NP-MRD: Showing NP-Card for Ribothymidine (NP0000964)

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Record Information

Version

1.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2020-11-24 22:19:43 UTC

NP-MRD ID

NP0000964

Secondary Accession Numbers

None

Natural Product 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>
NP0000964

> <DATABASE_NAME>
NP-MRD

> <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

View in JSmol

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

Chemical Formula

C₁₀H₁₄N₂O₆

Average Mass

258.2280 Da

Monoisotopic Mass

258.08519 Da

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

1463-10-1

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

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
Ctenodiscus crispatus	LOTUS Database	35616633
Dimocarpus longan	LOTUS Database	35616633
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Homo sapiens	LOTUS Database	35616633
Hyacinthoides non-scripta	LOTUS Database	35616633
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Leptasterias polaris	LOTUS Database	35616633
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
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 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	183 - 187 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

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

External Links

HMDB ID

HMDB0000884

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

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. [PubMed:2119230 ]
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. [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. [PubMed:12218021 ]
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. [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. [PubMed:9792789 ]
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. [PubMed:6603316 ]
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. [PubMed:3506820 ]
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. [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. [PubMed:17044778 ]
Liu Z, Liu S, Xie Z, Blum W, Perrotti D, Paschka P, Klisovic R, Byrd J, Chan KK, Marcucci G: Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method. Nucleic Acids Res. 2007;35(5):e31. Epub 2007 Jan 30. [PubMed:17264127 ]

Showing NP-Card for Ribothymidine (NP0000964)

MOL for NP0000964 (Ribothymidine)

3D MOL for NP0000964 (Ribothymidine)

3D SDF for NP0000964 (Ribothymidine)

3D-SDF for NP0000964 (Ribothymidine)

PDB for NP0000964 (Ribothymidine)

3D PDB for NP0000964 (Ribothymidine)

SMILES for NP0000964 (Ribothymidine)

INCHI for NP0000964 (Ribothymidine)

Structure for NP0000964 (Ribothymidine)

3D Structure for NP0000964 (Ribothymidine)