NP-MRD: Showing NP-Card for 5-Methylcytidine (NP0000250)

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Record Information

Version

1.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2021-10-07 20:40:07 UTC

NP-MRD ID

NP0000250

Secondary Accession Numbers

None

Natural Product 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.

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>
NP0000250

> <DATABASE_NAME>
NP-MRD

> <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

Synonyms

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

Chemical Formula

C₁₀H₁₅N₃O₅

Average Mass

257.2432 Da

Monoisotopic Mass

257.10117 Da

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

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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 )

Physical Properties

State

Solid

Experimental 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 CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).

Predicted 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

External Links

HMDB ID

HMDB0000982

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

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 ]
Ohshiro T, Konno M, Asai A, Komoto Y, Yamagata A, Doki Y, Eguchi H, Ofusa K, Taniguchi M, Ishii H: Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC. Sci Rep. 2021 Sep 29;11(1):19304. doi: 10.1038/s41598-021-98805-z. [PubMed:34588546 ]

Showing NP-Card for 5-Methylcytidine (NP0000250)

MOL for NP0000250 (5-Methylcytidine)

3D MOL for NP0000250 (5-Methylcytidine)

3D SDF for NP0000250 (5-Methylcytidine)

3D-SDF for NP0000250 (5-Methylcytidine)

PDB for NP0000250 (5-Methylcytidine)

3D PDB for NP0000250 (5-Methylcytidine)

SMILES for NP0000250 (5-Methylcytidine)

INCHI for NP0000250 (5-Methylcytidine)

Structure for NP0000250 (5-Methylcytidine)

3D Structure for NP0000250 (5-Methylcytidine)