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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:49:17 UTC

Update Date

2021-09-26 22:56:07 UTC

HMDB ID

HMDB0246808

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-Hydroxymethyl-2'-deoxyuridine

Description

4-hydroxy-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-1,2-dihydropyrimidin-2-one 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 4-hydroxy-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-1,2-dihydropyrimidin-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-hydroxymethyl-2'-deoxyuridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Hydroxymethyl-2'-deoxyuridine 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

HMDB0258024
     RDKit          3D
1-[(2S,5S)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)pyrimidin...
 32 33  0  0  0  0  0  0  0  0999 V2000
    0.0224   -2.6034    0.2795 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9201   -1.7923    0.1297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1592   -2.2783   -0.0298 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2365   -1.4893   -0.1977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5205   -1.9749   -0.3634 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0494   -0.1300   -0.2046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1760    0.8159   -0.3831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6903    2.1197   -0.3475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7756    0.3671   -0.0406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7175   -0.4652    0.1256 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5704    0.1260    0.2893 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3621    0.1914   -1.0123 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7462    0.5521   -0.4602 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8600    1.9401   -0.6034 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6054    0.1889    0.9840 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7956   -0.5278    1.5429 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9064    0.2776    1.3769 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4280   -0.5596    1.1108 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9656   -2.5941    0.2926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5702    0.6288   -1.4223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9774    0.6609    0.3685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5620    2.4433    0.5767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6159    1.4545   -0.0448 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4835    1.1630    0.6671 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9877    0.9510   -1.7016 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4442   -0.8043   -1.4787 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5309    0.0048   -0.9952 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9660    2.3096   -0.3730 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4259    1.1235    1.5745 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6384   -0.6529    2.6333 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9067   -1.5300    1.1120 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2563    0.0839    0.4494 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 10  2  1  0
 18 11  1  0
  5 19  1  0
  7 20  1  0
  7 21  1  0
  8 22  1  0
  9 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 14 28  1  0
 15 29  1  0
 16 30  1  0
 16 31  1  0
 17 32  1  0
M  END


  Mrv1652310061716212D          

 18 19  0  0  0  0            999 V2000
   -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
   -0.6110   -1.8216    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
   -0.1261   -2.4890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3874    1.5082    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  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  1  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  2  1  0  0  0  0
 12  8  1  0  0  0  0
 12 10  1  0  0  0  0
 13  3  1  0  0  0  0
 14  4  1  0  0  0  0
 15  6  1  0  0  0  0
 16  9  1  0  0  0  0
 17 10  2  0  0  0  0
 18  7  1  0  0  0  0
 18  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246808

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1OC(CC1O)N1C=C(CO)C(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N2O6/c13-3-5-2-12(10(17)11-9(5)16)8-1-6(15)7(4-14)18-8/h2,6-8,13-15H,1,3-4H2,(H,11,16,17)

> <INCHI_KEY>
IPAVKOYJGUMINP-UHFFFAOYSA-N

> <FORMULA>
C10H14N2O6

> <MOLECULAR_WEIGHT>
258.23

> <EXACT_MASS>
258.085186179

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.984408837333888

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.92

> <JCHEM_LOGP>
-2.0323239416666663

> <ALOGPS_LOGS>
-0.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.864621117696089

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.1380270443011025

> <JCHEM_PKA_STRONGEST_BASIC>
-2.832648454914132

> <JCHEM_POLAR_SURFACE_AREA>
122.82000000000001

> <JCHEM_REFRACTIVITY>
57.5084

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.66e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0258024
     RDKit          3D
1-[(2S,5S)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)pyrimidin...
 32 33  0  0  0  0  0  0  0  0999 V2000
    0.0224   -2.6034    0.2795 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9201   -1.7923    0.1297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1592   -2.2783   -0.0298 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2365   -1.4893   -0.1977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5205   -1.9749   -0.3634 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0494   -0.1300   -0.2046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1760    0.8159   -0.3831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6903    2.1197   -0.3475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7756    0.3671   -0.0406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7175   -0.4652    0.1256 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5704    0.1260    0.2893 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3621    0.1914   -1.0123 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7462    0.5521   -0.4602 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8600    1.9401   -0.6034 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6054    0.1889    0.9840 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7956   -0.5278    1.5429 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9064    0.2776    1.3769 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4280   -0.5596    1.1108 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9656   -2.5941    0.2926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5702    0.6288   -1.4223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9774    0.6609    0.3685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5620    2.4433    0.5767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6159    1.4545   -0.0448 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4835    1.1630    0.6671 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9877    0.9510   -1.7016 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4442   -0.8043   -1.4787 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5309    0.0048   -0.9952 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9660    2.3096   -0.3730 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4259    1.1235    1.5745 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6384   -0.6529    2.6333 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9067   -1.5300    1.1120 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2563    0.0839    0.4494 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 10  2  1  0
 18 11  1  0
  5 19  1  0
  7 20  1  0
  7 21  1  0
  8 22  1  0
  9 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 14 28  1  0
 15 29  1  0
 16 30  1  0
 16 31  1  0
 17 32  1  0
M  END

HEADER    PROTEIN                                 06-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-OCT-17         0                                  
HETATM    1  C   UNK     0      -1.222   3.370   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.419  -0.748   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.141  -3.400   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      -0.235  -4.646   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -6.323   2.815   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -2.468   5.815   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.923  -3.078   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.365   2.227   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -3.238   1.905   0.000  0.00  0.00           O+0
CONECT    1    6    8                                                       
CONECT    2    5   12                                                       
CONECT    3    5   13                                                       
CONECT    4    7   14                                                       
CONECT    5    2    3    9                                                  
CONECT    6    1    7   15                                                  
CONECT    7    4    6   18                                                  
CONECT    8    1   12   18                                                  
CONECT    9    5   11   16                                                  
CONECT   10   11   12   17                                                  
CONECT   11    9   10                                                       
CONECT   12    2    8   10                                                  
CONECT   13    3                                                            
CONECT   14    4                                                            
CONECT   15    6                                                            
CONECT   16    9                                                            
CONECT   17   10                                                            
CONECT   18    7    8                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0258024
HETATM    1  O1  UNL     1       0.022  -2.603   0.279  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.920  -1.792   0.130  1.00  0.00           C  
HETATM    3  N1  UNL     1      -2.159  -2.278  -0.030  1.00  0.00           N  
HETATM    4  C2  UNL     1      -3.237  -1.489  -0.198  1.00  0.00           C  
HETATM    5  O2  UNL     1      -4.520  -1.975  -0.363  1.00  0.00           O  
HETATM    6  C3  UNL     1      -3.049  -0.130  -0.205  1.00  0.00           C  
HETATM    7  C4  UNL     1      -4.176   0.816  -0.383  1.00  0.00           C  
HETATM    8  O3  UNL     1      -3.690   2.120  -0.347  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.776   0.367  -0.041  1.00  0.00           C  
HETATM   10  N2  UNL     1      -0.717  -0.465   0.126  1.00  0.00           N  
HETATM   11  C6  UNL     1       0.570   0.126   0.289  1.00  0.00           C  
HETATM   12  C7  UNL     1       1.362   0.191  -1.012  1.00  0.00           C  
HETATM   13  C8  UNL     1       2.746   0.552  -0.460  1.00  0.00           C  
HETATM   14  O4  UNL     1       2.860   1.940  -0.603  1.00  0.00           O  
HETATM   15  C9  UNL     1       2.605   0.189   0.984  1.00  0.00           C  
HETATM   16  C10 UNL     1       3.796  -0.528   1.543  1.00  0.00           C  
HETATM   17  O5  UNL     1       4.906   0.278   1.377  1.00  0.00           O  
HETATM   18  O6  UNL     1       1.428  -0.560   1.111  1.00  0.00           O  
HETATM   19  H1  UNL     1      -4.966  -2.594   0.293  1.00  0.00           H  
HETATM   20  H2  UNL     1      -4.570   0.629  -1.422  1.00  0.00           H  
HETATM   21  H3  UNL     1      -4.977   0.661   0.369  1.00  0.00           H  
HETATM   22  H4  UNL     1      -3.562   2.443   0.577  1.00  0.00           H  
HETATM   23  H5  UNL     1      -1.616   1.455  -0.045  1.00  0.00           H  
HETATM   24  H6  UNL     1       0.483   1.163   0.667  1.00  0.00           H  
HETATM   25  H7  UNL     1       0.988   0.951  -1.702  1.00  0.00           H  
HETATM   26  H8  UNL     1       1.444  -0.804  -1.479  1.00  0.00           H  
HETATM   27  H9  UNL     1       3.531   0.005  -0.995  1.00  0.00           H  
HETATM   28  H10 UNL     1       1.966   2.310  -0.373  1.00  0.00           H  
HETATM   29  H11 UNL     1       2.426   1.123   1.574  1.00  0.00           H  
HETATM   30  H12 UNL     1       3.638  -0.653   2.633  1.00  0.00           H  
HETATM   31  H13 UNL     1       3.907  -1.530   1.112  1.00  0.00           H  
HETATM   32  H14 UNL     1       5.256   0.084   0.449  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4    4
CONECT    4    5    6
CONECT    5   19
CONECT    6    7    9    9
CONECT    7    8   20   21
CONECT    8   22
CONECT    9   10   23
CONECT   10   11
CONECT   11   12   18   24
CONECT   12   13   25   26
CONECT   13   14   15   27
CONECT   14   28
CONECT   15   16   18   29
CONECT   16   17   30   31
CONECT   17   32
END

HMDB0258024
     RDKit          3D
1-[(2S,5S)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)pyrimidin...
 32 33  0  0  0  0  0  0  0  0999 V2000
    0.0224   -2.6034    0.2795 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9201   -1.7923    0.1297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1592   -2.2783   -0.0298 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2365   -1.4893   -0.1977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5205   -1.9749   -0.3634 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0494   -0.1300   -0.2046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1760    0.8159   -0.3831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6903    2.1197   -0.3475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7756    0.3671   -0.0406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7175   -0.4652    0.1256 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5704    0.1260    0.2893 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3621    0.1914   -1.0123 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7462    0.5521   -0.4602 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8600    1.9401   -0.6034 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6054    0.1889    0.9840 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7956   -0.5278    1.5429 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9064    0.2776    1.3769 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4280   -0.5596    1.1108 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9656   -2.5941    0.2926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5702    0.6288   -1.4223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9774    0.6609    0.3685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5620    2.4433    0.5767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6159    1.4545   -0.0448 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4835    1.1630    0.6671 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9877    0.9510   -1.7016 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4442   -0.8043   -1.4787 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5309    0.0048   -0.9952 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9660    2.3096   -0.3730 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4259    1.1235    1.5745 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6384   -0.6529    2.6333 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9067   -1.5300    1.1120 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2563    0.0839    0.4494 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 10  2  1  0
 18 11  1  0
  5 19  1  0
  7 20  1  0
  7 21  1  0
  8 22  1  0
  9 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 14 28  1  0
 15 29  1  0
 16 30  1  0
 16 31  1  0
 17 32  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2'-Deoxy-5-(hydroxymethyl)uridine	MeSH
5-Hydroxymethyl-2'-deoxyuridine	MeSH
5-Hydroxymethyldeoxyuridine	MeSH

Chemical Formula

C₁₀H₁₄N₂O₆

Average Molecular Weight

258.23

Monoisotopic Molecular Weight

258.085186179

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OCC1OC(CC1O)N1C=C(CO)C(O)=NC1=O

InChI Identifier

InChI=1S/C10H14N2O6/c13-3-5-2-12(10(17)11-9(5)16)8-1-6(15)7(4-14)18-8/h2,6-8,13-15H,1,3-4H2,(H,11,16,17)

InChI Key

IPAVKOYJGUMINP-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
Oxolane
Vinylogous amide
Heteroaromatic compound
Lactam
Urea
Secondary alcohol
Azacycle
Organoheterocyclic compound
Oxacycle
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Primary alcohol
Alcohol
Organooxygen compound
Organonitrogen compound
Aromatic 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	-1.9	ALOGPS
logP	-2	ChemAxon
logS	-0.99	ALOGPS
pKa (Strongest Acidic)	7.14	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	122.82 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	57.51 m³·mol⁻¹	ChemAxon
Polarizability	23.98 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]+	153.479	30932474
DeepCCS	[M-H]-	151.121	30932474
DeepCCS	[M-2H]-	185.718	30932474
DeepCCS	[M+Na]+	161.581	30932474
AllCCS	[M+H]+	156.7	32859911
AllCCS	[M+H-H2O]+	153.1	32859911
AllCCS	[M+NH4]+	160.1	32859911
AllCCS	[M+Na]+	161.1	32859911
AllCCS	[M-H]-	156.0	32859911
AllCCS	[M+Na-2H]-	156.0	32859911
AllCCS	[M+HCOO]-	156.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxymethyl-2'-deoxyuridine	OCC1OC(CC1O)N1C=C(CO)C(O)=NC1=O	2191.4	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine	OCC1OC(CC1O)N1C=C(CO)C(O)=NC1=O	2191.2	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine	OCC1OC(CC1O)N1C=C(CO)C(O)=NC1=O	2602.7	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine	OCC1OC(CC1O)N1C=C(CO)C(O)=NC1=O	2602.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O	2574.2	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O	2532.7	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O	4030.1	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=C(CO)C(O)=NC2=O)OC1CO	2607.8	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=C(CO)C(O)=NC2=O)OC1CO	2531.5	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=C(CO)C(O)=NC2=O)OC1CO	3958.4	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #3	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O	2562.6	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #3	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O	2526.6	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #3	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O	4089.0	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #4	C[Si](C)(C)OC1=NC(=O)N(C2CC(O)C(CO)O2)C=C1CO	2503.9	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #4	C[Si](C)(C)OC1=NC(=O)N(C2CC(O)C(CO)O2)C=C1CO	2488.1	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TMS,isomer #4	C[Si](C)(C)OC1=NC(=O)N(C2CC(O)C(CO)O2)C=C1CO	4143.8	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #1	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C)O2)C(=O)N=C1O	2535.0	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #1	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C)O2)C(=O)N=C1O	2625.3	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #1	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C)O2)C(=O)N=C1O	3492.7	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #2	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C)=NC2=O)CC1O	2487.5	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #2	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C)=NC2=O)CC1O	2587.3	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #2	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C)=NC2=O)CC1O	3575.0	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O[Si](C)(C)C	2566.9	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O[Si](C)(C)C	2586.9	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O[Si](C)(C)C	3345.0	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #4	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO)O2)C(=O)N=C1O	2567.4	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #4	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO)O2)C(=O)N=C1O	2605.7	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #4	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO)O2)C(=O)N=C1O	3441.1	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #5	C[Si](C)(C)OC1=NC(=O)N(C2CC(O[Si](C)(C)C)C(CO)O2)C=C1CO	2500.4	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #5	C[Si](C)(C)OC1=NC(=O)N(C2CC(O[Si](C)(C)C)C(CO)O2)C=C1CO	2554.8	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #5	C[Si](C)(C)OC1=NC(=O)N(C2CC(O[Si](C)(C)C)C(CO)O2)C=C1CO	3527.0	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #6	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O[Si](C)(C)C	2528.2	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #6	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O[Si](C)(C)C	2585.2	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TMS,isomer #6	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O[Si](C)(C)C	3627.1	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #1	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O2)C(=O)N=C1O	2498.1	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #1	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O2)C(=O)N=C1O	2625.1	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #1	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O2)C(=O)N=C1O	2993.3	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #2	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C	2486.0	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #2	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C	2665.4	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #2	C[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C	3213.7	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C)=NC2=O)CC1O[Si](C)(C)C	2459.7	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C)=NC2=O)CC1O[Si](C)(C)C	2586.8	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C)=NC2=O)CC1O[Si](C)(C)C	3090.1	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #4	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO)O2)C(=O)N=C1O[Si](C)(C)C	2503.3	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #4	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO)O2)C(=O)N=C1O[Si](C)(C)C	2602.8	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TMS,isomer #4	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO)O2)C(=O)N=C1O[Si](C)(C)C	3167.0	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,4TMS,isomer #1	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C	2462.2	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,4TMS,isomer #1	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C	2608.6	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,4TMS,isomer #1	C[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C	2820.8	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O	2838.1	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O	2756.3	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O	3971.0	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=C(CO)C(O)=NC2=O)OC1CO	2871.0	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=C(CO)C(O)=NC2=O)OC1CO	2758.0	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=C(CO)C(O)=NC2=O)OC1CO	3915.3	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O	2817.2	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O	2748.4	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O	4022.9	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC1=NC(=O)N(C2CC(O)C(CO)O2)C=C1CO	2765.3	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC1=NC(=O)N(C2CC(O)C(CO)O2)C=C1CO	2732.8	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC1=NC(=O)N(C2CC(O)C(CO)O2)C=C1CO	4025.6	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O	2988.5	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O	3066.0	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O	3515.4	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C(C)(C)C)=NC2=O)CC1O	2951.8	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C(C)(C)C)=NC2=O)CC1O	3043.1	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C(C)(C)C)=NC2=O)CC1O	3555.6	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O[Si](C)(C)C(C)(C)C	3047.9	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O[Si](C)(C)C(C)(C)C	3027.3	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O)=NC2=O)CC1O[Si](C)(C)C(C)(C)C	3393.3	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO)O2)C(=O)N=C1O	3020.4	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO)O2)C(=O)N=C1O	3047.5	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO)O2)C(=O)N=C1O	3464.2	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC1=NC(=O)N(C2CC(O[Si](C)(C)C(C)(C)C)C(CO)O2)C=C1CO	2969.7	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC1=NC(=O)N(C2CC(O[Si](C)(C)C(C)(C)C)C(CO)O2)C=C1CO	3026.6	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC1=NC(=O)N(C2CC(O[Si](C)(C)C(C)(C)C)C(CO)O2)C=C1CO	3507.5	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	2964.0	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3046.5	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3599.8	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O	3194.3	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O	3271.4	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O	3233.0	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3168.9	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3309.0	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3365.0	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C(C)(C)C)=NC2=O)CC1O[Si](C)(C)C(C)(C)C	3157.5	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C(C)(C)C)=NC2=O)CC1O[Si](C)(C)C(C)(C)C	3252.8	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(CO)C(O[Si](C)(C)C(C)(C)C)=NC2=O)CC1O[Si](C)(C)C(C)(C)C	3277.7	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3178.4	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3259.7	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3322.7	Standard polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3340.2	Semi standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3422.3	Standard non polar	33892256
5-Hydroxymethyl-2'-deoxyuridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C	3177.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 4-hydroxy-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-1,2-dihydropyrimidin-2-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-002f-9560000000-eca63775e836a6ee2cfd	2018-04-09	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-hydroxy-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-1,2-dihydropyrimidin-2-one GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-hydroxy-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-1,2-dihydropyrimidin-2-one GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	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 - 5-Hydroxymethyl-2'-deoxyuridine 10V, Positive-QTOF	splash10-0006-0900000000-0d5928885f5f472a635b	2018-04-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 20V, Positive-QTOF	splash10-004i-0900000000-6053e6d4e872a4fee26d	2018-04-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 40V, Positive-QTOF	splash10-002f-0900000000-652dab39dc8b3f2952c6	2018-04-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 10V, Negative-QTOF	splash10-0c29-0490000000-ddbfb529fb65ebbd60d6	2018-04-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 20V, Negative-QTOF	splash10-00kr-1920000000-ca57253d5fc5d17764b2	2018-04-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 40V, Negative-QTOF	splash10-0006-9300000000-372a9094192ab19376cf	2018-04-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 10V, Positive-QTOF	splash10-0a4i-0190000000-c04e1083ff9d9db7aadd	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 20V, Positive-QTOF	splash10-004i-0900000000-9095ce0e7f76e2662ec8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 40V, Positive-QTOF	splash10-0ar1-6900000000-677f20ff41c0544e634c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 10V, Negative-QTOF	splash10-0a4i-0290000000-d602fc36d892a52cf370	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 20V, Negative-QTOF	splash10-00dl-3920000000-0d6aab4a0691b8ffad90	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxymethyl-2'-deoxyuridine 40V, Negative-QTOF	splash10-0006-9500000000-7450c98d467a0677eef7	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
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, 100 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	¹³C NMR Spectrum (1D, 1000 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, 200 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, 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	¹³C NMR Spectrum (1D, 500 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	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	¹H NMR Spectrum (1D, 700 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	¹³C NMR Spectrum (1D, 800 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	¹H NMR Spectrum (1D, 900 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

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

4372656

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5201346

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 5-Hydroxymethyl-2'-deoxyuridine (HMDB0246808)

MOL for HMDB0246808 (5-Hydroxymethyl-2'-deoxyuridine)

3D MOL for HMDB0246808 (5-Hydroxymethyl-2'-deoxyuridine)

3D SDF for HMDB0246808 (5-Hydroxymethyl-2'-deoxyuridine)

3D-SDF for HMDB0246808 (5-Hydroxymethyl-2'-deoxyuridine)

PDB for HMDB0246808 (5-Hydroxymethyl-2'-deoxyuridine)

3D PDB for HMDB0246808 (5-Hydroxymethyl-2'-deoxyuridine)

SMILES for HMDB0246808 (5-Hydroxymethyl-2'-deoxyuridine)

INCHI for HMDB0246808 (5-Hydroxymethyl-2'-deoxyuridine)

Structure for HMDB0246808 (5-Hydroxymethyl-2'-deoxyuridine)

3D Structure for HMDB0246808 (5-Hydroxymethyl-2'-deoxyuridine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra