0    8664.2168666.867   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0    8662.8828666.097   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0    8662.8828664.556   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8664.2168663.787   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8665.5508664.556   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0    8665.5508666.097   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0    8668.1348665.942   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0    8666.8888666.848   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8667.3648668.312   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8668.9048668.312   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8669.3798666.848   0.000  0.00  0.00           C+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3    4   18                                                       
CONECT    4    3                                                            
CONECT    5    8                                                            
CONECT    6    9                                                            
CONECT    7   10                                                            
CONECT    8    9   13    5                                                  
CONECT    9    8   10    6                                                  
CONECT   10   11    9    7                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13    8   12   15                                                  
CONECT   14   15   18                                                       
CONECT   15   16   14   13                                                  
CONECT   16   15   17    1                                                  
CONECT   17   16   18    2                                                  
CONECT   18   17   14    3                                                  
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0240577
HETATM    1  C1  UNL     1       3.699   1.907  -0.218  1.00  0.00           C  
HETATM    2  N1  UNL     1       2.915   0.689  -0.111  1.00  0.00           N  
HETATM    3  C2  UNL     1       3.539  -0.444   0.259  1.00  0.00           C  
HETATM    4  N2  UNL     1       4.816  -0.471   0.521  1.00  0.00           N  
HETATM    5  C3  UNL     1       2.769  -1.586   0.352  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.413  -1.544   0.071  1.00  0.00           C  
HETATM    7  N3  UNL     1       0.813  -0.388  -0.299  1.00  0.00           N  
HETATM    8  C5  UNL     1      -0.590  -0.318  -0.596  1.00  0.00           C  
HETATM    9  O1  UNL     1      -1.125   0.866  -0.059  1.00  0.00           O  
HETATM   10  C6  UNL     1      -2.483   0.696  -0.322  1.00  0.00           C  
HETATM   11  C7  UNL     1      -3.329   1.678   0.471  1.00  0.00           C  
HETATM   12  O2  UNL     1      -3.118   1.484   1.828  1.00  0.00           O  
HETATM   13  C8  UNL     1      -2.791  -0.738   0.098  1.00  0.00           C  
HETATM   14  O3  UNL     1      -3.596  -1.293  -0.873  1.00  0.00           O  
HETATM   15  C9  UNL     1      -1.399  -1.383   0.103  1.00  0.00           C  
HETATM   16  O4  UNL     1      -1.461  -2.515  -0.686  1.00  0.00           O  
HETATM   17  C10 UNL     1       1.591   0.703  -0.379  1.00  0.00           C  
HETATM   18  O5  UNL     1       1.051   1.790  -0.723  1.00  0.00           O  
HETATM   19  H1  UNL     1       4.288   1.833  -1.149  1.00  0.00           H  
HETATM   20  H2  UNL     1       2.991   2.772  -0.372  1.00  0.00           H  
HETATM   21  H3  UNL     1       4.300   2.114   0.679  1.00  0.00           H  
HETATM   22  H4  UNL     1       5.368   0.392   0.444  1.00  0.00           H  
HETATM   23  H5  UNL     1       3.225  -2.521   0.646  1.00  0.00           H  
HETATM   24  H6  UNL     1       0.779  -2.421   0.134  1.00  0.00           H  
HETATM   25  H7  UNL     1      -0.783  -0.298  -1.680  1.00  0.00           H  
HETATM   26  H8  UNL     1      -2.623   0.853  -1.401  1.00  0.00           H  
HETATM   27  H9  UNL     1      -4.378   1.493   0.206  1.00  0.00           H  
HETATM   28  H10 UNL     1      -3.048   2.690   0.143  1.00  0.00           H  
HETATM   29  H11 UNL     1      -3.987   1.594   2.292  1.00  0.00           H  
HETATM   30  H12 UNL     1      -3.242  -0.751   1.099  1.00  0.00           H  
HETATM   31  H13 UNL     1      -3.159  -1.976  -1.424  1.00  0.00           H  
HETATM   32  H14 UNL     1      -1.027  -1.551   1.114  1.00  0.00           H  
HETATM   33  H15 UNL     1      -1.418  -3.356  -0.168  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3   17
CONECT    3    4    4    5
CONECT    4   22
CONECT    5    6    6   23
CONECT    6    7   24
CONECT    7    8   17
CONECT    8    9   15   25
CONECT    9   10
CONECT   10   11   13   26
CONECT   11   12   27   28
CONECT   12   29
CONECT   13   14   15   30
CONECT   14   31
CONECT   15   16   32
CONECT   16   33
CONECT   17   18   18
END

HMDB0240577
     RDKit          3D
3-Methylcytidine
 33 34  0  0  0  0  0  0  0  0999 V2000
    3.6987    1.9070   -0.2177 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9150    0.6889   -0.1111 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5387   -0.4443    0.2590 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8160   -0.4711    0.5207 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7694   -1.5858    0.3519 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4135   -1.5436    0.0711 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8127   -0.3882   -0.2992 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5897   -0.3175   -0.5955 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1249    0.8655   -0.0589 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4828    0.6955   -0.3223 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3291    1.6779    0.4708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1182    1.4840    1.8279 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7913   -0.7378    0.0982 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5965   -1.2930   -0.8735 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3995   -1.3831    0.1029 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4612   -2.5150   -0.6855 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5912    0.7035   -0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0515    1.7897   -0.7227 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2882    1.8330   -1.1494 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9914    2.7716   -0.3716 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3002    2.1144    0.6791 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3680    0.3923    0.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2246   -2.5215    0.6456 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7791   -2.4208    0.1339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7826   -0.2984   -1.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6234    0.8534   -1.4007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3779    1.4928    0.2056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0481    2.6904    0.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9866    1.5938    2.2918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2424   -0.7509    1.0990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1589   -1.9758   -1.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0272   -1.5512    1.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4178   -3.3558   -0.1675 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17  2  1  0
 15  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  8 25  1  6
 10 26  1  6
 11 27  1  0
 11 28  1  0
 12 29  1  0
 13 30  1  1
 14 31  1  0
 15 32  1  1
 16 33  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3-Methyl-4,N(4)-didehydro-3,4-dihydrocytidine	ChEBI
N3-Methylcytidine	HMDB
3-Methylcytidine	HMDB

Chemical Formula

C₁₀H₁₅N₃O₅

Average Molecular Weight

257.246

Monoisotopic Molecular Weight

257.101170595

IUPAC Name

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

Traditional Name

3-methylcytidine

CAS Registry Number

2140-64-9

SMILES

CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O

InChI Identifier

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

InChI Key

RDPUKVRQKWBSPK-ZOQUXTDFSA-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
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Urea
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

methylcytidine (CHEBI:20129 )

Ontology

Not Available

Placenta (HMDB: HMDB0240577)

Excreta

Biofluid or Excreta

Urine (PMID: 27805021)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.7	ALOGPS
logP	-1.8	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	-0.018	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	117.32 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	69.93 m³·mol⁻¹	ChemAxon
Polarizability	24.43 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
DeepCCS	[M+H]+	159.075	30932474
DeepCCS	[M-H]-	156.717	30932474
DeepCCS	[M-2H]-	190.844	30932474
DeepCCS	[M+Na]+	166.961	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Methylcytidine	CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	3789.1	Standard polar	33892256
3-Methylcytidine	CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	2299.8	Standard non polar	33892256
3-Methylcytidine	CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	2544.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Methylcytidine,1TMS,isomer #1	CN1C(=N)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O)C1=O	2451.3	Semi standard non polar	33892256
3-Methylcytidine,1TMS,isomer #2	CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O)C1=O	2455.3	Semi standard non polar	33892256
3-Methylcytidine,1TMS,isomer #3	CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C)C1=O	2437.8	Semi standard non polar	33892256
3-Methylcytidine,1TMS,isomer #4	CN1C(=N[Si](C)(C)C)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	2446.5	Semi standard non polar	33892256
3-Methylcytidine,2TMS,isomer #1	CN1C(=N)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O)C1=O	2434.1	Semi standard non polar	33892256
3-Methylcytidine,2TMS,isomer #2	CN1C(=N)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C)C1=O	2428.5	Semi standard non polar	33892256
3-Methylcytidine,2TMS,isomer #3	CN1C(=N[Si](C)(C)C)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O)C1=O	2412.3	Semi standard non polar	33892256
3-Methylcytidine,2TMS,isomer #4	CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O	2425.4	Semi standard non polar	33892256
3-Methylcytidine,2TMS,isomer #5	CN1C(=N[Si](C)(C)C)C=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O)C1=O	2412.2	Semi standard non polar	33892256
3-Methylcytidine,2TMS,isomer #6	CN1C(=N[Si](C)(C)C)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C)C1=O	2413.7	Semi standard non polar	33892256
3-Methylcytidine,3TMS,isomer #1	CN1C(=N)C=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)C1=O	2425.5	Semi standard non polar	33892256
3-Methylcytidine,3TMS,isomer #2	CN1C(=N[Si](C)(C)C)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O)C1=O	2400.0	Semi standard non polar	33892256
3-Methylcytidine,3TMS,isomer #3	CN1C(=N[Si](C)(C)C)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H]2O[Si](C)(C)C)C1=O	2410.4	Semi standard non polar	33892256
3-Methylcytidine,3TMS,isomer #4	CN1C(=N[Si](C)(C)C)C=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O	2382.9	Semi standard non polar	33892256
3-Methylcytidine,4TMS,isomer #1	CN1C(=N[Si](C)(C)C)C=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)C1=O	2412.3	Semi standard non polar	33892256
3-Methylcytidine,4TMS,isomer #1	CN1C(=N[Si](C)(C)C)C=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)C1=O	2647.9	Standard non polar	33892256
3-Methylcytidine,4TMS,isomer #1	CN1C(=N[Si](C)(C)C)C=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)C1=O	2895.3	Standard polar	33892256
3-Methylcytidine,1TBDMS,isomer #1	CN1C(=N)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O)C1=O	2706.4	Semi standard non polar	33892256
3-Methylcytidine,1TBDMS,isomer #2	CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C1=O	2689.5	Semi standard non polar	33892256
3-Methylcytidine,1TBDMS,isomer #3	CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C1=O	2688.3	Semi standard non polar	33892256
3-Methylcytidine,1TBDMS,isomer #4	CN1C(=N[Si](C)(C)C(C)(C)C)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	2718.3	Semi standard non polar	33892256
3-Methylcytidine,2TBDMS,isomer #1	CN1C(=N)C=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)C1=O	2909.8	Semi standard non polar	33892256
3-Methylcytidine,2TBDMS,isomer #2	CN1C(=N)C=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)C1=O	2907.1	Semi standard non polar	33892256
3-Methylcytidine,2TBDMS,isomer #3	CN1C(=N[Si](C)(C)C(C)(C)C)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]2O)C1=O	2909.1	Semi standard non polar	33892256
3-Methylcytidine,2TBDMS,isomer #4	CN1C(=N)C=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)C1=O	2892.6	Semi standard non polar	33892256
3-Methylcytidine,2TBDMS,isomer #5	CN1C(=N[Si](C)(C)C(C)(C)C)C=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C1=O	2907.5	Semi standard non polar	33892256
3-Methylcytidine,2TBDMS,isomer #6	CN1C(=N[Si](C)(C)C(C)(C)C)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C1=O	2899.9	Semi standard non polar	33892256
3-Methylcytidine,3TBDMS,isomer #1	CN1C(=N)C=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)C1=O	3126.2	Semi standard non polar	33892256
3-Methylcytidine,3TBDMS,isomer #2	CN1C(=N[Si](C)(C)C(C)(C)C)C=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)C1=O	3115.0	Semi standard non polar	33892256
3-Methylcytidine,3TBDMS,isomer #3	CN1C(=N[Si](C)(C)C(C)(C)C)C=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)C1=O	3121.5	Semi standard non polar	33892256
3-Methylcytidine,3TBDMS,isomer #4	CN1C(=N[Si](C)(C)C(C)(C)C)C=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)C1=O	3104.2	Semi standard non polar	33892256
3-Methylcytidine,4TBDMS,isomer #1	CN1C(=N[Si](C)(C)C(C)(C)C)C=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)C1=O	3299.8	Semi standard non polar	33892256
3-Methylcytidine,4TBDMS,isomer #1	CN1C(=N[Si](C)(C)C(C)(C)C)C=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)C1=O	3395.1	Standard non polar	33892256
3-Methylcytidine,4TBDMS,isomer #1	CN1C(=N[Si](C)(C)C(C)(C)C)C=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)C1=O	3256.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylcytidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylcytidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3-Methylcytidine 35V, Positive-QTOF	splash10-004i-0900000000-6f98cd51f22dda9b60d6	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3-Methylcytidine 35V, Negative-QTOF	splash10-0urc-1900000000-4ac88b500f3678e07429	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytidine 10V, Negative-QTOF	splash10-014i-0900000000-ab6f7c5ad4035e6cf4cd	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytidine 20V, Negative-QTOF	splash10-01b9-5900000000-5b26fa5276ea7866f919	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytidine 40V, Negative-QTOF	splash10-00kg-9200000000-865cf06b478bdb40c62c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytidine 10V, Positive-QTOF	splash10-004i-1900000000-72526dc613a3c811599b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytidine 20V, Positive-QTOF	splash10-00di-2900000000-e010f2121713a9ab3ee9	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytidine 40V, Positive-QTOF	splash10-004i-5900000000-49ec4e26b45f6a396d5d	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Placenta

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27805021	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

21864863

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

5-Methylcytidine

METLIN ID

Not Available

PubChem Compound

14237477

PDB ID

Not Available

ChEBI ID

20129

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Zhu Y, Wang P, Sha W, Sang S: Urinary Biomarkers of Whole Grain Wheat Intake Identified by Non-targeted and Targeted Metabolomics Approaches. Sci Rep. 2016 Nov 2;6:36278. doi: 10.1038/srep36278. [PubMed:27805021 ]
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 3-Methylcytidine (HMDB0240577)

MOL for HMDB0240577 (3-Methylcytidine)

3D MOL for HMDB0240577 (3-Methylcytidine)

3D SDF for HMDB0240577 (3-Methylcytidine)

3D-SDF for HMDB0240577 (3-Methylcytidine)

PDB for HMDB0240577 (3-Methylcytidine)

3D PDB for HMDB0240577 (3-Methylcytidine)

SMILES for HMDB0240577 (3-Methylcytidine)

INCHI for HMDB0240577 (3-Methylcytidine)

Structure for HMDB0240577 (3-Methylcytidine)

3D Structure for HMDB0240577 (3-Methylcytidine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra