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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 22:58:58 UTC

Update Date

2021-09-26 22:54:41 UTC

HMDB ID

HMDB0245937

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3-Methylthymidine

Description

1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,5-dimethyl-1,2,3,4-tetrahydropyrimidine-2,4-dione 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. Based on a literature review very few articles have been published on 1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,5-dimethyl-1,2,3,4-tetrahydropyrimidine-2,4-dione. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-methylthymidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-Methylthymidine 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

HMDB0245937
     RDKit          3D
3-Methylthymidine
 34 35  0  0  0  0  0  0  0  0999 V2000
   -3.7847   -1.7063    0.3833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8002   -0.6261    0.1939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4699   -0.8919   -0.0134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5799    0.0858   -0.1847 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8228   -0.0872   -0.4062 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2172   -1.4523   -0.8664 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7354   -1.3661   -0.6357 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2925   -2.6152   -0.4823 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7577   -0.5365    0.6245 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8984    0.4349    0.6592 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7650    1.3100   -0.3952 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5599    0.1157    0.7304 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0360    1.3732   -0.1475 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2371    2.3349   -0.3036 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3213    1.6663    0.0517 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7484    3.0681    0.0811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2247    0.6846    0.2253 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4200    1.0257    0.4086 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3255   -2.4401    1.1059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6968   -1.3371    0.8868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9852   -2.2673   -0.5356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1323   -1.8991   -0.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1140    0.6298   -1.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9923   -1.6545   -1.9210 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8711   -2.2543   -0.1810 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2161   -0.7632   -1.4382 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0519   -2.9495    0.4226 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8112   -1.2702    1.4775 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7985    1.0258    1.5952 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8841   -0.0760    0.6979 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3718    2.1797   -0.1256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8971    3.6629    0.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8303    3.3900   -0.9622 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    3.2052    0.6583 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  1  0
 15 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  0
  6 24  1  0
  6 25  1  0
  7 26  1  0
  8 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
 16 32  1  0
 16 33  1  0
 16 34  1  0
M  END


  Mrv1533004241523462D          

 18 19  0  0  0  0            999 V2000
    0.1067    4.7652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    4.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    3.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    3.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512    3.1152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    4.3527    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    4.7652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    5.5902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512    4.7652    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
   -0.6548    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
   -1.7347    1.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197    0.3532    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8841   -0.4005    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4248    0.3532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  7 10  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 11 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 13 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245937

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(=O)N(C=C(C)C1=O)C1CC(O)C(CO)O1

> <INCHI_IDENTIFIER>
InChI=1S/C11H16N2O5/c1-6-4-13(11(17)12(2)10(6)16)9-3-7(15)8(5-14)18-9/h4,7-9,14-15H,3,5H2,1-2H3

> <INCHI_KEY>
JCVDICFLPGDHAT-UHFFFAOYSA-N

> <FORMULA>
C11H16N2O5

> <MOLECULAR_WEIGHT>
256.258

> <EXACT_MASS>
256.105921623

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
25.51274435157203

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,5-dimethyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-1.14

> <JCHEM_LOGP>
-0.8953775236666662

> <ALOGPS_LOGS>
-0.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.787555381900546

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.894924423418356

> <JCHEM_PKA_STRONGEST_BASIC>
-2.978083590090309

> <JCHEM_POLAR_SURFACE_AREA>
90.31000000000002

> <JCHEM_REFRACTIVITY>
60.30870000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.16e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,5-dimethylpyrimidine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0245937
     RDKit          3D
3-Methylthymidine
 34 35  0  0  0  0  0  0  0  0999 V2000
   -3.7847   -1.7063    0.3833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8002   -0.6261    0.1939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4699   -0.8919   -0.0134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5799    0.0858   -0.1847 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8228   -0.0872   -0.4062 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2172   -1.4523   -0.8664 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7354   -1.3661   -0.6357 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2925   -2.6152   -0.4823 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7577   -0.5365    0.6245 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8984    0.4349    0.6592 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7650    1.3100   -0.3952 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5599    0.1157    0.7304 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0360    1.3732   -0.1475 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2371    2.3349   -0.3036 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3213    1.6663    0.0517 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7484    3.0681    0.0811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2247    0.6846    0.2253 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4200    1.0257    0.4086 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3255   -2.4401    1.1059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6968   -1.3371    0.8868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9852   -2.2673   -0.5356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1323   -1.8991   -0.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1140    0.6298   -1.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9923   -1.6545   -1.9210 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8711   -2.2543   -0.1810 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2161   -0.7632   -1.4382 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0519   -2.9495    0.4226 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8112   -1.2702    1.4775 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7985    1.0258    1.5952 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8841   -0.0760    0.6979 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3718    2.1797   -0.1256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8971    3.6629    0.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8303    3.3900   -0.9622 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    3.2052    0.6583 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  1  0
 15 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  0
  6 24  1  0
  6 25  1  0
  7 26  1  0
  8 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
 16 32  1  0
 16 33  1  0
 16 34  1  0
M  END

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       0.199   8.895   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.134   8.125   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.134   6.585   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -2.468   5.815   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -3.802   6.585   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -5.136   5.815   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -3.802   8.125   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -2.468   8.895   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.468  10.435   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -5.136   8.895   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.468   4.275   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.222   3.370   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.698   1.905   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -3.238   1.905   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -3.714   3.370   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -4.143   0.659   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -3.517  -0.748   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -0.793   0.659   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   10                                                  
CONECT    8    7    2    9                                                  
CONECT    9    8                                                            
CONECT   10    7                                                            
CONECT   11    4   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14   11                                                       
CONECT   16   14   17                                                       
CONECT   17   16                                                            
CONECT   18   13                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0245937
HETATM    1  C1  UNL     1      -3.785  -1.706   0.383  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.800  -0.626   0.194  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.470  -0.892  -0.013  1.00  0.00           C  
HETATM    4  N1  UNL     1      -0.580   0.086  -0.185  1.00  0.00           N  
HETATM    5  C4  UNL     1       0.823  -0.087  -0.406  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.217  -1.452  -0.866  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.735  -1.366  -0.636  1.00  0.00           C  
HETATM    8  O1  UNL     1       3.292  -2.615  -0.482  1.00  0.00           O  
HETATM    9  C7  UNL     1       2.758  -0.536   0.624  1.00  0.00           C  
HETATM   10  C8  UNL     1       3.898   0.435   0.659  1.00  0.00           C  
HETATM   11  O2  UNL     1       3.765   1.310  -0.395  1.00  0.00           O  
HETATM   12  O3  UNL     1       1.560   0.116   0.730  1.00  0.00           O  
HETATM   13  C9  UNL     1      -1.036   1.373  -0.147  1.00  0.00           C  
HETATM   14  O4  UNL     1      -0.237   2.335  -0.304  1.00  0.00           O  
HETATM   15  N2  UNL     1      -2.321   1.666   0.052  1.00  0.00           N  
HETATM   16  C10 UNL     1      -2.748   3.068   0.081  1.00  0.00           C  
HETATM   17  C11 UNL     1      -3.225   0.685   0.225  1.00  0.00           C  
HETATM   18  O5  UNL     1      -4.420   1.026   0.409  1.00  0.00           O  
HETATM   19  H1  UNL     1      -3.325  -2.440   1.106  1.00  0.00           H  
HETATM   20  H2  UNL     1      -4.697  -1.337   0.887  1.00  0.00           H  
HETATM   21  H3  UNL     1      -3.985  -2.267  -0.536  1.00  0.00           H  
HETATM   22  H4  UNL     1      -1.132  -1.899  -0.039  1.00  0.00           H  
HETATM   23  H5  UNL     1       1.114   0.630  -1.221  1.00  0.00           H  
HETATM   24  H6  UNL     1       0.992  -1.655  -1.921  1.00  0.00           H  
HETATM   25  H7  UNL     1       0.871  -2.254  -0.181  1.00  0.00           H  
HETATM   26  H8  UNL     1       3.216  -0.763  -1.438  1.00  0.00           H  
HETATM   27  H9  UNL     1       3.052  -2.949   0.423  1.00  0.00           H  
HETATM   28  H10 UNL     1       2.811  -1.270   1.478  1.00  0.00           H  
HETATM   29  H11 UNL     1       3.799   1.026   1.595  1.00  0.00           H  
HETATM   30  H12 UNL     1       4.884  -0.076   0.698  1.00  0.00           H  
HETATM   31  H13 UNL     1       3.372   2.180  -0.126  1.00  0.00           H  
HETATM   32  H14 UNL     1      -1.897   3.663   0.524  1.00  0.00           H  
HETATM   33  H15 UNL     1      -2.830   3.390  -0.962  1.00  0.00           H  
HETATM   34  H16 UNL     1      -3.670   3.205   0.658  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3    3   17
CONECT    3    4   22
CONECT    4    5   13
CONECT    5    6   12   23
CONECT    6    7   24   25
CONECT    7    8    9   26
CONECT    8   27
CONECT    9   10   12   28
CONECT   10   11   29   30
CONECT   11   31
CONECT   13   14   14   15
CONECT   15   16   17
CONECT   16   32   33   34
CONECT   17   18   18
END

HMDB0245937
     RDKit          3D
3-Methylthymidine
 34 35  0  0  0  0  0  0  0  0999 V2000
   -3.7847   -1.7063    0.3833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8002   -0.6261    0.1939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4699   -0.8919   -0.0134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5799    0.0858   -0.1847 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8228   -0.0872   -0.4062 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2172   -1.4523   -0.8664 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7354   -1.3661   -0.6357 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2925   -2.6152   -0.4823 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7577   -0.5365    0.6245 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8984    0.4349    0.6592 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7650    1.3100   -0.3952 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5599    0.1157    0.7304 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0360    1.3732   -0.1475 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2371    2.3349   -0.3036 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3213    1.6663    0.0517 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7484    3.0681    0.0811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2247    0.6846    0.2253 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4200    1.0257    0.4086 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3255   -2.4401    1.1059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6968   -1.3371    0.8868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9852   -2.2673   -0.5356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1323   -1.8991   -0.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1140    0.6298   -1.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9923   -1.6545   -1.9210 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8711   -2.2543   -0.1810 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2161   -0.7632   -1.4382 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0519   -2.9495    0.4226 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8112   -1.2702    1.4775 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7985    1.0258    1.5952 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8841   -0.0760    0.6979 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3718    2.1797   -0.1256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8971    3.6629    0.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8303    3.3900   -0.9622 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    3.2052    0.6583 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  1  0
 15 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  0
  6 24  1  0
  6 25  1  0
  7 26  1  0
  8 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
 16 32  1  0
 16 33  1  0
 16 34  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₁H₁₆N₂O₅

Average Molecular Weight

256.258

Monoisotopic Molecular Weight

256.105921623

IUPAC Name

1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,5-dimethyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,5-dimethylpyrimidine-2,4-dione

CAS Registry Number

Not Available

SMILES

CN1C(=O)N(C=C(C)C1=O)C1CC(O)C(CO)O1

InChI Identifier

InChI=1S/C11H16N2O5/c1-6-4-13(11(17)12(2)10(6)16)9-3-7(15)8(5-14)18-9/h4,7-9,14-15H,3,5H2,1-2H3

InChI Key

JCVDICFLPGDHAT-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

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (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	-1.1	ALOGPS
logP	-0.9	ChemAxon
logS	-0.35	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	90.31 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	60.31 m³·mol⁻¹	ChemAxon
Polarizability	25.51 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]+	159.849	30932474
DeepCCS	[M-H]-	157.491	30932474
DeepCCS	[M-2H]-	190.873	30932474
DeepCCS	[M+Na]+	165.942	30932474
AllCCS	[M+H]+	157.8	32859911
AllCCS	[M+H-H2O]+	154.1	32859911
AllCCS	[M+NH4]+	161.1	32859911
AllCCS	[M+Na]+	162.1	32859911
AllCCS	[M-H]-	158.8	32859911
AllCCS	[M+Na-2H]-	158.9	32859911
AllCCS	[M+HCOO]-	159.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Methylthymidine	CN1C(=O)N(C=C(C)C1=O)C1CC(O)C(CO)O1	2778.5	Standard polar	33892256
3-Methylthymidine	CN1C(=O)N(C=C(C)C1=O)C1CC(O)C(CO)O1	1961.9	Standard non polar	33892256
3-Methylthymidine	CN1C(=O)N(C=C(C)C1=O)C1CC(O)C(CO)O1	2240.4	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 - 3-Methylthymidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9440000000-10b18900258f4431f428	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylthymidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylthymidine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylthymidine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylthymidine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylthymidine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylthymidine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylthymidine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylthymidine 10V, Positive-QTOF	splash10-052f-2970000000-76115d5698d6f67733d4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylthymidine 20V, Positive-QTOF	splash10-0005-8900000000-cddab4aad926f404f607	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylthymidine 40V, Positive-QTOF	splash10-052g-9800000000-53c58b92ee08e9a835f8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylthymidine 10V, Negative-QTOF	splash10-0aor-0970000000-d74ffa3ad6875fd1084e	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylthymidine 20V, Negative-QTOF	splash10-0089-8900000000-a84829d8277baaedfd38	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylthymidine 40V, Negative-QTOF	splash10-0pbc-9510000000-c4243c2b9439d2999b3f	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)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

1612

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

1675

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 3-Methylthymidine (HMDB0245937)

MOL for HMDB0245937 (3-Methylthymidine)

3D MOL for HMDB0245937 (3-Methylthymidine)

3D SDF for HMDB0245937 (3-Methylthymidine)

3D-SDF for HMDB0245937 (3-Methylthymidine)

PDB for HMDB0245937 (3-Methylthymidine)

3D PDB for HMDB0245937 (3-Methylthymidine)

SMILES for HMDB0245937 (3-Methylthymidine)

INCHI for HMDB0245937 (3-Methylthymidine)

Structure for HMDB0245937 (3-Methylthymidine)

3D Structure for HMDB0245937 (3-Methylthymidine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra