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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 00:32:04 UTC

Update Date

2021-09-26 22:57:16 UTC

HMDB ID

HMDB0247529

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-

Description

Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- 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 Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-. This compound has been identified in human blood as reported by (PMID: 31557052 ). Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'r)- is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- 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

HMDB0247529
     RDKit          3D
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-
 31 32  0  0  0  0  0  0  0  0999 V2000
   -0.9849   -2.3651   -0.7413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7239   -0.8746   -0.6635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1997   -0.3929   -1.8488 F   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0745   -0.2091   -0.4008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4319    0.6419   -1.4453 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9082    0.5168    0.9086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6405    1.8264    0.8063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4560    2.5355    1.9724 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5624    0.6349    1.0997 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0631   -0.4711    0.5330 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4277   -0.0977    0.2376 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9307    1.1440    0.3779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2484    1.4387    0.0777 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0786    0.4391   -0.3788 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3016    0.6933   -0.6618 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5743   -0.7915   -0.5162 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2946   -1.0182   -0.2113 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8869   -2.2181   -0.3687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7187   -2.8964    0.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4768   -2.8175   -1.6399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0804   -2.5714   -0.9266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8833   -0.9369   -0.2788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8659    0.0428   -2.1336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3510   -0.0376    1.7696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7341    1.5740    0.7536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4186    2.3960   -0.1033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5239    2.3446    2.2894 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0718   -1.3394    1.2449 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2826    1.9240    0.7342 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6626    2.4327    0.1868 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2121   -1.5470   -0.8642 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 10  2  1  0
 17 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
 10 28  1  0
 12 29  1  0
 13 30  1  0
 16 31  1  0
M  END


  Mrv1652309112102322D          

 18 19  0  0  0  0            999 V2000
    0.1624   -0.6244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3507   -2.0195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1353   -1.7646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3068   -0.9576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0915   -0.7027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6937   -0.4056    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9091   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2960   -0.1085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665   -0.6244    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
  7 13  1  0  0  0  0
 13 14  2  0  0  0  0
  4 15  1  0  0  0  0
 15 16  1  0  0  0  0
  3 17  1  0  0  0  0
  2 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0247529

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1(F)C(O)C(CO)OC1N1C=CC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H13FN2O5/c1-10(11)7(16)5(4-14)18-8(10)13-3-2-6(15)12-9(13)17/h2-3,5,7-8,14,16H,4H2,1H3,(H,12,15,17)

> <INCHI_KEY>
ARKKGZQTGXJVKW-UHFFFAOYSA-N

> <FORMULA>
C10H13FN2O5

> <MOLECULAR_WEIGHT>
260.221

> <EXACT_MASS>
260.08084969

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
23.10741907867278

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.00

> <JCHEM_LOGP>
-1.2435736993333326

> <ALOGPS_LOGS>
-0.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.60279538390181

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.849589481908572

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9807895232439874

> <JCHEM_POLAR_SURFACE_AREA>
99.10000000000001

> <JCHEM_REFRACTIVITY>
55.5117

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.27e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[3-fluoro-4-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]-3H-pyrimidine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0247529
     RDKit          3D
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-
 31 32  0  0  0  0  0  0  0  0999 V2000
   -0.9849   -2.3651   -0.7413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7239   -0.8746   -0.6635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1997   -0.3929   -1.8488 F   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0745   -0.2091   -0.4008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4319    0.6419   -1.4453 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9082    0.5168    0.9086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6405    1.8264    0.8063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4560    2.5355    1.9724 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5624    0.6349    1.0997 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0631   -0.4711    0.5330 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4277   -0.0977    0.2376 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9307    1.1440    0.3779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2484    1.4387    0.0777 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0786    0.4391   -0.3788 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3016    0.6933   -0.6618 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5743   -0.7915   -0.5162 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2946   -1.0182   -0.2113 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8869   -2.2181   -0.3687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7187   -2.8964    0.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4768   -2.8175   -1.6399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0804   -2.5714   -0.9266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8833   -0.9369   -0.2788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8659    0.0428   -2.1336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3510   -0.0376    1.7696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7341    1.5740    0.7536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4186    2.3960   -0.1033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5239    2.3446    2.2894 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0718   -1.3394    1.2449 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2826    1.9240    0.7342 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6626    2.4327    0.1868 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2121   -1.5470   -0.8642 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 10  2  1  0
 17 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
 10 28  1  0
 12 29  1  0
 13 30  1  0
 16 31  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       0.303  -1.166   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.564  -4.680   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.377  -2.739   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -2.521  -3.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.986  -3.294   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.306  -1.788   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -5.771  -1.312   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0      -3.162  -0.757   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -1.697  -1.233   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.553  -0.202   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.009  -5.926   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.540  -5.765   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.044  -2.739   0.000  0.00  0.00           O+0
HETATM   18  F   UNK     0       2.364  -1.166   0.000  0.00  0.00           F+0
CONECT    1    2                                                            
CONECT    2    1    3    6   18                                             
CONECT    3    2    4   17                                                  
CONECT    4    3    5   15                                                  
CONECT    5    4    6                                                       
CONECT    6    5    2    7                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12    7   14                                                  
CONECT   14   13                                                            
CONECT   15    4   16                                                       
CONECT   16   15                                                            
CONECT   17    3                                                            
CONECT   18    2                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0247529
HETATM    1  C1  UNL     1      -0.985  -2.365  -0.741  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.724  -0.875  -0.664  1.00  0.00           C  
HETATM    3  F1  UNL     1      -0.200  -0.393  -1.849  1.00  0.00           F  
HETATM    4  C3  UNL     1      -2.075  -0.209  -0.401  1.00  0.00           C  
HETATM    5  O1  UNL     1      -2.432   0.642  -1.445  1.00  0.00           O  
HETATM    6  C4  UNL     1      -1.908   0.517   0.909  1.00  0.00           C  
HETATM    7  C5  UNL     1      -2.641   1.826   0.806  1.00  0.00           C  
HETATM    8  O2  UNL     1      -2.456   2.536   1.972  1.00  0.00           O  
HETATM    9  O3  UNL     1      -0.562   0.635   1.100  1.00  0.00           O  
HETATM   10  C6  UNL     1       0.063  -0.471   0.533  1.00  0.00           C  
HETATM   11  N1  UNL     1       1.428  -0.098   0.238  1.00  0.00           N  
HETATM   12  C7  UNL     1       1.931   1.144   0.378  1.00  0.00           C  
HETATM   13  C8  UNL     1       3.248   1.439   0.078  1.00  0.00           C  
HETATM   14  C9  UNL     1       4.079   0.439  -0.379  1.00  0.00           C  
HETATM   15  O4  UNL     1       5.302   0.693  -0.662  1.00  0.00           O  
HETATM   16  N2  UNL     1       3.574  -0.792  -0.516  1.00  0.00           N  
HETATM   17  C10 UNL     1       2.295  -1.018  -0.211  1.00  0.00           C  
HETATM   18  O5  UNL     1       1.887  -2.218  -0.369  1.00  0.00           O  
HETATM   19  H1  UNL     1      -0.719  -2.896   0.191  1.00  0.00           H  
HETATM   20  H2  UNL     1      -0.477  -2.818  -1.640  1.00  0.00           H  
HETATM   21  H3  UNL     1      -2.080  -2.571  -0.927  1.00  0.00           H  
HETATM   22  H4  UNL     1      -2.883  -0.937  -0.279  1.00  0.00           H  
HETATM   23  H5  UNL     1      -2.866   0.043  -2.134  1.00  0.00           H  
HETATM   24  H6  UNL     1      -2.351  -0.038   1.770  1.00  0.00           H  
HETATM   25  H7  UNL     1      -3.734   1.574   0.754  1.00  0.00           H  
HETATM   26  H8  UNL     1      -2.419   2.396  -0.103  1.00  0.00           H  
HETATM   27  H9  UNL     1      -1.524   2.345   2.289  1.00  0.00           H  
HETATM   28  H10 UNL     1       0.072  -1.339   1.245  1.00  0.00           H  
HETATM   29  H11 UNL     1       1.283   1.924   0.734  1.00  0.00           H  
HETATM   30  H12 UNL     1       3.663   2.433   0.187  1.00  0.00           H  
HETATM   31  H13 UNL     1       4.212  -1.547  -0.864  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3    4   10
CONECT    4    5    6   22
CONECT    5   23
CONECT    6    7    9   24
CONECT    7    8   25   26
CONECT    8   27
CONECT    9   10
CONECT   10   11   28
CONECT   11   12   17
CONECT   12   13   13   29
CONECT   13   14   30
CONECT   14   15   15   16
CONECT   16   17   31
CONECT   17   18   18
END

HMDB0247529
     RDKit          3D
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-
 31 32  0  0  0  0  0  0  0  0999 V2000
   -0.9849   -2.3651   -0.7413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7239   -0.8746   -0.6635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1997   -0.3929   -1.8488 F   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0745   -0.2091   -0.4008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4319    0.6419   -1.4453 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9082    0.5168    0.9086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6405    1.8264    0.8063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4560    2.5355    1.9724 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5624    0.6349    1.0997 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0631   -0.4711    0.5330 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4277   -0.0977    0.2376 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9307    1.1440    0.3779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2484    1.4387    0.0777 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0786    0.4391   -0.3788 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3016    0.6933   -0.6618 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5743   -0.7915   -0.5162 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2946   -1.0182   -0.2113 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8869   -2.2181   -0.3687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7187   -2.8964    0.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4768   -2.8175   -1.6399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0804   -2.5714   -0.9266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8833   -0.9369   -0.2788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8659    0.0428   -2.1336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3510   -0.0376    1.7696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7341    1.5740    0.7536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4186    2.3960   -0.1033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5239    2.3446    2.2894 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0718   -1.3394    1.2449 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2826    1.9240    0.7342 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6626    2.4327    0.1868 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2121   -1.5470   -0.8642 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 10  2  1  0
 17 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
 10 28  1  0
 12 29  1  0
 13 30  1  0
 16 31  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₀H₁₃FN₂O₅

Average Molecular Weight

260.221

Monoisotopic Molecular Weight

260.08084969

IUPAC Name

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

Traditional Name

1-[3-fluoro-4-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]-3H-pyrimidine-2,4-dione

CAS Registry Number

Not Available

SMILES

CC1(F)C(O)C(CO)OC1N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C10H13FN2O5/c1-10(11)7(16)5(4-14)18-8(10)13-3-2-6(15)12-9(13)17/h2-3,5,7-8,14,16H,4H2,1H3,(H,12,15,17)

InChI Key

ARKKGZQTGXJVKW-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
Heteroaromatic compound
Vinylogous amide
Fluorohydrin
Halohydrin
Lactam
Secondary alcohol
Urea
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Primary alcohol
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organofluoride
Organohalogen compound
Alkyl halide
Organic nitrogen compound
Alkyl fluoride
Alcohol
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)

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	0	ALOGPS
logP	-1.2	ChemAxon
logS	-0.31	ALOGPS
pKa (Strongest Acidic)	9.85	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	99.1 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.51 m³·mol⁻¹	ChemAxon
Polarizability	23.11 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]+	156.589	30932474
DeepCCS	[M-H]-	154.231	30932474
DeepCCS	[M-2H]-	187.44	30932474
DeepCCS	[M+Na]+	162.683	30932474
AllCCS	[M+H]+	157.2	32859911
AllCCS	[M+H-H2O]+	153.5	32859911
AllCCS	[M+NH4]+	160.6	32859911
AllCCS	[M+Na]+	161.6	32859911
AllCCS	[M-H]-	155.9	32859911
AllCCS	[M+Na-2H]-	155.9	32859911
AllCCS	[M+HCOO]-	156.0	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.6741 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.72 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	815.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	247.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	91.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	158.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	59.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	297.0 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	280.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	130.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	632.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	231.5 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	989.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	193.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	203.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	427.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	220.4 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	159.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-	CC1(F)C(O)C(CO)OC1N1C=CC(=O)NC1=O	2835.7	Standard polar	33892256
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-	CC1(F)C(O)C(CO)OC1N1C=CC(=O)NC1=O	2005.5	Standard non polar	33892256
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-	CC1(F)C(O)C(CO)OC1N1C=CC(=O)NC1=O	2294.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-,3TMS,isomer #1	CC1(F)C(O[Si](C)(C)C)C(CO[Si](C)(C)C)OC1N1C=CC(=O)N([Si](C)(C)C)C1=O	2330.2	Semi standard non polar	33892256
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-,3TMS,isomer #1	CC1(F)C(O[Si](C)(C)C)C(CO[Si](C)(C)C)OC1N1C=CC(=O)N([Si](C)(C)C)C1=O	2356.0	Standard non polar	33892256
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-,3TMS,isomer #1	CC1(F)C(O[Si](C)(C)C)C(CO[Si](C)(C)C)OC1N1C=CC(=O)N([Si](C)(C)C)C1=O	2270.0	Standard polar	33892256
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-,3TBDMS,isomer #1	CC1(F)C(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)OC1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O	3003.3	Semi standard non polar	33892256
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-,3TBDMS,isomer #1	CC1(F)C(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)OC1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O	2908.3	Standard non polar	33892256
Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-,3TBDMS,isomer #1	CC1(F)C(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)OC1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O	2605.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (Non-derivatized) - 70eV, Positive	splash10-05be-9210000000-4d1f0c7837e4e4050ce8	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- GC-MS (TBDMS_2_3) - 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 - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- 10V, Negative-QTOF	splash10-0bt9-2970000000-0c7c61417da791425c2a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- 20V, Negative-QTOF	splash10-01p6-5940000000-dd1a86d955334e51dc9d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- 40V, Negative-QTOF	splash10-0006-9200000000-3d539661e4cfef4006f5	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- 10V, Positive-QTOF	splash10-03di-0390000000-44cae17d0242a73c97ae	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- 20V, Positive-QTOF	splash10-03di-6910000000-811c1cdcc18cba4c42d9	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- 40V, Positive-QTOF	splash10-03fr-4900000000-7eaf03928eeee6fb9105	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	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	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	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	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

23257777

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44399265

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 Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)- (HMDB0247529)

MOL for HMDB0247529 (Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-)

3D MOL for HMDB0247529 (Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-)

3D SDF for HMDB0247529 (Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-)

3D-SDF for HMDB0247529 (Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-)

PDB for HMDB0247529 (Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-)

3D PDB for HMDB0247529 (Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-)

SMILES for HMDB0247529 (Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-)

INCHI for HMDB0247529 (Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-)

Structure for HMDB0247529 (Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-)

3D Structure for HMDB0247529 (Uridine, 2'-deoxy-2'-fluoro-2'-methyl-, (2'R)-)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra