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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-07-04 18:55:25 UTC

Update Date

2021-09-14 15:45:02 UTC

HMDB ID

HMDB0060727

Secondary Accession Numbers

HMDB60727

Metabolite Identification

Common Name

2',2'-Difluorodeoxyuridine

Description

2',2'-Difluorodeoxyuridine 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. 2',2'-Difluorodeoxyuridine is an extremely weak basic (essentially neutral) compound (based on its pKa). It is marketed as Gemzar by Eli Lilly and Company. Gemcitabine is a nucleoside analog used as chemotherapy. 2',2'-Difluorodeoxyuridine is a metabolite of gemcitabine.

Structure

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

HMDB0060727
     RDKit          3D
2',2'-Difluorodeoxyuridine
 28 29  0  0  0  0  0  0  0  0999 V2000
    1.0021    0.4152   -2.2588 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8465    0.0965   -1.3627 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0991   -0.2912   -1.6820 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0074   -0.6326   -0.7477 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2869   -1.0261   -1.1219 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5943   -0.5672    0.5675 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2920   -0.1627    0.8741 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4141    0.1703   -0.0901 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1023    0.5736    0.2969 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7423    0.7200   -0.8161 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0244    0.7819   -0.3379 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0293    0.0825   -1.2224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2834    0.2261   -0.6148 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0615    0.1305    1.0129 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0215   -0.8538    1.1200 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6464   -0.4562    1.0984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2181   -0.5722    2.3859 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6344   -1.6347    0.3935 F   0  0  0  0  0  0  0  0  0  0  0  0
    6.0813   -0.4000   -1.1480 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3066   -0.8363    1.3282 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9937   -0.1197    1.9035 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0970    1.5469    0.8424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3321    1.8609   -0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8253   -1.0150   -1.2620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0796    0.4919   -2.2327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3945    1.1306   -0.2188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1366    0.8931    1.8074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6940   -0.5525    1.7901 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
  8  2  1  0
 16  9  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
  9 22  1  1
 11 23  1  1
 12 24  1  0
 12 25  1  0
 13 26  1  0
 14 27  1  1
 15 28  1  0
M  END

  Mrv0541 07041311552D          

 18 19  0  0  0  0            999 V2000
   -0.0986   -0.5887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6860   -0.8436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6486   -1.9986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2701    0.2183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1276    0.5154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1562    0.6571    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    2.3462    0.6571    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    0.3430    0.7703    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4691   -1.9124    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0547    0.4732    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7407    1.0674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  6  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  9  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  9  1  0  0  0  0
 11  9  1  0  0  0  0
 12  5  2  0  0  0  0
 12  8  1  0  0  0  0
 13  2  1  0  0  0  0
  7 13  1  6  0  0  0
 13  8  1  0  0  0  0
 14  3  1  0  0  0  0
 15  5  1  0  0  0  0
  6 16  1  6  0  0  0
 17  8  2  0  0  0  0
 18  4  1  0  0  0  0
 18  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060727

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@@H]1O[C@H](N2C=CC(O)=NC2=O)C(F)(F)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H10F2N2O5/c10-9(11)6(16)4(3-14)18-7(9)13-2-1-5(15)12-8(13)17/h1-2,4,6-7,14,16H,3H2,(H,12,15,17)/t4-,6+,7-/m0/s1

> <INCHI_KEY>
FIRDBEQIJQERSE-JHYUDYDFSA-N

> <FORMULA>
C9H10F2N2O5

> <MOLECULAR_WEIGHT>
264.1829

> <EXACT_MASS>
264.05577785

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
21.24211620545631

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2S,4R,5S)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
0.27

> <JCHEM_LOGP>
-0.7167636809999999

> <ALOGPS_LOGS>
-0.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.51709647595163

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.305237770370759

> <JCHEM_PKA_STRONGEST_BASIC>
-2.983187864329431

> <JCHEM_POLAR_SURFACE_AREA>
102.59000000000002

> <JCHEM_REFRACTIVITY>
51.592800000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.81e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2S,4R,5S)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060727
     RDKit          3D
2',2'-Difluorodeoxyuridine
 28 29  0  0  0  0  0  0  0  0999 V2000
    1.0021    0.4152   -2.2588 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8465    0.0965   -1.3627 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0991   -0.2912   -1.6820 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0074   -0.6326   -0.7477 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2869   -1.0261   -1.1219 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5943   -0.5672    0.5675 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2920   -0.1627    0.8741 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4141    0.1703   -0.0901 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1023    0.5736    0.2969 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7423    0.7200   -0.8161 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0244    0.7819   -0.3379 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0293    0.0825   -1.2224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2834    0.2261   -0.6148 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0615    0.1305    1.0129 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0215   -0.8538    1.1200 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6464   -0.4562    1.0984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2181   -0.5722    2.3859 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6344   -1.6347    0.3935 F   0  0  0  0  0  0  0  0  0  0  0  0
    6.0813   -0.4000   -1.1480 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3066   -0.8363    1.3282 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9937   -0.1197    1.9035 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0970    1.5469    0.8424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3321    1.8609   -0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8253   -1.0150   -1.2620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0796    0.4919   -2.2327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3945    1.1306   -0.2188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1366    0.8931    1.8074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6940   -0.5525    1.7901 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
  8  2  1  0
 16  9  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
  9 22  1  1
 11 23  1  1
 12 24  1  0
 12 25  1  0
 13 26  1  0
 14 27  1  1
 15 28  1  0
M  END

HEADER    PROTEIN                                 04-JUL-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUL-13         0                                  
HETATM    1  C   UNK     0      -0.184  -1.099   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.281  -1.575   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.811  -3.731   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.906  -2.485   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.504   0.407   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.105   0.962   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM   10  F   UNK     0       5.892   1.227   0.000  0.00  0.00           F+0
HETATM   11  F   UNK     0       4.380   1.227   0.000  0.00  0.00           F+0
HETATM   12  N   UNK     0       0.640   1.438   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       2.425  -0.544   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       8.342  -3.570   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -1.969   0.883   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       7.846  -0.544   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.249   1.992   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.366  -2.485   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1   13                                                       
CONECT    3    4   14                                                       
CONECT    4    3    6   18                                                  
CONECT    5    1   12   15                                                  
CONECT    6    4    9   16                                                  
CONECT    7    9   13   18                                                  
CONECT    8   12   13   17                                                  
CONECT    9    6    7   10   11                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    5    8                                                       
CONECT   13    2    7    8                                                  
CONECT   14    3                                                            
CONECT   15    5                                                            
CONECT   16    6                                                            
CONECT   17    8                                                            
CONECT   18    4    7                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0060727
HETATM    1  O1  UNL     1       1.002   0.415  -2.259  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.846   0.097  -1.363  1.00  0.00           C  
HETATM    3  N1  UNL     1       3.099  -0.291  -1.682  1.00  0.00           N  
HETATM    4  C2  UNL     1       4.007  -0.633  -0.748  1.00  0.00           C  
HETATM    5  O2  UNL     1       5.287  -1.026  -1.122  1.00  0.00           O  
HETATM    6  C3  UNL     1       3.594  -0.567   0.567  1.00  0.00           C  
HETATM    7  C4  UNL     1       2.292  -0.163   0.874  1.00  0.00           C  
HETATM    8  N2  UNL     1       1.414   0.170  -0.090  1.00  0.00           N  
HETATM    9  C5  UNL     1       0.102   0.574   0.297  1.00  0.00           C  
HETATM   10  O3  UNL     1      -0.742   0.720  -0.816  1.00  0.00           O  
HETATM   11  C6  UNL     1      -2.024   0.782  -0.338  1.00  0.00           C  
HETATM   12  C7  UNL     1      -3.029   0.083  -1.222  1.00  0.00           C  
HETATM   13  O4  UNL     1      -4.283   0.226  -0.615  1.00  0.00           O  
HETATM   14  C8  UNL     1      -2.062   0.130   1.013  1.00  0.00           C  
HETATM   15  O5  UNL     1      -3.022  -0.854   1.120  1.00  0.00           O  
HETATM   16  C9  UNL     1      -0.646  -0.456   1.098  1.00  0.00           C  
HETATM   17  F1  UNL     1      -0.218  -0.572   2.386  1.00  0.00           F  
HETATM   18  F2  UNL     1      -0.634  -1.635   0.393  1.00  0.00           F  
HETATM   19  H1  UNL     1       6.081  -0.400  -1.148  1.00  0.00           H  
HETATM   20  H2  UNL     1       4.307  -0.836   1.328  1.00  0.00           H  
HETATM   21  H3  UNL     1       1.994  -0.120   1.904  1.00  0.00           H  
HETATM   22  H4  UNL     1       0.097   1.547   0.842  1.00  0.00           H  
HETATM   23  H5  UNL     1      -2.332   1.861  -0.305  1.00  0.00           H  
HETATM   24  H6  UNL     1      -2.825  -1.015  -1.262  1.00  0.00           H  
HETATM   25  H7  UNL     1      -3.080   0.492  -2.233  1.00  0.00           H  
HETATM   26  H8  UNL     1      -4.394   1.131  -0.219  1.00  0.00           H  
HETATM   27  H9  UNL     1      -2.137   0.893   1.807  1.00  0.00           H  
HETATM   28  H10 UNL     1      -3.694  -0.552   1.790  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    4
CONECT    4    5    6
CONECT    5   19
CONECT    6    7    7   20
CONECT    7    8   21
CONECT    8    9
CONECT    9   10   16   22
CONECT   10   11
CONECT   11   12   14   23
CONECT   12   13   24   25
CONECT   13   26
CONECT   14   15   16   27
CONECT   15   28
CONECT   16   17   18
END

HMDB0060727
     RDKit          3D
2',2'-Difluorodeoxyuridine
 28 29  0  0  0  0  0  0  0  0999 V2000
    1.0021    0.4152   -2.2588 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8465    0.0965   -1.3627 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0991   -0.2912   -1.6820 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0074   -0.6326   -0.7477 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2869   -1.0261   -1.1219 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5943   -0.5672    0.5675 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2920   -0.1627    0.8741 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4141    0.1703   -0.0901 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1023    0.5736    0.2969 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7423    0.7200   -0.8161 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0244    0.7819   -0.3379 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0293    0.0825   -1.2224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2834    0.2261   -0.6148 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0615    0.1305    1.0129 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0215   -0.8538    1.1200 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6464   -0.4562    1.0984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2181   -0.5722    2.3859 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6344   -1.6347    0.3935 F   0  0  0  0  0  0  0  0  0  0  0  0
    6.0813   -0.4000   -1.1480 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3066   -0.8363    1.3282 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9937   -0.1197    1.9035 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0970    1.5469    0.8424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3321    1.8609   -0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8253   -1.0150   -1.2620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0796    0.4919   -2.2327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3945    1.1306   -0.2188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1366    0.8931    1.8074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6940   -0.5525    1.7901 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
  8  2  1  0
 16  9  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
  9 22  1  1
 11 23  1  1
 12 24  1  0
 12 25  1  0
 13 26  1  0
 14 27  1  1
 15 28  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2',2'-DFdU	MeSH
2',2'-Difluoro-2'-deoxyuridine	MeSH
2',2'-Difluorodeoxyuridine	MeSH

Chemical Formula

C₉H₁₀F₂N₂O₅

Average Molecular Weight

264.1829

Monoisotopic Molecular Weight

264.05577785

IUPAC Name

1-[(2S,4R,5S)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,2-dihydropyrimidin-2-one

Traditional Name

1-[(2S,4R,5S)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one

CAS Registry Number

Not Available

SMILES

OC[C@@H]1O[C@H](N2C=CC(O)=NC2=O)C(F)(F)[C@@H]1O

InChI Identifier

InChI=1S/C9H10F2N2O5/c10-9(11)6(16)4(3-14)18-7(9)13-2-1-5(15)12-8(13)17/h1-2,4,6-7,14,16H,3H2,(H,12,15,17)/t4-,6+,7-/m0/s1

InChI Key

FIRDBEQIJQERSE-JHYUDYDFSA-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
Tetrahydrofuran
Heteroaromatic compound
Vinylogous amide
Fluorohydrin
Halohydrin
Lactam
Secondary alcohol
Urea
Azacycle
Organoheterocyclic compound
Oxacycle
Organic oxide
Organic oxygen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organofluoride
Organohalogen compound
Alkyl halide
Organic nitrogen compound
Alkyl fluoride
Hydrocarbon derivative
Alcohol
Organopnictogen 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 (HMDB: HMDB0060727)

Organ

Kidney (HMDB: HMDB0060727)
Liver (HMDB: HMDB0060727)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060727)

Cellular substructure

Cytoplasm (HMDB: HMDB0060727)

Source

Endogenous

Endogenous (HMDB: HMDB0060727)

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
Water Solubility	28.1 g/L	ALOGPS
logP	0.27	ALOGPS
logP	-0.72	ChemAxon
logS	-0.97	ALOGPS
pKa (Strongest Acidic)	7.31	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	102.59 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	51.59 m³·mol⁻¹	ChemAxon
Polarizability	21.24 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]+	154.269	30932474
DeepCCS	[M-H]-	151.873	30932474
DeepCCS	[M-2H]-	186.476	30932474
DeepCCS	[M+Na]+	161.232	30932474
AllCCS	[M+H]+	157.8	32859911
AllCCS	[M+H-H2O]+	154.1	32859911
AllCCS	[M+NH4]+	161.2	32859911
AllCCS	[M+Na]+	162.2	32859911
AllCCS	[M-H]-	152.9	32859911
AllCCS	[M+Na-2H]-	152.8	32859911
AllCCS	[M+HCOO]-	152.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2',2'-Difluorodeoxyuridine	OC[C@@H]1O[C@H](N2C=CC(O)=NC2=O)C(F)(F)[C@@H]1O	2739.4	Standard polar	33892256
2',2'-Difluorodeoxyuridine	OC[C@@H]1O[C@H](N2C=CC(O)=NC2=O)C(F)(F)[C@@H]1O	1924.5	Standard non polar	33892256
2',2'-Difluorodeoxyuridine	OC[C@@H]1O[C@H](N2C=CC(O)=NC2=O)C(F)(F)[C@@H]1O	2230.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2',2'-Difluorodeoxyuridine,1TMS,isomer #1	C[Si](C)(C)OC[C@@H]1O[C@H](N2C=CC(O)=NC2=O)C(F)(F)[C@@H]1O	2110.2	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,1TMS,isomer #2	C[Si](C)(C)OC1=NC(=O)N([C@H]2O[C@@H](CO)[C@@H](O)C2(F)F)C=C1	2046.6	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,1TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@H](CO)O[C@H](N2C=CC(O)=NC2=O)C1(F)F	2102.5	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,2TMS,isomer #1	C[Si](C)(C)OC[C@@H]1O[C@H](N2C=CC(O[Si](C)(C)C)=NC2=O)C(F)(F)[C@@H]1O	2070.7	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,2TMS,isomer #2	C[Si](C)(C)OC[C@@H]1O[C@H](N2C=CC(O)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C	2102.0	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,2TMS,isomer #3	C[Si](C)(C)OC1=NC(=O)N([C@H]2O[C@@H](CO)[C@@H](O[Si](C)(C)C)C2(F)F)C=C1	2068.6	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,3TMS,isomer #1	C[Si](C)(C)OC[C@@H]1O[C@H](N2C=CC(O[Si](C)(C)C)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C	2105.9	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](N2C=CC(O)=NC2=O)C(F)(F)[C@@H]1O	2315.5	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=NC(=O)N([C@H]2O[C@@H](CO)[C@@H](O)C2(F)F)C=C1	2278.5	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](CO)O[C@H](N2C=CC(O)=NC2=O)C1(F)F	2324.7	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](N2C=CC(O[Si](C)(C)C(C)(C)C)=NC2=O)C(F)(F)[C@@H]1O	2514.5	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](N2C=CC(O)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C(C)(C)C	2516.4	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1=NC(=O)N([C@H]2O[C@@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)C2(F)F)C=C1	2488.8	Semi standard non polar	33892256
2',2'-Difluorodeoxyuridine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](N2C=CC(O[Si](C)(C)C(C)(C)C)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C(C)(C)C	2730.7	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 - 2',2'-Difluorodeoxyuridine GC-MS (Non-derivatized) - 70eV, Positive	splash10-004l-9210000000-669089dd9a3c33337c08	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2',2'-Difluorodeoxyuridine GC-MS (3 TMS) - 70eV, Positive	splash10-0fsr-2930100000-673b959e84f22ec738a6	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2',2'-Difluorodeoxyuridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2',2'-Difluorodeoxyuridine 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 - 2',2'-Difluorodeoxyuridine 10V, Positive-QTOF	splash10-03di-0900000000-eb08d1680db35c0793f7	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2',2'-Difluorodeoxyuridine 20V, Positive-QTOF	splash10-03di-7900000000-fb7cdeb30a1ffba66c61	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2',2'-Difluorodeoxyuridine 40V, Positive-QTOF	splash10-01xc-9100000000-24ce107de806149aaff0	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2',2'-Difluorodeoxyuridine 10V, Negative-QTOF	splash10-03dl-8890000000-55b9c4ea0fcf6911fba9	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2',2'-Difluorodeoxyuridine 20V, Negative-QTOF	splash10-01ox-9740000000-7f2210f4b2e827773076	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2',2'-Difluorodeoxyuridine 40V, Negative-QTOF	splash10-0006-9000000000-247de26426a920ac06a1	2017-10-06	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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, 900 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

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

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

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

92021386

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

Not Available

Showing metabocard for 2',2'-Difluorodeoxyuridine (HMDB0060727)

MOL for HMDB0060727 (2',2'-Difluorodeoxyuridine)

3D MOL for HMDB0060727 (2',2'-Difluorodeoxyuridine)

3D SDF for HMDB0060727 (2',2'-Difluorodeoxyuridine)

3D-SDF for HMDB0060727 (2',2'-Difluorodeoxyuridine)

PDB for HMDB0060727 (2',2'-Difluorodeoxyuridine)

3D PDB for HMDB0060727 (2',2'-Difluorodeoxyuridine)

SMILES for HMDB0060727 (2',2'-Difluorodeoxyuridine)

INCHI for HMDB0060727 (2',2'-Difluorodeoxyuridine)

Structure for HMDB0060727 (2',2'-Difluorodeoxyuridine)

3D Structure for HMDB0060727 (2',2'-Difluorodeoxyuridine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra