MiMeDB: Showing metabocard for Ribothymidine (MMDBc0000555)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:40:26 UTC

Update Date

2024-04-30 19:32:58 UTC

Metabolite ID

MMDBc0000555

Metabolite Identification

Common Name

Ribothymidine

Description

Ribothymidine is an endogenous methylated nucleoside found in human fluids; methylated purine bases are present in higher amounts in tumor-bearing patients compared to healthy controls.DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents. When chemical bonds to DNA, the DNA becomes damaged and proper and complete replication cannot occur to make the normal intended cell. A DNA adduct is an abnormal piece of DNA covalently-bonded to a cancer-causing chemical. This has shown to be the start of a cancerous cell, or carcinogenesis. DNA adducts in scientific experiments are used as bio-markers and as such are themselves measured to reflect quantitatively, for comparison, the amount of cancer in the subject. (PMID:3506820 , 17044778 , 17264127 , 16799933 ).

Structure

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

HMDB0000884
     RDKit          3D
Ribothymidine
 32 33  0  0  0  0  0  0  0  0999 V2000
   -3.9763    1.8296   -0.0536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1056    0.6347   -0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7314    0.6905    0.0793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9571   -0.4080    0.0781 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4485   -0.4406    0.2066 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0369    0.6564    0.7706 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4000    0.3297    0.7045 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2662    1.5578    0.8594 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9745    2.1152    2.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6171   -0.3958   -0.5810 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0217   -1.7072   -0.2723 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1879   -0.5295   -1.1189 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9914   -1.7299   -1.7542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6079   -1.5998   -0.0618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9627   -2.6800   -0.0738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9408   -1.6761   -0.1909 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7214   -0.5980   -0.1916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9813   -0.6754   -0.3140 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5431    1.8493   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4407    2.7655    0.1399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7665    1.6458    0.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2485    1.6425    0.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7651   -1.3366    0.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5959   -0.3078    1.6118 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3212    1.1809    0.9420 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1813    2.2616    0.0327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7874    1.3402    2.7157 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2807    0.0963   -1.2870 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6505   -2.0689   -0.9187 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0242    0.3600   -1.7507 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8388   -2.1881   -2.0198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4059   -2.6143   -0.2967 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  1  0
 17 18  2  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  1
  7 24  1  1
  8 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  6
 11 29  1  0
 12 30  1  6
 13 31  1  0
 16 32  1  0
M  END


  Mrv1652305271900282D          

 18 19  0  0  1  0            999 V2000
    8.9249   -8.1597    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8053   -7.9047    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3600   -9.6118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9754   -9.5256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8285   -6.8498    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2574   -4.3747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2574   -6.8498    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.5430   -5.6123    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.5900   -8.1597    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.8449   -8.9443    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.2574   -7.6748    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.6699   -8.9443    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.1549   -9.6118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9719   -6.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5430   -6.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9719   -5.6123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2574   -5.1997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6865   -5.1997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  9  2  1  1  0  0  0
 10  3  1  1  0  0  0
  4 13  1  0  0  0  0
  5 15  2  0  0  0  0
  6 17  2  0  0  0  0
 11  7  1  6  0  0  0
  7 14  1  0  0  0  0
  7 15  1  0  0  0  0
  8 15  1  0  0  0  0
  8 17  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  6  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000555

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m1/s1

> <INCHI_KEY>
DWRXFEITVBNRMK-JXOAFFINSA-N

> <FORMULA>
C10H14N2O6

> <MOLECULAR_WEIGHT>
258.228

> <EXACT_MASS>
258.08518619

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
24.10148861671833

> <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]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-1.71

> <JCHEM_LOGP>
-2.019691652333333

> <ALOGPS_LOGS>
-0.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.620574905993259

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.954822616778223

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9802996399088295

> <JCHEM_POLAR_SURFACE_AREA>
119.33

> <JCHEM_REFRACTIVITY>
56.92269999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.35e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thymidin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000884
     RDKit          3D
Ribothymidine
 32 33  0  0  0  0  0  0  0  0999 V2000
   -3.9763    1.8296   -0.0536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1056    0.6347   -0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7314    0.6905    0.0793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9571   -0.4080    0.0781 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4485   -0.4406    0.2066 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0369    0.6564    0.7706 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4000    0.3297    0.7045 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2662    1.5578    0.8594 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9745    2.1152    2.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6171   -0.3958   -0.5810 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0217   -1.7072   -0.2723 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1879   -0.5295   -1.1189 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9914   -1.7299   -1.7542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6079   -1.5998   -0.0618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9627   -2.6800   -0.0738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9408   -1.6761   -0.1909 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7214   -0.5980   -0.1916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9813   -0.6754   -0.3140 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5431    1.8493   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4407    2.7655    0.1399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7665    1.6458    0.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2485    1.6425    0.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7651   -1.3366    0.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5959   -0.3078    1.6118 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3212    1.1809    0.9420 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1813    2.2616    0.0327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7874    1.3402    2.7157 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2807    0.0963   -1.2870 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6505   -2.0689   -0.9187 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0242    0.3600   -1.7507 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8388   -2.1881   -2.0198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4059   -2.6143   -0.2967 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  1  0
 17 18  2  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  1
  7 24  1  1
  8 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  6
 11 29  1  0
 12 30  1  6
 13 31  1  0
 16 32  1  0
M  END

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      16.660 -15.231   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      12.703 -14.755   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      13.739 -17.942   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      18.621 -17.781   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      12.747 -12.786   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      15.414  -8.166   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      15.414 -12.786   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      14.080 -10.476   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      14.168 -15.231   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.644 -16.696   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.414 -14.326   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      16.184 -16.696   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      17.089 -17.942   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      16.748 -12.016   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      14.080 -12.016   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      16.748 -10.476   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      15.414  -9.706   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      18.081  -9.706   0.000  0.00  0.00           C+0
CONECT    1   11   12                                                       
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   13                                                            
CONECT    5   15                                                            
CONECT    6   17                                                            
CONECT    7   11   14   15                                                  
CONECT    8   15   17                                                       
CONECT    9    2   10   11                                                  
CONECT   10    3    9   12                                                  
CONECT   11    1    7    9                                                  
CONECT   12    1   10   13                                                  
CONECT   13    4   12                                                       
CONECT   14    7   16                                                       
CONECT   15    5    7    8                                                  
CONECT   16   14   17   18                                                  
CONECT   17    6    8   16                                                  
CONECT   18   16                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0000884
HETATM    1  C1  UNL     1      -3.976   1.830  -0.054  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.106   0.635  -0.052  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.731   0.691   0.079  1.00  0.00           C  
HETATM    4  N1  UNL     1      -0.957  -0.408   0.078  1.00  0.00           N  
HETATM    5  C4  UNL     1       0.448  -0.441   0.207  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.037   0.656   0.771  1.00  0.00           O  
HETATM    7  C5  UNL     1       2.400   0.330   0.705  1.00  0.00           C  
HETATM    8  C6  UNL     1       3.266   1.558   0.859  1.00  0.00           C  
HETATM    9  O2  UNL     1       2.975   2.115   2.107  1.00  0.00           O  
HETATM   10  C7  UNL     1       2.617  -0.396  -0.581  1.00  0.00           C  
HETATM   11  O3  UNL     1       3.022  -1.707  -0.272  1.00  0.00           O  
HETATM   12  C8  UNL     1       1.188  -0.530  -1.119  1.00  0.00           C  
HETATM   13  O4  UNL     1       0.991  -1.730  -1.754  1.00  0.00           O  
HETATM   14  C9  UNL     1      -1.608  -1.600  -0.062  1.00  0.00           C  
HETATM   15  O5  UNL     1      -0.963  -2.680  -0.074  1.00  0.00           O  
HETATM   16  N2  UNL     1      -2.941  -1.676  -0.191  1.00  0.00           N  
HETATM   17  C10 UNL     1      -3.721  -0.598  -0.192  1.00  0.00           C  
HETATM   18  O6  UNL     1      -4.981  -0.675  -0.314  1.00  0.00           O  
HETATM   19  H1  UNL     1      -4.543   1.849  -1.025  1.00  0.00           H  
HETATM   20  H2  UNL     1      -3.441   2.765   0.140  1.00  0.00           H  
HETATM   21  H3  UNL     1      -4.767   1.646   0.729  1.00  0.00           H  
HETATM   22  H4  UNL     1      -1.249   1.643   0.188  1.00  0.00           H  
HETATM   23  H5  UNL     1       0.765  -1.337   0.798  1.00  0.00           H  
HETATM   24  H6  UNL     1       2.596  -0.308   1.612  1.00  0.00           H  
HETATM   25  H7  UNL     1       4.321   1.181   0.942  1.00  0.00           H  
HETATM   26  H8  UNL     1       3.181   2.262   0.033  1.00  0.00           H  
HETATM   27  H9  UNL     1       2.787   1.340   2.716  1.00  0.00           H  
HETATM   28  H10 UNL     1       3.281   0.096  -1.287  1.00  0.00           H  
HETATM   29  H11 UNL     1       3.650  -2.069  -0.919  1.00  0.00           H  
HETATM   30  H12 UNL     1       1.024   0.360  -1.751  1.00  0.00           H  
HETATM   31  H13 UNL     1       1.839  -2.188  -2.020  1.00  0.00           H  
HETATM   32  H14 UNL     1      -3.406  -2.614  -0.297  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   32
CONECT   17   18   18
END

HMDB0000884
     RDKit          3D
Ribothymidine
 32 33  0  0  0  0  0  0  0  0999 V2000
   -3.9763    1.8296   -0.0536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1056    0.6347   -0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7314    0.6905    0.0793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9571   -0.4080    0.0781 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4485   -0.4406    0.2066 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0369    0.6564    0.7706 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4000    0.3297    0.7045 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2662    1.5578    0.8594 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9745    2.1152    2.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6171   -0.3958   -0.5810 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0217   -1.7072   -0.2723 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1879   -0.5295   -1.1189 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9914   -1.7299   -1.7542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6079   -1.5998   -0.0618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9627   -2.6800   -0.0738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9408   -1.6761   -0.1909 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7214   -0.5980   -0.1916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9813   -0.6754   -0.3140 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5431    1.8493   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4407    2.7655    0.1399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7665    1.6458    0.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2485    1.6425    0.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7651   -1.3366    0.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5959   -0.3078    1.6118 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3212    1.1809    0.9420 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1813    2.2616    0.0327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7874    1.3402    2.7157 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2807    0.0963   -1.2870 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6505   -2.0689   -0.9187 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0242    0.3600   -1.7507 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8388   -2.1881   -2.0198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4059   -2.6143   -0.2967 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  1  0
 17 18  2  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  1
  7 24  1  1
  8 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  6
 11 29  1  0
 12 30  1  6
 13 31  1  0
 16 32  1  0
M  END

Synonyms

Value	Source
1-(beta-D-Ribofuranosyl)thymine	ChEBI
Ribosylthymidine	ChEBI
t	ChEBI
Thymine riboside	ChEBI
1-(b-D-Ribofuranosyl)thymine	Generator
1-(Β-D-ribofuranosyl)thymine	Generator
1-b-D-Ribofuranosylthymine	HMDB
1-beta-delta-Ribofuranosylthymine	HMDB
5-Methyl-1-beta-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-Methyl-1-beta-delta-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-Methyl-uridine	HMDB
5-Methyluridine	HMDB
b-D-Ribofuranoside thymine-1	HMDB
beta-D-Ribofuranoside	HMDB
beta-delta-Ribofuranoside	HMDB
beta-delta-Ribofuranoside thymine-1	HMDB
Ribosylthymine	HMDB
Thymine ribofuranoside	HMDB
Thymine ribonucleoside	HMDB
Thymine-1 beta-D-ribofuranosylthymine	HMDB
Thymine-1 beta-delta-ribofuranosylthymine	HMDB

Molecular Formula

C₁₀H₁₄N₂O₆

Average Mass

258.228

Monoisotopic Mass

258.08518619

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

thymidin

CAS Registry Number

Not Available

SMILES

CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O

InChI Identifier

InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m1/s1

InChI Key

DWRXFEITVBNRMK-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
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Vinylogous amide
Tetrahydrofuran
Heteroaromatic compound
Urea
Secondary alcohol
Lactam
Organoheterocyclic compound
Oxacycle
Azacycle
Hydrocarbon derivative
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Primary alcohol
Alcohol
Organic oxygen compound
Organic oxide
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

methyluridine (CHEBI:45996 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	135 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-2	ChemAxon
logS	-0.28	ALOGPS
pKa (Strongest Acidic)	9.95	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	119.33 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	56.92 m³·mol⁻¹	ChemAxon
Polarizability	24.1 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-05bf-9420000000-897dab8f4bbf7b8e664c	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0kp0-6879400000-656a0a43be4a2cd044e7	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_5) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-0900000000-1653ad80c56ae3727f92	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-004i-2900000000-826774188d3e78ca38f2	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0a6r-9800000000-f5daf31a98b364b70f8c	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0090000000-f186cfbb52edc03ff4de	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-004i-0900000000-9f7398feab5dd8950264	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-893019db60499c0a9602	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-004i-2900000000-461a9c94bf89e5b47970	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0900000000-1db6a34eff49b044d944	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-004i-1900000000-1c2ee21cd9d3515f7124	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-056r-1970000000-ba6f9aa1164c365abfa2	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-01u0-8900000000-a63ffd4c990b9c9a543a	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-004i-4900000000-71ebad0df798bf2ac282	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-06w9-8900000000-3c0ceb68319de86fc30f	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-004i-1900000000-45b9a7b5e831351a1fe0	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-e1eddf8b44309a38eebb	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0910000000-90f6da130f49fa9df29d	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-5900000000-203a4367756530615ffd	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004j-9800000000-13e51659da01285bdc7f	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a6r-1490000000-4ba707a2228996f9f9f7	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-6920000000-a25c60ade61d6d32f0f1	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001m-9100000000-37e601ae2d82d72111e7	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-f08754aed5978a645b7c	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-3910000000-01ae005a14dd4c188d46	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a6r-9700000000-513e87b6fba58d79ef98	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-056r-0950000000-b4a8bf9fcddaedc20b74	2021-09-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-05	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Feces
Placenta
Urine

Tissue Locations

Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0196289	tRNA (uracil(54)-C(5))-methyltransferase homolog	Enzyme	Q96GJ1	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Verrucomicrobia	1	Human feces; Human stool; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Firmicutes	4	Human feces; Human stool; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference
Animal	Milk	Bos taurus	FooDB	31437929

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Units	Age	Sex	Health Condition	Data Source	Reference
Human Urine	Detected and Quantified	0.51	0.53	umol/mmol creatinine	Adult (>18 years old)	Both	Breast cancer	HMDB	15607313
Human Urine	Detected and Quantified	0.28	0.17	umol/mmol creatinine	Adult (>18 years old)	Female	Normal	HMDB	15607313
Human Blood	Detected and Quantified	0.200	0.098	uM	Adult (>18 years old)	Not Specified	Normal	HMDB	Xu, G., Enderle, H., Liebich, H., Lu, P. Study of normal and modified nucleosides in serum by RP-HPLC. Chromatographia (2000), 52(3/4), 152-158.
Human Placenta	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified				Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified				Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified				Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0000884

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022298

KNApSAcK ID

Not Available

Chemspider ID

393058

KEGG Compound ID

Not Available

BioCyc ID

CPD-15123

BiGG ID

Not Available

Wikipedia Link

5-methyluridine

METLIN ID

5843

PubChem Compound

445408

PDB ID

Not Available

ChEBI ID

45996

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Avraham Y, Grossowicz N, Yashphe J: Purification and characterization of uridine and thymidine phosphorylase from Lactobacillus casei. Biochim Biophys Acta. 1990 Sep 3;1040(2):287-93. doi: 10.1016/0167-4838(90)90089-x. [PubMed:2119230 ]
Morris GS, Simmonds HA, Davies PM: Use of biological fluids for the rapid diagnosis of potentially lethal inherited disorders of human purine and pyrimidine metabolism. Biomed Chromatogr. 1986 Jun;1(3):109-18. doi: 10.1002/bmc.1130010305. [PubMed:3506820 ]
Weisbart RH, Garrett RA, Liebling MR, Barnett EV, Paulus HE, Katz DH: Specificity of anti-nucleoside antibodies in systemic lupus erythematosus. Clin Immunol Immunopathol. 1983 Jun;27(3):403-11. doi: 10.1016/0090-1229(83)90092-2. [PubMed:6603316 ]
Hacia JG, Woski SA, Fidanza J, Edgemon K, Hunt N, McGall G, Fodor SP, Collins FS: Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates. Nucleic Acids Res. 1998 Nov 1;26(21):4975-82. doi: 10.1093/nar/26.21.4975. [PubMed:9776762 ]
Mori T, Guo MW, Li X, Xu JP, Mori E: Isolation and identification of apoptosis inducing nucleosides from CD57(+)HLA-DRbright natural suppressor cell line. Biochem Biophys Res Commun. 1998 Oct 20;251(2):416-22. doi: 10.1006/bbrc.1998.9423. [PubMed:9792789 ]
Lang TT, Selner M, Young JD, Cass CE: Acquisition of human concentrative nucleoside transporter 2 (hcnt2) activity by gene transfer confers sensitivity to fluoropyrimidine nucleosides in drug-resistant leukemia cells. Mol Pharmacol. 2001 Nov;60(5):1143-52. doi: 10.1124/mol.60.5.1143. [PubMed:11641443 ]
Urbonavicius J, Durand JM, Bjork GR: Three modifications in the D and T arms of tRNA influence translation in Escherichia coli and expression of virulence genes in Shigella flexneri. J Bacteriol. 2002 Oct;184(19):5348-57. doi: 10.1128/JB.184.19.5348-5357.2002. [PubMed:12218021 ]
Cho SH, Jung BH, Lee SH, Lee WY, Kong G, Chung BC: Direct determination of nucleosides in the urine of patients with breast cancer using column-switching liquid chromatography-tandem mass spectrometry. Biomed Chromatogr. 2006 Nov;20(11):1229-36. doi: 10.1002/bmc.689. [PubMed:16799933 ]
Yang TH, Hu ML: Intracellular levels of S-adenosylhomocysteine but not homocysteine are highly correlated to the expression of nm23-H1 and the level of 5-methyldeoxycytidine in human hepatoma cells with different invasion activities. Nutr Cancer. 2006;55(2):224-31. doi: 10.1207/s15327914nc5502_14. [PubMed:17044778 ]
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Showing metabocard for Ribothymidine (MMDBc0000555)

MOL for #<Metabolite:0x00007fd12c408328>

3D MOL for #<Metabolite:0x00007fd12c408328>

3D SDF for #<Metabolite:0x00007fd12c408328>

3D-SDF for #<Metabolite:0x00007fd12c408328>

PDB for #<Metabolite:0x00007fd12c408328>

3D PDB for #<Metabolite:0x00007fd12c408328>

SMILES for #<Metabolite:0x00007fd12c408328>

INCHI for #<Metabolite:0x00007fd12c408328>

Structure for #<Metabolite:0x00007fd12c408328>

3D Structure for #<Metabolite:0x00007fd12c408328>