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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (12) Show 12 proteins XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-08-27 00:49:52 UTC

Update Date

2022-09-22 18:34:34 UTC

HMDB ID

HMDB0242132

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2'-O-Methylcytidine

Description

2'-O-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. Based on a literature review a significant number of articles have been published on 2'-O-Methylcytidine.

Structure

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

HMDB0242132
     RDKit          3D
2'-O-Methylcytidine
 33 34  0  0  0  0  0  0  0  0999 V2000
   -0.0419    3.0237   -0.5078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4613    2.1062    0.4165 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8340    0.8920   -0.0911 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2665    0.5127    0.2813 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6237    1.1874    1.4461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1303   -0.9624    0.5950 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1724   -1.7849   -0.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9677   -3.1249    0.1904 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8364   -1.3237    0.2207 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1001   -0.2373    0.6425 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2793   -0.2870    0.3400 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7698   -1.1812   -0.5262 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1201   -1.2528   -0.8421 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9760   -0.3599   -0.2304 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2614   -0.3742   -0.4845 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4510    0.5256    0.6348 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1223    0.5717    0.9246 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7143    1.5417    1.8409 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7878    3.2891   -1.2720 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8316    2.5698   -1.0613 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3472    3.9127    0.0439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7540    0.7922   -1.1826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9668    0.7049   -0.5498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3283    0.7156    2.2553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2051   -1.1555    1.6849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1657   -1.5120    0.2788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1947   -1.6083   -1.2003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7939   -3.5700    0.4413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3180   -0.0880    1.7196 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1365   -1.9034   -1.0321 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5374   -1.9660   -1.5379 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6413   -1.0717   -1.1597 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.4178    2.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  3
 14 16  1  0
 16 17  2  0
 17 18  1  0
 10  3  1  0
 17 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  6
  4 23  1  6
  5 24  1  0
  6 25  1  1
  7 26  1  0
  7 27  1  0
  8 28  1  0
 10 29  1  1
 12 30  1  0
 13 31  1  0
 15 32  1  0
 18 33  1  0
M  END


  Mrv1652308272102592D          

 22 23  0  0  1  0            999 V2000
    1.1276    0.5154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5477    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0161    0.3129    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004   -1.1299    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7132   -2.0662    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  5  4  1  1  0  0  0
  6  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 11  6  2  0  0  0  0
 12  6  1  0  0  0  0
 12 10  2  0  0  0  0
 13  3  1  0  0  0  0
  9 13  1  1  0  0  0
 13 10  1  0  0  0  0
 14  4  1  0  0  0  0
  7 15  1  6  0  0  0
 16 10  1  0  0  0  0
 17  1  1  0  0  0  0
  8 17  1  6  0  0  0
 18  5  1  0  0  0  0
 18  9  1  0  0  0  0
  5 19  1  6  0  0  0
  7 20  1  1  0  0  0
  8 21  1  1  0  0  0
  9 22  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0242132

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@]1(CO)O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(OC)[C@]1([H])O

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

> <INCHI_KEY>
RFCQJGFZUQFYRF-ZOQUXTDFSA-N

> <FORMULA>
C10H15N3O5

> <MOLECULAR_WEIGHT>
257.246

> <EXACT_MASS>
257.101170595

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
24.498456085701697

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-ol

> <ALOGPS_LOGP>
-2.11

> <JCHEM_LOGP>
-1.176253320333333

> <ALOGPS_LOGS>
-2.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.003440267553966

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.896091552377536

> <JCHEM_PKA_STRONGEST_BASIC>
2.509764066448414

> <JCHEM_POLAR_SURFACE_AREA>
118.60000000000001

> <JCHEM_REFRACTIVITY>
70.7085

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-4-iminopyrimidin-2-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0242132
     RDKit          3D
2'-O-Methylcytidine
 33 34  0  0  0  0  0  0  0  0999 V2000
   -0.0419    3.0237   -0.5078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4613    2.1062    0.4165 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8340    0.8920   -0.0911 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2665    0.5127    0.2813 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6237    1.1874    1.4461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1303   -0.9624    0.5950 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1724   -1.7849   -0.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9677   -3.1249    0.1904 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8364   -1.3237    0.2207 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1001   -0.2373    0.6425 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2793   -0.2870    0.3400 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7698   -1.1812   -0.5262 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1201   -1.2528   -0.8421 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9760   -0.3599   -0.2304 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2614   -0.3742   -0.4845 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4510    0.5256    0.6348 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1223    0.5717    0.9246 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7143    1.5417    1.8409 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7878    3.2891   -1.2720 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8316    2.5698   -1.0613 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3472    3.9127    0.0439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7540    0.7922   -1.1826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9668    0.7049   -0.5498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3283    0.7156    2.2553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2051   -1.1555    1.6849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1657   -1.5120    0.2788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1947   -1.6083   -1.2003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7939   -3.5700    0.4413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3180   -0.0880    1.7196 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1365   -1.9034   -1.0321 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5374   -1.9660   -1.5379 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6413   -1.0717   -1.1597 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.4178    2.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  3
 14 16  1  0
 16 17  2  0
 17 18  1  0
 10  3  1  0
 17 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  6
  4 23  1  6
  5 24  1  0
  6 25  1  1
  7 26  1  0
  7 27  1  0
  8 28  1  0
 10 29  1  1
 12 30  1  0
 13 31  1  0
 15 32  1  0
 18 33  1  0
M  END

HEADER    PROTEIN                                 27-AUG-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-AUG-21         0                                  
HETATM    1  C   UNK     0       2.105   0.962   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.182  -6.383   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.087  -5.138   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.846  -0.544   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.650  -6.222   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.366  -2.485   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.929  -3.570   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.745  -7.468   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       1.024  -4.816   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       3.460  -3.731   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       8.166   0.962   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       5.136   1.425   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.302  -2.163   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.425  -0.544   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       5.906  -2.485   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       6.622   0.501   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.763   0.584   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       2.801  -2.109   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       5.065  -3.857   0.000  0.00  0.00           H+0
CONECT    1   17                                                            
CONECT    2    3    6                                                       
CONECT    3    2   13                                                       
CONECT    4    5   14                                                       
CONECT    5    4    7   18   19                                             
CONECT    6    2   11   12                                                  
CONECT    7    5    8   15   20                                             
CONECT    8    7    9   17   21                                             
CONECT    9    8   13   18   22                                             
CONECT   10   12   13   16                                                  
CONECT   11    6                                                            
CONECT   12    6   10                                                       
CONECT   13    3    9   10                                                  
CONECT   14    4                                                            
CONECT   15    7                                                            
CONECT   16   10                                                            
CONECT   17    1    8                                                       
CONECT   18    5    9                                                       
CONECT   19    5                                                            
CONECT   20    7                                                            
CONECT   21    8                                                            
CONECT   22    9                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

COMPND    HMDB0242132
HETATM    1  C1  UNL     1      -0.042   3.024  -0.508  1.00  0.00           C  
HETATM    2  O1  UNL     1      -0.461   2.106   0.417  1.00  0.00           O  
HETATM    3  C2  UNL     1      -0.834   0.892  -0.091  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.266   0.513   0.281  1.00  0.00           C  
HETATM    5  O2  UNL     1      -2.624   1.187   1.446  1.00  0.00           O  
HETATM    6  C4  UNL     1      -2.130  -0.962   0.595  1.00  0.00           C  
HETATM    7  C5  UNL     1      -3.172  -1.785  -0.127  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.968  -3.125   0.190  1.00  0.00           O  
HETATM    9  O4  UNL     1      -0.836  -1.324   0.221  1.00  0.00           O  
HETATM   10  C6  UNL     1      -0.100  -0.237   0.642  1.00  0.00           C  
HETATM   11  N1  UNL     1       1.279  -0.287   0.340  1.00  0.00           N  
HETATM   12  C7  UNL     1       1.770  -1.181  -0.526  1.00  0.00           C  
HETATM   13  C8  UNL     1       3.120  -1.253  -0.842  1.00  0.00           C  
HETATM   14  C9  UNL     1       3.976  -0.360  -0.230  1.00  0.00           C  
HETATM   15  N2  UNL     1       5.261  -0.374  -0.485  1.00  0.00           N  
HETATM   16  N3  UNL     1       3.451   0.526   0.635  1.00  0.00           N  
HETATM   17  C10 UNL     1       2.122   0.572   0.925  1.00  0.00           C  
HETATM   18  O5  UNL     1       1.714   1.542   1.841  1.00  0.00           O  
HETATM   19  H1  UNL     1      -0.788   3.289  -1.272  1.00  0.00           H  
HETATM   20  H2  UNL     1       0.832   2.570  -1.061  1.00  0.00           H  
HETATM   21  H3  UNL     1       0.347   3.913   0.044  1.00  0.00           H  
HETATM   22  H4  UNL     1      -0.754   0.792  -1.183  1.00  0.00           H  
HETATM   23  H5  UNL     1      -2.967   0.705  -0.550  1.00  0.00           H  
HETATM   24  H6  UNL     1      -2.328   0.716   2.255  1.00  0.00           H  
HETATM   25  H7  UNL     1      -2.205  -1.156   1.685  1.00  0.00           H  
HETATM   26  H8  UNL     1      -4.166  -1.512   0.279  1.00  0.00           H  
HETATM   27  H9  UNL     1      -3.195  -1.608  -1.200  1.00  0.00           H  
HETATM   28  H10 UNL     1      -3.794  -3.570   0.441  1.00  0.00           H  
HETATM   29  H11 UNL     1      -0.318  -0.088   1.720  1.00  0.00           H  
HETATM   30  H12 UNL     1       1.137  -1.903  -1.032  1.00  0.00           H  
HETATM   31  H13 UNL     1       3.537  -1.966  -1.538  1.00  0.00           H  
HETATM   32  H14 UNL     1       5.641  -1.072  -1.160  1.00  0.00           H  
HETATM   33  H15 UNL     1       1.760   1.418   2.837  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3
CONECT    3    4   10   22
CONECT    4    5    6   23
CONECT    5   24
CONECT    6    7    9   25
CONECT    7    8   26   27
CONECT    8   28
CONECT    9   10
CONECT   10   11   29
CONECT   11   12   17
CONECT   12   13   13   30
CONECT   13   14   31
CONECT   14   15   15   16
CONECT   15   32
CONECT   16   17   17
CONECT   17   18
CONECT   18   33
END

HMDB0242132
     RDKit          3D
2'-O-Methylcytidine
 33 34  0  0  0  0  0  0  0  0999 V2000
   -0.0419    3.0237   -0.5078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4613    2.1062    0.4165 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8340    0.8920   -0.0911 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2665    0.5127    0.2813 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6237    1.1874    1.4461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1303   -0.9624    0.5950 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1724   -1.7849   -0.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9677   -3.1249    0.1904 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8364   -1.3237    0.2207 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1001   -0.2373    0.6425 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2793   -0.2870    0.3400 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7698   -1.1812   -0.5262 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1201   -1.2528   -0.8421 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9760   -0.3599   -0.2304 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2614   -0.3742   -0.4845 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4510    0.5256    0.6348 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1223    0.5717    0.9246 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7143    1.5417    1.8409 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7878    3.2891   -1.2720 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8316    2.5698   -1.0613 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3472    3.9127    0.0439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7540    0.7922   -1.1826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9668    0.7049   -0.5498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3283    0.7156    2.2553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2051   -1.1555    1.6849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1657   -1.5120    0.2788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1947   -1.6083   -1.2003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7939   -3.5700    0.4413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3180   -0.0880    1.7196 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1365   -1.9034   -1.0321 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5374   -1.9660   -1.5379 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6413   -1.0717   -1.1597 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.4178    2.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  3
 14 16  1  0
 16 17  2  0
 17 18  1  0
 10  3  1  0
 17 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  6
  4 23  1  6
  5 24  1  0
  6 25  1  1
  7 26  1  0
  7 27  1  0
  8 28  1  0
 10 29  1  1
 12 30  1  0
 13 31  1  0
 15 32  1  0
 18 33  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
O(2')-Methylcytidine	ChEBI

Chemical Formula

C₁₀H₁₅N₃O₅

Average Molecular Weight

257.246

Monoisotopic Molecular Weight

257.101170595

IUPAC Name

1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-ol

Traditional Name

1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-4-iminopyrimidin-2-ol

CAS Registry Number

Not Available

SMILES

[H][C@]1(CO)O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(OC)[C@]1([H])O

InChI Identifier

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

InChI Key

RFCQJGFZUQFYRF-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
Aminopyrimidine
Pyrimidone
Imidolactam
Pyrimidine
Hydropyrimidine
Monosaccharide
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Dialkyl ether
Oxacycle
Azacycle
Organoheterocyclic compound
Ether
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Primary alcohol
Primary amine
Amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

methylcytidine (CHEBI:19228 )

Ontology

Not Available

Not Available

Not Available

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	-2.1	ALOGPS
logP	-1.2	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	5.9	ChemAxon
pKa (Strongest Basic)	2.51	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	118.6 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	70.71 m³·mol⁻¹	ChemAxon
Polarizability	24.5 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]+	157.907	30932474
DeepCCS	[M-H]-	155.512	30932474
DeepCCS	[M-2H]-	190.244	30932474
DeepCCS	[M+Na]+	165.423	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.2484 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.17 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	628.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	230.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	60.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	161.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	47.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	305.8 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	243.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	619.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	595.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	57.7 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	769.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	163.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	185.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	440.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	474.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	238.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2'-O-Methylcytidine	[H][C@]1(CO)O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(OC)[C@]1([H])O	3812.6	Standard polar	33892256
2'-O-Methylcytidine	[H][C@]1(CO)O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(OC)[C@]1([H])O	2444.2	Standard non polar	33892256
2'-O-Methylcytidine	[H][C@]1(CO)O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(OC)[C@]1([H])O	2464.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2'-O-Methylcytidine,4TMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=N[Si](C)(C)C)N=C1O[Si](C)(C)C	2334.1	Semi standard non polar	33892256
2'-O-Methylcytidine,4TMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=N[Si](C)(C)C)N=C1O[Si](C)(C)C	2511.8	Standard non polar	33892256
2'-O-Methylcytidine,4TMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=N[Si](C)(C)C)N=C1O[Si](C)(C)C	2924.2	Standard polar	33892256
2'-O-Methylcytidine,4TBDMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=N[Si](C)(C)C(C)(C)C)N=C1O[Si](C)(C)C(C)(C)C	3056.5	Semi standard non polar	33892256
2'-O-Methylcytidine,4TBDMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=N[Si](C)(C)C(C)(C)C)N=C1O[Si](C)(C)C(C)(C)C	3198.7	Standard non polar	33892256
2'-O-Methylcytidine,4TBDMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=N[Si](C)(C)C(C)(C)C)N=C1O[Si](C)(C)C(C)(C)C	3255.0	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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
Urine	Detected 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

133067

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

150971

PDB ID

Not Available

ChEBI ID

19228

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

Kong SW, Hernandez-Ferrer C: Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. Pac Symp Biocomput. 2020;25:587-598. [PubMed:31797630 ]

Only showing the first 10 proteins. There are 12 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details

1. Putative tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase

General function:: Involved in methyltransferase activity
Specific function:: Methylates the 2'-O-ribose of nucleotides at positions 32 and 34 of the tRNA anticodon loop of substrate tRNAs (By similarity).
Gene Name:: FTSJ1
Uniprot ID:: Q9UET6
Molecular weight:: 36078.76

Enzyme Details

2. tRNA:m(4)X modification enzyme TRM13 homolog

General function:: Involved in methyltransferase activity
Specific function:: tRNA methylase which 2'-O-methylates cytidine(4) in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine(4) in tRNA(His) (By similarity).
Gene Name:: TRMT13
Uniprot ID:: Q9NUP7
Molecular weight:: 54246.57

Enzyme Details

3. tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ

General function:: Not Available
Specific function:: Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA.
Gene Name:: TRMJ
Uniprot ID:: A1AE69
Molecular weight:: 27047.725

Enzyme Details

4. tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ

General function:: Not Available
Specific function:: Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA.
Gene Name:: TRMJ
Uniprot ID:: Q5PNG3
Molecular weight:: 26613.21

Enzyme Details

5. Ribosomal RNA small subunit methyltransferase I

General function:: Not Available
Specific function:: Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA.
Gene Name:: RSMI
Uniprot ID:: P9WGW7
Molecular weight:: 29664.73

Enzyme Details

6. tRNA (cytidine(34)-2'-O)-methyltransferase

General function:: Not Available
Specific function:: Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide.
Gene Name:: TRML
Uniprot ID:: C7BSD3
Molecular weight:: 18250.675

Enzyme Details

7. Ribosomal RNA large subunit methyltransferase M

General function:: Not Available
Specific function:: Catalyzes the 2'-O-methylation at nucleotide C2498 in 23S rRNA.
Gene Name:: RLMM
Uniprot ID:: C7BKL0
Molecular weight:: 42414.705

Enzyme Details

8. Ribosomal RNA large subunit methyltransferase M

General function:: Not Available
Specific function:: Catalyzes the 2'-O-methylation at nucleotide C2498 in 23S rRNA.
Gene Name:: RLMM
Uniprot ID:: A1AEZ3
Molecular weight:: 41824.825

Enzyme Details

9. tRNA (cytidine(56)-2'-O)-methyltransferase

General function:: Not Available
Specific function:: Specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of cytidine at position 56 in tRNAs.
Gene Name:: (GENBANK) CONSERVED HYPOTHETICAL PROTEIN
Uniprot ID:: Q2NF55
Molecular weight:: 19944.62

Enzyme Details

10. Ribosomal RNA large subunit methyltransferase M

General function:: Not Available
Specific function:: Catalyzes the 2'-O-methylation at nucleotide C2498 in 23S rRNA.
Gene Name:: RLMM
Uniprot ID:: Q5PEK5
Molecular weight:: 42006.015

Only showing the first 10 proteins. There are 12 proteins in total.

Show all enzymes and transporters

Showing metabocard for 2'-O-Methylcytidine (HMDB0242132)

MOL for HMDB0242132 (2'-O-Methylcytidine)

3D MOL for HMDB0242132 (2'-O-Methylcytidine)

3D SDF for HMDB0242132 (2'-O-Methylcytidine)

3D-SDF for HMDB0242132 (2'-O-Methylcytidine)

PDB for HMDB0242132 (2'-O-Methylcytidine)

3D PDB for HMDB0242132 (2'-O-Methylcytidine)

SMILES for HMDB0242132 (2'-O-Methylcytidine)

INCHI for HMDB0242132 (2'-O-Methylcytidine)

Structure for HMDB0242132 (2'-O-Methylcytidine)

3D Structure for HMDB0242132 (2'-O-Methylcytidine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes