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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 19:10:53 UTC

Update Date

2021-09-26 23:14:40 UTC

HMDB ID

HMDB0258011

Secondary Accession Numbers

None

Metabolite Identification

Common Name

[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid

Description

fluoro({[3-hydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid 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 fluoro({[3-hydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). [(2r,3s,5r)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically [(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid 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

HMDB0258011
     RDKit          3D
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluoroph...
 32 33  0  0  0  0  0  0  0  0999 V2000
   -5.7223   -0.6817   -1.5394 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5614   -0.5725   -1.0399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4277   -0.6687    0.3330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629   -0.5476    0.8515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0666   -0.3408    0.0678 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8056   -0.2324    0.7331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6195    1.1826    1.2510 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8985    1.2717    1.3134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3197    2.2290    0.3981 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3420   -0.0894    0.7670 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6563    0.0347    0.0436 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9315   -1.1585   -0.5979 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3823   -1.1318   -1.4408 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.4877   -2.4022   -2.2559 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4978    0.1793   -2.4889 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7127   -1.0912   -0.4262 F   0  0  0  0  0  0  0  0  0  0  0  0
    0.2877   -0.3746   -0.1001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2394   -0.2545   -1.2467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2061   -0.0608   -1.9692 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4737   -0.3685   -1.8030 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2789   -0.8339    0.9975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0582   -0.6229    1.9268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7186   -0.9783    1.5590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0416    1.8873    0.4919 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0904    1.3025    2.2373 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2804    1.4168    2.3222 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8552    2.0185   -0.4638 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3753   -0.8557    1.5436 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6541    0.9125   -0.6225 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4387    0.1822    0.8222 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9549    0.9478   -2.0514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6017   -0.2988   -2.8457 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
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  1  0
 17  6  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 15 31  1  0
 20 32  1  0
M  END


  Mrv1652309112121112D          

 20 21  0  0  0  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   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
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034   -3.0882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884   -3.7557    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9733   -4.4231    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1558   -3.2708    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8209   -4.2406    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 O   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
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
  6 12  1  0  0  0  0
 12 13  2  0  0  0  0
  3 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 16 19  1  0  0  0  0
  2 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258011

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1CC(OC1COP(O)(F)=O)N1C=CC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H12FN2O7P/c10-20(16,17)18-4-6-5(13)3-8(19-6)12-2-1-7(14)11-9(12)15/h1-2,5-6,8,13H,3-4H2,(H,16,17)(H,11,14,15)

> <INCHI_KEY>
QYAKHWNNJJLYOP-UHFFFAOYSA-N

> <FORMULA>
C9H12FN2O7P

> <MOLECULAR_WEIGHT>
310.174

> <EXACT_MASS>
310.036615895

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
25.278665032141035

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphinoyl fluoride

> <ALOGPS_LOGP>
-1.29

> <JCHEM_LOGP>
-1.1603630459999994

> <ALOGPS_LOGS>
-1.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.855726019314842

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.3389171320170359

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2403486880313332

> <JCHEM_POLAR_SURFACE_AREA>
125.4

> <JCHEM_REFRACTIVITY>
60.8645

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.41e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphinoyl fluoride

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0258011
     RDKit          3D
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluoroph...
 32 33  0  0  0  0  0  0  0  0999 V2000
   -5.7223   -0.6817   -1.5394 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5614   -0.5725   -1.0399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4277   -0.6687    0.3330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629   -0.5476    0.8515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0666   -0.3408    0.0678 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8056   -0.2324    0.7331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6195    1.1826    1.2510 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8985    1.2717    1.3134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3197    2.2290    0.3981 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3420   -0.0894    0.7670 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6563    0.0347    0.0436 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9315   -1.1585   -0.5979 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3823   -1.1318   -1.4408 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.4877   -2.4022   -2.2559 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4978    0.1793   -2.4889 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7127   -1.0912   -0.4262 F   0  0  0  0  0  0  0  0  0  0  0  0
    0.2877   -0.3746   -0.1001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2394   -0.2545   -1.2467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2061   -0.0608   -1.9692 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4737   -0.3685   -1.8030 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2789   -0.8339    0.9975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0582   -0.6229    1.9268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7186   -0.9783    1.5590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0416    1.8873    0.4919 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0904    1.3025    2.2373 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2804    1.4168    2.3222 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8552    2.0185   -0.4638 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3753   -0.8557    1.5436 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6541    0.9125   -0.6225 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4387    0.1822    0.8222 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9549    0.9478   -2.0514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6017   -0.2988   -2.8457 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
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  1  0
 17  6  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 15 31  1  0
 20 32  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       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.088  -3.215   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.342  -5.926   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.873  -5.765   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0      -2.778  -7.011   0.000  0.00  0.00           P+0
HETATM   17  O   UNK     0      -3.683  -8.257   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -4.024  -6.105   0.000  0.00  0.00           O+0
HETATM   19  F   UNK     0      -1.532  -7.916   0.000  0.00  0.00           F+0
HETATM   20  O   UNK     0       3.009  -5.926   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3   20                                                  
CONECT    3    2    4   14                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11    6   13                                                  
CONECT   13   12                                                            
CONECT   14    3   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16                                                            
CONECT   20    2                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

COMPND    HMDB0258011
HETATM    1  O1  UNL     1      -5.722  -0.682  -1.539  1.00  0.00           O  
HETATM    2  C1  UNL     1      -4.561  -0.573  -1.040  1.00  0.00           C  
HETATM    3  C2  UNL     1      -4.428  -0.669   0.333  1.00  0.00           C  
HETATM    4  C3  UNL     1      -3.163  -0.548   0.851  1.00  0.00           C  
HETATM    5  N1  UNL     1      -2.067  -0.341   0.068  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.806  -0.232   0.733  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.620   1.183   1.251  1.00  0.00           C  
HETATM    8  C6  UNL     1       0.898   1.272   1.313  1.00  0.00           C  
HETATM    9  O2  UNL     1       1.320   2.229   0.398  1.00  0.00           O  
HETATM   10  C7  UNL     1       1.342  -0.089   0.767  1.00  0.00           C  
HETATM   11  C8  UNL     1       2.656   0.035   0.044  1.00  0.00           C  
HETATM   12  O3  UNL     1       2.931  -1.158  -0.598  1.00  0.00           O  
HETATM   13  P1  UNL     1       4.382  -1.132  -1.441  1.00  0.00           P  
HETATM   14  O4  UNL     1       4.488  -2.402  -2.256  1.00  0.00           O  
HETATM   15  O5  UNL     1       4.498   0.179  -2.489  1.00  0.00           O  
HETATM   16  F1  UNL     1       5.713  -1.091  -0.426  1.00  0.00           F  
HETATM   17  O6  UNL     1       0.288  -0.375  -0.100  1.00  0.00           O  
HETATM   18  C9  UNL     1      -2.239  -0.254  -1.247  1.00  0.00           C  
HETATM   19  O7  UNL     1      -1.206  -0.061  -1.969  1.00  0.00           O  
HETATM   20  N2  UNL     1      -3.474  -0.368  -1.803  1.00  0.00           N  
HETATM   21  H1  UNL     1      -5.279  -0.834   0.998  1.00  0.00           H  
HETATM   22  H2  UNL     1      -3.058  -0.623   1.927  1.00  0.00           H  
HETATM   23  H3  UNL     1      -0.719  -0.978   1.559  1.00  0.00           H  
HETATM   24  H4  UNL     1      -1.042   1.887   0.492  1.00  0.00           H  
HETATM   25  H5  UNL     1      -1.090   1.302   2.237  1.00  0.00           H  
HETATM   26  H6  UNL     1       1.280   1.417   2.322  1.00  0.00           H  
HETATM   27  H7  UNL     1       0.855   2.019  -0.464  1.00  0.00           H  
HETATM   28  H8  UNL     1       1.375  -0.856   1.544  1.00  0.00           H  
HETATM   29  H9  UNL     1       2.654   0.912  -0.623  1.00  0.00           H  
HETATM   30  H10 UNL     1       3.439   0.182   0.822  1.00  0.00           H  
HETATM   31  H11 UNL     1       4.955   0.948  -2.051  1.00  0.00           H  
HETATM   32  H12 UNL     1      -3.602  -0.299  -2.846  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   20
CONECT    3    4    4   21
CONECT    4    5   22
CONECT    5    6   18
CONECT    6    7   17   23
CONECT    7    8   24   25
CONECT    8    9   10   26
CONECT    9   27
CONECT   10   11   17   28
CONECT   11   12   29   30
CONECT   12   13
CONECT   13   14   14   15   16
CONECT   15   31
CONECT   18   19   19   20
CONECT   20   32
END

HMDB0258011
     RDKit          3D
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluoroph...
 32 33  0  0  0  0  0  0  0  0999 V2000
   -5.7223   -0.6817   -1.5394 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5614   -0.5725   -1.0399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4277   -0.6687    0.3330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629   -0.5476    0.8515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0666   -0.3408    0.0678 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8056   -0.2324    0.7331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6195    1.1826    1.2510 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8985    1.2717    1.3134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3197    2.2290    0.3981 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3420   -0.0894    0.7670 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6563    0.0347    0.0436 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9315   -1.1585   -0.5979 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3823   -1.1318   -1.4408 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.4877   -2.4022   -2.2559 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4978    0.1793   -2.4889 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7127   -1.0912   -0.4262 F   0  0  0  0  0  0  0  0  0  0  0  0
    0.2877   -0.3746   -0.1001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2394   -0.2545   -1.2467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2061   -0.0608   -1.9692 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4737   -0.3685   -1.8030 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2789   -0.8339    0.9975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0582   -0.6229    1.9268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7186   -0.9783    1.5590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0416    1.8873    0.4919 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0904    1.3025    2.2373 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2804    1.4168    2.3222 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8552    2.0185   -0.4638 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3753   -0.8557    1.5436 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6541    0.9125   -0.6225 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4387    0.1822    0.8222 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9549    0.9478   -2.0514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6017   -0.2988   -2.8457 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
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  1  0
 17  6  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 15 31  1  0
 20 32  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Fluoro({[3-hydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinate	Generator
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinate	Generator

Chemical Formula

C₉H₁₂FN₂O₇P

Average Molecular Weight

310.174

Monoisotopic Molecular Weight

310.036615895

IUPAC Name

{[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphinoyl fluoride

Traditional Name

[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphinoyl fluoride

CAS Registry Number

Not Available

SMILES

OC1CC(OC1COP(O)(F)=O)N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C9H12FN2O7P/c10-20(16,17)18-4-6-5(13)3-8(19-6)12-2-1-7(14)11-9(12)15/h1-2,5-6,8,13H,3-4H2,(H,16,17)(H,11,14,15)

InChI Key

QYAKHWNNJJLYOP-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
Hydroxypyrimidine
Pyrimidone
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Oxolane
Heteroaromatic compound
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Azacycle
Hydrocarbon derivative
Organic oxide
Alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
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	-1.3	ALOGPS
logP	-1.2	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	-0.34	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	125.4 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	60.86 m³·mol⁻¹	ChemAxon
Polarizability	25.28 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]+	154.752	30932474
DeepCCS	[M-H]-	152.394	30932474
DeepCCS	[M-2H]-	185.279	30932474
DeepCCS	[M+Na]+	160.846	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid	OC1CC(OC1COP(O)(F)=O)N1C=CC(=O)NC1=O	3638.6	Standard polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid	OC1CC(OC1COP(O)(F)=O)N1C=CC(=O)NC1=O	2165.3	Standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid	OC1CC(OC1COP(O)(F)=O)N1C=CC(=O)NC1=O	2689.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TMS,isomer #1	C[Si](C)(C)OC1CC(N2C=CC(=O)[NH]C2=O)OC1COP(=O)(F)O[Si](C)(C)C	2570.7	Semi standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TMS,isomer #1	C[Si](C)(C)OC1CC(N2C=CC(=O)[NH]C2=O)OC1COP(=O)(F)O[Si](C)(C)C	2600.5	Standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TMS,isomer #1	C[Si](C)(C)OC1CC(N2C=CC(=O)[NH]C2=O)OC1COP(=O)(F)O[Si](C)(C)C	3045.5	Standard polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C)C2=O)OC1COP(=O)(O)F	2556.2	Semi standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C)C2=O)OC1COP(=O)(O)F	2671.9	Standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C)C2=O)OC1COP(=O)(O)F	3298.4	Standard polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TMS,isomer #3	C[Si](C)(C)OP(=O)(F)OCC1OC(N2C=CC(=O)N([Si](C)(C)C)C2=O)CC1O	2602.6	Semi standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TMS,isomer #3	C[Si](C)(C)OP(=O)(F)OCC1OC(N2C=CC(=O)N([Si](C)(C)C)C2=O)CC1O	2683.2	Standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TMS,isomer #3	C[Si](C)(C)OP(=O)(F)OCC1OC(N2C=CC(=O)N([Si](C)(C)C)C2=O)CC1O	3170.5	Standard polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,3TMS,isomer #1	C[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C)C2=O)OC1COP(=O)(F)O[Si](C)(C)C	2608.1	Semi standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,3TMS,isomer #1	C[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C)C2=O)OC1COP(=O)(F)O[Si](C)(C)C	2703.7	Standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,3TMS,isomer #1	C[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C)C2=O)OC1COP(=O)(F)O[Si](C)(C)C	2819.5	Standard polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(=O)[NH]C2=O)OC1COP(=O)(F)O[Si](C)(C)C(C)(C)C	3006.0	Semi standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(=O)[NH]C2=O)OC1COP(=O)(F)O[Si](C)(C)C(C)(C)C	3046.0	Standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(=O)[NH]C2=O)OC1COP(=O)(F)O[Si](C)(C)C(C)(C)C	3232.2	Standard polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)OC1COP(=O)(O)F	3011.0	Semi standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)OC1COP(=O)(O)F	3101.0	Standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)OC1COP(=O)(O)F	3378.5	Standard polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(F)OCC1OC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1O	3035.0	Semi standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(F)OCC1OC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1O	3096.5	Standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(F)OCC1OC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1O	3274.1	Standard polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)OC1COP(=O)(F)O[Si](C)(C)C(C)(C)C	3265.8	Semi standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)OC1COP(=O)(F)O[Si](C)(C)C(C)(C)C	3303.6	Standard non polar	33892256
[(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)OC1COP(=O)(F)O[Si](C)(C)C(C)(C)C	3052.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - [(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-01ow-9510000000-eafa48b5464bc05f3fe9	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - [(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - [(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - [(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - [(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - [(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - [(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - [(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

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 [(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid (HMDB0258011)

MOL for HMDB0258011 ([(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid)

3D MOL for HMDB0258011 ([(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid)

3D SDF for HMDB0258011 ([(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid)

3D-SDF for HMDB0258011 ([(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid)

PDB for HMDB0258011 ([(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid)

3D PDB for HMDB0258011 ([(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid)

SMILES for HMDB0258011 ([(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid)

INCHI for HMDB0258011 ([(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid)

Structure for HMDB0258011 ([(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid)

3D Structure for HMDB0258011 ([(2R,3S,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-fluorophosphinic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra