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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 12:49:25 UTC

Update Date

2021-09-26 23:07:30 UTC

HMDB ID

HMDB0253921

Secondary Accession Numbers

None

Metabolite Identification

Common Name

L-Thymidine

Description

Thymine 2-desoxyriboside belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Thymine 2-desoxyriboside is an extremely weak basic (essentially neutral) compound (based on its pKa). In humans, thymine 2-desoxyriboside is involved in the metabolic disorder called the beta-ureidopropionase deficiency pathway. Outside of the human body, Thymine 2-desoxyriboside has been detected, but not quantified in, a few different foods, such as green beans, pulses, and yellow wax beans. This could make thymine 2-desoxyriboside a potential biomarker for the consumption of these foods. This compound has been identified in human blood as reported by (PMID: 31557052 ). L-thymidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically L-Thymidine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0253921
     RDKit          3D
L-Thymidine
 31 32  0  0  0  0  0  0  0  0999 V2000
    4.1731   -0.9255   -0.5767 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0554   -0.1682    0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7399   -0.5990   -0.1379 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7375    0.1094    0.4069 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6533   -0.2737    0.2964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9529   -0.9236   -1.0431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4577   -0.6961   -1.1314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1014   -1.7197   -0.4484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6242    0.5678   -0.3453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5979    0.3854    0.8262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6632    1.5813    1.5226 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4000    0.9004    0.2009 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0106    1.2354    1.0951 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0767    1.9210    1.6189 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2705    1.6776    1.2555 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2894    0.9872    0.7205 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6171    1.3946    0.8525 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0804   -0.9419    0.0866 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8712   -1.9884   -0.6788 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4823   -0.5537   -1.5681 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5279   -1.4895   -0.6826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9879   -0.9337    1.1154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4780   -0.3260   -1.8499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6858   -1.9837   -1.0709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7950   -0.6089   -2.1818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5907   -2.3354   -1.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9742    1.3953   -0.9999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1653   -0.3716    1.5110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5814    0.0336    0.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1114    2.2788    1.0867 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8884    2.3706    0.7081 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
  7  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  4 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 16  2  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  0
 17 31  1  0
M  END


  Mrv1652305221920222D          

 17 18  0  0  0  0            999 V2000
   -0.6110   -1.8216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7604   -0.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7743    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2754   -1.0679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5450   -0.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3957    0.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8806   -0.2280    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4248    0.3532    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9458    2.8672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0300   -1.6491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7312    1.1931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  2  1  0  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  2  1  0  0  0  0
  9  5  1  0  0  0  0
 11  9  2  0  0  0  0
 11 10  1  0  0  0  0
 12  3  1  0  0  0  0
 12  8  1  0  0  0  0
 12 10  1  0  0  0  0
 13  4  1  0  0  0  0
 14  6  1  0  0  0  0
 15  9  1  0  0  0  0
 16 10  2  0  0  0  0
 17  7  1  0  0  0  0
 17  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253921

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)

> <INCHI_KEY>
IQFYYKKMVGJFEH-UHFFFAOYSA-N

> <FORMULA>
C10H14N2O5

> <MOLECULAR_WEIGHT>
242.2286

> <EXACT_MASS>
242.090271568

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
23.082519034975338

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-hydroxy-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.66

> <JCHEM_LOGP>
-0.7515527849999996

> <ALOGPS_LOGS>
-1.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.894901584189796

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.518974365070233

> <JCHEM_PKA_STRONGEST_BASIC>
-2.978083819508636

> <JCHEM_POLAR_SURFACE_AREA>
102.59000000000002

> <JCHEM_REFRACTIVITY>
55.7337

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.98e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-hydroxy-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0253921
     RDKit          3D
L-Thymidine
 31 32  0  0  0  0  0  0  0  0999 V2000
    4.1731   -0.9255   -0.5767 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0554   -0.1682    0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7399   -0.5990   -0.1379 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7375    0.1094    0.4069 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6533   -0.2737    0.2964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9529   -0.9236   -1.0431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4577   -0.6961   -1.1314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1014   -1.7197   -0.4484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6242    0.5678   -0.3453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5979    0.3854    0.8262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6632    1.5813    1.5226 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4000    0.9004    0.2009 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0106    1.2354    1.0951 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0767    1.9210    1.6189 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2705    1.6776    1.2555 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2894    0.9872    0.7205 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6171    1.3946    0.8525 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0804   -0.9419    0.0866 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8712   -1.9884   -0.6788 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4823   -0.5537   -1.5681 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5279   -1.4895   -0.6826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9879   -0.9337    1.1154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4780   -0.3260   -1.8499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6858   -1.9837   -1.0709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7950   -0.6089   -2.1818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5907   -2.3354   -1.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9742    1.3953   -0.9999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1653   -0.3716    1.5110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5814    0.0336    0.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1114    2.2788    1.0867 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8884    2.3706    0.7081 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
  7  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  4 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 16  2  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  0
 17 31  1  0
M  END

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0      -1.141  -3.400   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.222   3.370   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.419  -0.748   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.179   3.846   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.514  -1.993   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.468   4.275   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.714   3.370   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.698   1.905   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.017  -1.832   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.739   0.820   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       1.644  -0.426   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -0.793   0.659   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0      -5.499   5.352   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -2.468   5.815   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.923  -3.078   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.365   2.227   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -3.238   1.905   0.000  0.00  0.00           O+0
CONECT    1    5                                                            
CONECT    2    6    8                                                       
CONECT    3    5   12                                                       
CONECT    4    7   13                                                       
CONECT    5    1    3    9                                                  
CONECT    6    2    7   14                                                  
CONECT    7    4    6   17                                                  
CONECT    8    2   12   17                                                  
CONECT    9    5   11   15                                                  
CONECT   10   11   12   16                                                  
CONECT   11    9   10                                                       
CONECT   12    3    8   10                                                  
CONECT   13    4                                                            
CONECT   14    6                                                            
CONECT   15    9                                                            
CONECT   16   10                                                            
CONECT   17    7    8                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0253921
HETATM    1  C1  UNL     1       4.173  -0.925  -0.577  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.055  -0.168   0.010  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.740  -0.599  -0.138  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.737   0.109   0.407  1.00  0.00           N  
HETATM    5  C4  UNL     1      -0.653  -0.274   0.296  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.953  -0.924  -1.043  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.458  -0.696  -1.131  1.00  0.00           C  
HETATM    8  O1  UNL     1      -3.101  -1.720  -0.448  1.00  0.00           O  
HETATM    9  C7  UNL     1      -2.624   0.568  -0.345  1.00  0.00           C  
HETATM   10  C8  UNL     1      -3.598   0.385   0.826  1.00  0.00           C  
HETATM   11  O2  UNL     1      -3.663   1.581   1.523  1.00  0.00           O  
HETATM   12  O3  UNL     1      -1.400   0.900   0.201  1.00  0.00           O  
HETATM   13  C9  UNL     1       1.011   1.235   1.095  1.00  0.00           C  
HETATM   14  O4  UNL     1       0.077   1.921   1.619  1.00  0.00           O  
HETATM   15  N2  UNL     1       2.271   1.678   1.255  1.00  0.00           N  
HETATM   16  C10 UNL     1       3.289   0.987   0.721  1.00  0.00           C  
HETATM   17  O5  UNL     1       4.617   1.395   0.852  1.00  0.00           O  
HETATM   18  H1  UNL     1       5.080  -0.942   0.087  1.00  0.00           H  
HETATM   19  H2  UNL     1       3.871  -1.988  -0.679  1.00  0.00           H  
HETATM   20  H3  UNL     1       4.482  -0.554  -1.568  1.00  0.00           H  
HETATM   21  H4  UNL     1       1.528  -1.489  -0.683  1.00  0.00           H  
HETATM   22  H5  UNL     1      -0.988  -0.934   1.115  1.00  0.00           H  
HETATM   23  H6  UNL     1      -0.478  -0.326  -1.850  1.00  0.00           H  
HETATM   24  H7  UNL     1      -0.686  -1.984  -1.071  1.00  0.00           H  
HETATM   25  H8  UNL     1      -2.795  -0.609  -2.182  1.00  0.00           H  
HETATM   26  H9  UNL     1      -3.591  -2.335  -1.076  1.00  0.00           H  
HETATM   27  H10 UNL     1      -2.974   1.395  -1.000  1.00  0.00           H  
HETATM   28  H11 UNL     1      -3.165  -0.372   1.511  1.00  0.00           H  
HETATM   29  H12 UNL     1      -4.581   0.034   0.477  1.00  0.00           H  
HETATM   30  H13 UNL     1      -3.111   2.279   1.087  1.00  0.00           H  
HETATM   31  H14 UNL     1       4.888   2.371   0.708  1.00  0.00           H  
CONECT    1    2   18   19   20
CONECT    2    3    3   16
CONECT    3    4   21
CONECT    4    5   13
CONECT    5    6   12   22
CONECT    6    7   23   24
CONECT    7    8    9   25
CONECT    8   26
CONECT    9   10   12   27
CONECT   10   11   28   29
CONECT   11   30
CONECT   13   14   14   15
CONECT   15   16   16
CONECT   16   17
CONECT   17   31
END

HMDB0253921
     RDKit          3D
L-Thymidine
 31 32  0  0  0  0  0  0  0  0999 V2000
    4.1731   -0.9255   -0.5767 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0554   -0.1682    0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7399   -0.5990   -0.1379 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7375    0.1094    0.4069 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6533   -0.2737    0.2964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9529   -0.9236   -1.0431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4577   -0.6961   -1.1314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1014   -1.7197   -0.4484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6242    0.5678   -0.3453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5979    0.3854    0.8262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6632    1.5813    1.5226 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4000    0.9004    0.2009 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0106    1.2354    1.0951 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0767    1.9210    1.6189 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2705    1.6776    1.2555 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2894    0.9872    0.7205 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6171    1.3946    0.8525 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0804   -0.9419    0.0866 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8712   -1.9884   -0.6788 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4823   -0.5537   -1.5681 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5279   -1.4895   -0.6826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9879   -0.9337    1.1154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4780   -0.3260   -1.8499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6858   -1.9837   -1.0709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7950   -0.6089   -2.1818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5907   -2.3354   -1.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9742    1.3953   -0.9999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1653   -0.3716    1.5110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5814    0.0336    0.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1114    2.2788    1.0867 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8884    2.3706    0.7081 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
  7  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  4 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 16  2  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  0
 17 31  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₀H₁₄N₂O₅

Average Molecular Weight

242.2286

Monoisotopic Molecular Weight

242.090271568

IUPAC Name

4-hydroxy-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one

Traditional Name

4-hydroxy-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one

CAS Registry Number

Not Available

SMILES

CC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O

InChI Identifier

InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)

InChI Key

IQFYYKKMVGJFEH-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Pyrimidone
Hydropyrimidine
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Vinylogous amide
Lactam
Secondary alcohol
Urea
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a pyrimidine-related compound (THYMIDINE )
a deoxynucleoside (THYMIDINE )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.7	ALOGPS
logP	-0.75	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	7.52	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	102.59 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.73 m³·mol⁻¹	ChemAxon
Polarizability	23.08 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]+	155.066	30932474
DeepCCS	[M-H]-	152.708	30932474
DeepCCS	[M-2H]-	186.424	30932474
DeepCCS	[M+Na]+	161.326	30932474
AllCCS	[M+H]+	154.3	32859911
AllCCS	[M+H-H2O]+	150.5	32859911
AllCCS	[M+NH4]+	157.8	32859911
AllCCS	[M+Na]+	158.9	32859911
AllCCS	[M-H]-	154.2	32859911
AllCCS	[M+Na-2H]-	154.3	32859911
AllCCS	[M+HCOO]-	154.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.4167 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.95 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	845.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	227.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	95.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	158.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	70.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	276.1 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	285.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	133.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	632.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	159.1 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	902.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	193.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	187.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	438.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	178.5 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	156.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
L-Thymidine	CC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O	3482.1	Standard polar	33892256
L-Thymidine	CC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O	2117.5	Standard non polar	33892256
L-Thymidine	CC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O	2355.9	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9520000000-4f5fdf466b2300e3cc3e	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Thymidine GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-01dj-9300000000-6e24b5b6d36e07dd73d0	2014-09-20	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 10V, Positive-QTOF	splash10-004i-0900000000-9c9e9e6d7f74fb1f2757	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 20V, Positive-QTOF	splash10-004i-4900000000-3b1e6c50c2450e123648	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 40V, Positive-QTOF	splash10-004i-6900000000-b04537b00f6e00caad37	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 10V, Negative-QTOF	splash10-052g-1940000000-8fce8753136d1a1982ae	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 20V, Negative-QTOF	splash10-0ufu-3920000000-1a2bd5708f88b9808da6	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 40V, Negative-QTOF	splash10-000x-9200000000-d9db5a1484e9c4936d30	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 10V, Positive-QTOF	splash10-004i-1900000000-bcb24421d7b0162d607d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 20V, Positive-QTOF	splash10-057j-7900000000-ddd5f450835af7ef5edf	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 40V, Positive-QTOF	splash10-0a4i-5900000000-c6ee0c9772bd68aa7c3f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 10V, Negative-QTOF	splash10-002f-1980000000-a20f517efa944c15889c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 20V, Negative-QTOF	splash10-002f-9400000000-0daaa361f245163aeaec	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Thymidine 40V, Negative-QTOF	splash10-0006-9400000000-de7ded95723d9abbf35f	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

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

FDB012757

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

1134

PDB ID

Not Available

ChEBI ID

Not Available

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for L-Thymidine (HMDB0253921)

MOL for HMDB0253921 (L-Thymidine)

3D MOL for HMDB0253921 (L-Thymidine)

3D SDF for HMDB0253921 (L-Thymidine)

3D-SDF for HMDB0253921 (L-Thymidine)

PDB for HMDB0253921 (L-Thymidine)

3D PDB for HMDB0253921 (L-Thymidine)

SMILES for HMDB0253921 (L-Thymidine)

INCHI for HMDB0253921 (L-Thymidine)

Structure for HMDB0253921 (L-Thymidine)

3D Structure for HMDB0253921 (L-Thymidine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra