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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-17 01:00:20 UTC

Update Date

2021-09-14 15:18:57 UTC

HMDB ID

HMDB0060406

Secondary Accession Numbers

HMDB60406

Metabolite Identification

Common Name

5'-Deoxy-5-fluorouridine

Description

5'-Deoxy-5-fluorouridine, also known as 5'-DFUR or 5-fluoro-5'-deoxyuridine, belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives. 5'-Deoxy-5-fluorouridine is an extremely weak basic (essentially neutral) compound (based on its pKa). 5'-Deoxy-5-fluorouridine is a metabolite of capecitabine. Within humans, 5'-deoxy-5-fluorouridine participates in a number of enzymatic reactions. In particular, 5'-deoxy-5-fluorouridine can be converted into fluorouracil and 5-deoxyribose-1-phosphate through the action of the enzyme thymidine phosphorylase. In addition, 5'-deoxy-5-fluorouridine and meprobamate can be biosynthesized from capecitabine through its interaction with the enzymes liver carboxylesterase 1 and cytidine deaminase. Capecitabine is a prodrug, that is enzymatically converted to 5-fluorouracil in the tumor, where it inhibits DNA synthesis and slows growth of tumor tissue. In humans, 5'-deoxy-5-fluorouridine is involved in capecitabine action pathway. Capecitabine (Xeloda, Roche) is an orally-administered chemotherapeutic agent used in the treatment of metastatic breast and colorectal cancers.

Structure

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

HMDB0060406
     RDKit          3D
5'-Deoxy-5-fluorouridine
 28 29  0  0  0  0  0  0  0  0999 V2000
   -2.4296    1.7476    0.4596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1265    0.6236   -0.5266 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8073    0.6409   -0.8618 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2025   -0.5388   -0.4331 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1221   -0.2128   -0.0264 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7748    0.7710   -0.6768 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0502    1.1476   -0.3502 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7022    2.1381   -1.0078 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.7035    0.5005    0.6854 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0059    0.8754    1.0290 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0406   -0.4686    1.3149 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7700   -0.8292    0.9743 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1579   -1.7390    1.5710 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0791   -1.1444    0.5988 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1285   -2.5377    0.5505 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4597   -0.6835    0.1042 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9169   -1.5426   -0.9008 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2634    1.3834    1.1178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5570    1.9804    1.1007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8241    2.6462   -0.0609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7367    0.8228   -1.4365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1969   -1.2161   -1.3176 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2855    1.3058   -1.5042 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6148    1.0726    0.2226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9567   -0.7475    1.6186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6486   -2.9048   -0.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1723   -0.6120    0.9416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7213   -2.4788   -0.6403 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  2  0
 11 12  1  0
 12 13  2  0
  4 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16  2  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  6
  4 22  1  6
  6 23  1  0
 10 24  1  0
 14 25  1  1
 15 26  1  0
 16 27  1  1
 17 28  1  0
M  END


  Mrv0541 05161318002D          

 17 18  0  0  0  0            999 V2000
    0.1298    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0401    0.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5251   -0.2280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1895   -0.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8841   -0.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3455   -0.1418    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3690   -1.0679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197    0.3532    0.0000 N   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
   -2.7743    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6744   -1.6491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0636   -0.4867    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  1  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  8  6  1  0  0  0  0
 10  4  1  0  0  0  0
 11  7  2  0  0  0  0
 11  9  1  0  0  0  0
 12  2  1  0  0  0  0
  8 12  1  1  0  0  0
 12  9  1  0  0  0  0
  5 13  1  6  0  0  0
  6 14  1  6  0  0  0
 15  7  1  0  0  0  0
 16  9  2  0  0  0  0
 17  3  1  0  0  0  0
 17  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060406

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H11FN2O5/c1-3-5(13)6(14)8(17-3)12-2-4(10)7(15)11-9(12)16/h2-3,5-6,8,13-14H,1H3,(H,11,15,16)/t3-,5-,6-,8-/m1/s1

> <INCHI_KEY>
ZWAOHEXOSAUJHY-ZIYNGMLESA-N

> <FORMULA>
C9H11FN2O5

> <MOLECULAR_WEIGHT>
246.1924

> <EXACT_MASS>
246.065199677

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
21.05696053068467

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-methyloxolan-2-yl]-5-fluoro-4-hydroxy-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-0.82

> <JCHEM_LOGP>
-0.8013884606666666

> <ALOGPS_LOGS>
-1.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.587272330418951

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.2036954432895195

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6273746253685584

> <JCHEM_POLAR_SURFACE_AREA>
102.59000000000002

> <JCHEM_REFRACTIVITY>
51.546499999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.36e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
doxifluridine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060406
     RDKit          3D
5'-Deoxy-5-fluorouridine
 28 29  0  0  0  0  0  0  0  0999 V2000
   -2.4296    1.7476    0.4596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1265    0.6236   -0.5266 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8073    0.6409   -0.8618 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2025   -0.5388   -0.4331 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1221   -0.2128   -0.0264 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7748    0.7710   -0.6768 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0502    1.1476   -0.3502 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7022    2.1381   -1.0078 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.7035    0.5005    0.6854 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0059    0.8754    1.0290 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0406   -0.4686    1.3149 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7700   -0.8292    0.9743 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1579   -1.7390    1.5710 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0791   -1.1444    0.5988 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1285   -2.5377    0.5505 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4597   -0.6835    0.1042 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9169   -1.5426   -0.9008 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2634    1.3834    1.1178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5570    1.9804    1.1007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8241    2.6462   -0.0609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7367    0.8228   -1.4365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1969   -1.2161   -1.3176 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2855    1.3058   -1.5042 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6148    1.0726    0.2226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9567   -0.7475    1.6186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6486   -2.9048   -0.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1723   -0.6120    0.9416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7213   -2.4788   -0.6403 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  2  0
 11 12  1  0
 12 13  2  0
  4 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16  2  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  6
  4 22  1  6
  6 23  1  0
 10 24  1  0
 14 25  1  1
 15 26  1  0
 16 27  1  1
 17 28  1  0
M  END

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0       0.242   3.846   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.675   0.820   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.222   3.370   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.580  -0.426   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.468   4.275   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.714   3.370   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.954  -1.833   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.238   1.905   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.517  -0.748   0.000  0.00  0.00           C+0
HETATM   10  F   UNK     0      -8.112  -0.265   0.000  0.00  0.00           F+0
HETATM   11  N   UNK     0      -4.422  -1.993   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -4.143   0.659   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0      -2.468   5.815   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -5.179   3.846   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -6.859  -3.078   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.985  -0.909   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.698   1.905   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2    4   12                                                       
CONECT    3    1    5   17                                                  
CONECT    4    2    7   10                                                  
CONECT    5    3    6   13                                                  
CONECT    6    5    8   14                                                  
CONECT    7    4   11   15                                                  
CONECT    8    6   12   17                                                  
CONECT    9   11   12   16                                                  
CONECT   10    4                                                            
CONECT   11    7    9                                                       
CONECT   12    2    8    9                                                  
CONECT   13    5                                                            
CONECT   14    6                                                            
CONECT   15    7                                                            
CONECT   16    9                                                            
CONECT   17    3    8                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0060406
HETATM    1  C1  UNL     1      -2.430   1.748   0.460  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.127   0.624  -0.527  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.807   0.641  -0.862  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.203  -0.539  -0.433  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.122  -0.213  -0.026  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.775   0.771  -0.677  1.00  0.00           C  
HETATM    7  C5  UNL     1       3.050   1.148  -0.350  1.00  0.00           C  
HETATM    8  F1  UNL     1       3.702   2.138  -1.008  1.00  0.00           F  
HETATM    9  C6  UNL     1       3.704   0.500   0.685  1.00  0.00           C  
HETATM   10  O2  UNL     1       5.006   0.875   1.029  1.00  0.00           O  
HETATM   11  N2  UNL     1       3.041  -0.469   1.315  1.00  0.00           N  
HETATM   12  C7  UNL     1       1.770  -0.829   0.974  1.00  0.00           C  
HETATM   13  O3  UNL     1       1.158  -1.739   1.571  1.00  0.00           O  
HETATM   14  C8  UNL     1      -1.079  -1.144   0.599  1.00  0.00           C  
HETATM   15  O4  UNL     1      -1.129  -2.538   0.551  1.00  0.00           O  
HETATM   16  C9  UNL     1      -2.460  -0.683   0.104  1.00  0.00           C  
HETATM   17  O5  UNL     1      -2.917  -1.543  -0.901  1.00  0.00           O  
HETATM   18  H1  UNL     1      -3.263   1.383   1.118  1.00  0.00           H  
HETATM   19  H2  UNL     1      -1.557   1.980   1.101  1.00  0.00           H  
HETATM   20  H3  UNL     1      -2.824   2.646  -0.061  1.00  0.00           H  
HETATM   21  H4  UNL     1      -2.737   0.823  -1.436  1.00  0.00           H  
HETATM   22  H5  UNL     1      -0.197  -1.216  -1.318  1.00  0.00           H  
HETATM   23  H6  UNL     1       1.285   1.306  -1.504  1.00  0.00           H  
HETATM   24  H7  UNL     1       5.615   1.073   0.223  1.00  0.00           H  
HETATM   25  H8  UNL     1      -0.957  -0.748   1.619  1.00  0.00           H  
HETATM   26  H9  UNL     1      -0.649  -2.905  -0.218  1.00  0.00           H  
HETATM   27  H10 UNL     1      -3.172  -0.612   0.942  1.00  0.00           H  
HETATM   28  H11 UNL     1      -2.721  -2.479  -0.640  1.00  0.00           H  
CONECT    1    2   18   19   20
CONECT    2    3   16   21
CONECT    3    4
CONECT    4    5   14   22
CONECT    5    6   12
CONECT    6    7    7   23
CONECT    7    8    9
CONECT    9   10   11   11
CONECT   10   24
CONECT   11   12
CONECT   12   13   13
CONECT   14   15   16   25
CONECT   15   26
CONECT   16   17   27
CONECT   17   28
END

HMDB0060406
     RDKit          3D
5'-Deoxy-5-fluorouridine
 28 29  0  0  0  0  0  0  0  0999 V2000
   -2.4296    1.7476    0.4596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1265    0.6236   -0.5266 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8073    0.6409   -0.8618 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2025   -0.5388   -0.4331 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1221   -0.2128   -0.0264 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7748    0.7710   -0.6768 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0502    1.1476   -0.3502 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7022    2.1381   -1.0078 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.7035    0.5005    0.6854 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0059    0.8754    1.0290 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0406   -0.4686    1.3149 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7700   -0.8292    0.9743 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1579   -1.7390    1.5710 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0791   -1.1444    0.5988 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1285   -2.5377    0.5505 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4597   -0.6835    0.1042 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9169   -1.5426   -0.9008 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2634    1.3834    1.1178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5570    1.9804    1.1007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8241    2.6462   -0.0609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7367    0.8228   -1.4365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1969   -1.2161   -1.3176 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2855    1.3058   -1.5042 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6148    1.0726    0.2226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9567   -0.7475    1.6186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6486   -2.9048   -0.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1723   -0.6120    0.9416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7213   -2.4788   -0.6403 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  2  0
 11 12  1  0
 12 13  2  0
  4 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16  2  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  6
  4 22  1  6
  6 23  1  0
 10 24  1  0
 14 25  1  1
 15 26  1  0
 16 27  1  1
 17 28  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1-(beta-D-5-Desoxyribofuranoxyl)-5-fluoruracil	ChEBI
5'-DFUR	ChEBI
5'-DFUrd	ChEBI
5-Fluoro-5'-deoxyuridine	ChEBI
Doxifluridina	ChEBI
Doxifluridinum	ChEBI
Furtulon	ChEBI
Ro 21-9738	ChEBI
Ro 219738	ChEBI
Doxifluridine	Kegg
1-(b-D-5-Desoxyribofuranoxyl)-5-fluoruracil	Generator
1-(Β-D-5-desoxyribofuranoxyl)-5-fluoruracil	Generator
5'-Deoxy-5'-fluorouridine	HMDB
5'-Fluoro-5'-deoxyuridine	HMDB
Doxyfluridine	HMDB
5'-Deoxy-5-fluorouridine	MeSH

Chemical Formula

C₉H₁₁FN₂O₅

Average Molecular Weight

246.1924

Monoisotopic Molecular Weight

246.065199677

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-methyloxolan-2-yl]-5-fluoro-4-hydroxy-1,2-dihydropyrimidin-2-one

Traditional Name

doxifluridine

CAS Registry Number

Not Available

SMILES

C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(O)=NC1=O

InChI Identifier

InChI=1S/C9H11FN2O5/c1-3-5(13)6(14)8(17-3)12-2-4(10)7(15)11-9(12)16/h2-3,5-6,8,13-14H,1H3,(H,11,15,16)/t3-,5-,6-,8-/m1/s1

InChI Key

ZWAOHEXOSAUJHY-ZIYNGMLESA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

5'-deoxyribonucleosides

Sub Class

Not Available

Direct Parent

5'-deoxyribonucleosides

Alternative Parents

Substituents

5'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
Halopyrimidine
Pyrimidone
Aryl fluoride
Aryl halide
Pyrimidine
Hydropyrimidine
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Urea
Secondary alcohol
1,2-diol
Lactam
Oxacycle
Azacycle
Organoheterocyclic compound
Organopnictogen compound
Organohalogen compound
Organofluoride
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

organofluorine compound (CHEBI:31521 )
pyrimidine 5'-deoxyribonucleoside (CHEBI:31521 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0060406)

Organ

Liver (HMDB: HMDB0060406)
Kidney (HMDB: HMDB0060406)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060406)

Cellular substructure

Cytoplasm (HMDB: HMDB0060406)

Source

Endogenous

Endogenous (HMDB: HMDB0060406)

Process

Naturally occurring process

Biological process

Biochemical pathway

Drug action pathway

Capecitabine Action Pathway (PathBank: SMP0000469)

Metabolic pathway

Capecitabine Metabolism Pathway (PathBank: SMP0000607)

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
Water Solubility	5.36 g/L	ALOGPS
logP	-0.82	ALOGPS
logP	-0.8	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	6.2	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	102.59 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	51.55 m³·mol⁻¹	ChemAxon
Polarizability	21.06 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	155.464	30932474
DeepCCS	[M-H]-	153.068	30932474
DeepCCS	[M-2H]-	186.409	30932474
DeepCCS	[M+Na]+	161.495	30932474
AllCCS	[M+H]+	154.4	32859911
AllCCS	[M+H-H2O]+	150.6	32859911
AllCCS	[M+NH4]+	158.0	32859911
AllCCS	[M+Na]+	159.0	32859911
AllCCS	[M-H]-	151.0	32859911
AllCCS	[M+Na-2H]-	151.0	32859911
AllCCS	[M+HCOO]-	151.0	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	2.27 minutes	32390414
Predicted by Siyang on May 30, 2022	9.3089 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.89 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	841.9 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	84.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	158.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	68.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	273.8 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	295.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	113.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	637.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	265.6 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	847.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	190.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	190.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	433.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	262.8 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	84.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5'-Deoxy-5-fluorouridine	C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(O)=NC1=O	3504.9	Standard polar	33892256
5'-Deoxy-5-fluorouridine	C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(O)=NC1=O	2082.2	Standard non polar	33892256
5'-Deoxy-5-fluorouridine	C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(O)=NC1=O	2157.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5'-Deoxy-5-fluorouridine,1TMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(O)=NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2098.9	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,1TMS,isomer #2	C[C@H]1O[C@@H](N2C=C(F)C(O)=NC2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2118.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,1TMS,isomer #3	C[C@H]1O[C@@H](N2C=C(F)C(O[Si](C)(C)C)=NC2=O)[C@H](O)[C@@H]1O	2063.0	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,2TMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(O[Si](C)(C)C)=NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2098.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,2TMS,isomer #2	C[C@H]1O[C@@H](N2C=C(F)C(O)=NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2119.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,2TMS,isomer #3	C[C@H]1O[C@@H](N2C=C(F)C(O[Si](C)(C)C)=NC2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2112.0	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,3TMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(O[Si](C)(C)C)=NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2151.1	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,1TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(O)=NC2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2352.9	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,1TBDMS,isomer #2	C[C@H]1O[C@@H](N2C=C(F)C(O)=NC2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2371.5	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,1TBDMS,isomer #3	C[C@H]1O[C@@H](N2C=C(F)C(O[Si](C)(C)C(C)(C)C)=NC2=O)[C@H](O)[C@@H]1O	2298.0	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,2TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(O[Si](C)(C)C(C)(C)C)=NC2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2573.0	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,2TBDMS,isomer #2	C[C@H]1O[C@@H](N2C=C(F)C(O)=NC2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2612.3	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,2TBDMS,isomer #3	C[C@H]1O[C@@H](N2C=C(F)C(O[Si](C)(C)C(C)(C)C)=NC2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2583.5	Semi standard non polar	33892256
5'-Deoxy-5-fluorouridine,3TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(O[Si](C)(C)C(C)(C)C)=NC2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2801.7	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Deoxy-5-fluorouridine GC-MS (Non-derivatized) - 70eV, Positive	splash10-056u-9210000000-68ddd4a6bcf1d8ff7c3f	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Deoxy-5-fluorouridine GC-MS (3 TMS) - 70eV, Positive	splash10-00tk-6976700000-d826a815dab6401bbc3d	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Deoxy-5-fluorouridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Deoxy-5-fluorouridine 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'-Deoxy-5-fluorouridine 10V, Positive-QTOF	splash10-001i-0910000000-7e78eab45706c44d825f	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 20V, Positive-QTOF	splash10-001i-1900000000-17e125f0d2b5d65e776e	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 40V, Positive-QTOF	splash10-03e9-9400000000-4647ffbb75476b52110a	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 10V, Negative-QTOF	splash10-004l-5950000000-62edf53c23a7fcae3dde	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 20V, Negative-QTOF	splash10-004i-4930000000-e1442f1a62dab8ca8e79	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 40V, Negative-QTOF	splash10-0006-9100000000-583eee0dde55403044a4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 10V, Positive-QTOF	splash10-0002-9810000000-af33e0acf393f434b2b4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 20V, Positive-QTOF	splash10-001s-9800000000-ebb571742c6aab84653b	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 40V, Positive-QTOF	splash10-00ec-8900000000-11063d9f21aa7c8eb3df	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 10V, Negative-QTOF	splash10-004j-1890000000-1de9ab4256d6804b8f6a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 20V, Negative-QTOF	splash10-0006-9600000000-64d7705d227c428a4b7c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorouridine 40V, Negative-QTOF	splash10-0006-9100000000-a2671dc87d34b4b003e3	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)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Name	SMPDB/PathBank	KEGG
Capecitabine Action Pathway		Not Available
Capecitabine Metabolism Pathway		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB12947

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C12739

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

18343

PDB ID

Not Available

ChEBI ID

31521

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

Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Enzymes

Enzyme Details

1. Thymidine phosphorylase

General function:: Involved in transferase activity, transferring glycosyl groups
Specific function:: May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:: TYMP
Uniprot ID:: P19971
Molecular weight:: 49954.965

Reactions

5'-Deoxy-5-fluorouridine + Phosphate → Fluorouracil + 5-Deoxyribose-1-phosphate	details

Enzyme Details

2. Cytidine deaminase

General function:: Involved in zinc ion binding
Specific function:: This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
Gene Name:: CDA
Uniprot ID:: P32320
Molecular weight:: 16184.545

Reactions

5'-Deoxy-5-fluorocytidine + Water → 5'-Deoxy-5-fluorouridine + Ammonia	details

Showing metabocard for 5'-Deoxy-5-fluorouridine (HMDB0060406)

MOL for HMDB0060406 (5'-Deoxy-5-fluorouridine)

3D MOL for HMDB0060406 (5'-Deoxy-5-fluorouridine)

3D SDF for HMDB0060406 (5'-Deoxy-5-fluorouridine)

3D-SDF for HMDB0060406 (5'-Deoxy-5-fluorouridine)

PDB for HMDB0060406 (5'-Deoxy-5-fluorouridine)

3D PDB for HMDB0060406 (5'-Deoxy-5-fluorouridine)

SMILES for HMDB0060406 (5'-Deoxy-5-fluorouridine)

INCHI for HMDB0060406 (5'-Deoxy-5-fluorouridine)

Structure for HMDB0060406 (5'-Deoxy-5-fluorouridine)

3D Structure for HMDB0060406 (5'-Deoxy-5-fluorouridine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions

Reactions