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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-17 01:00:16 UTC

Update Date

2021-09-14 15:18:57 UTC

HMDB ID

HMDB0060405

Secondary Accession Numbers

HMDB60405

Metabolite Identification

Common Name

5'-Deoxy-5-fluorocytidine

Description

5'-Deoxy-5-fluorocytidine 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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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-fluorocytidine is an extremely weak basic (essentially neutral) compound (based on its pKa). 5'-Deoxy-5-fluorocytidine exists in all living organisms, ranging from bacteria to humans. Capecitabine (Xeloda, Roche) is an orally-administered chemotherapeutic agent used in the treatment of metastatic breast and colorectal cancers. 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. 5'-Deoxy-5-fluorocytidine is a metabolite of capecitabine.

Structure

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

HMDB0060405
     RDKit          3D
5'-Deoxy-5-fluorocytidine
 29 30  0  0  0  0  0  0  0  0999 V2000
   -3.4202   -1.1097   -0.5148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3106   -0.3322    0.0854 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1092   -1.0349    0.1804 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2552   -0.0629    0.6635 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1378   -0.3628    0.4079 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0200    0.6201    0.7178 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3700    0.4743    0.5284 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2840    1.4322    0.8251 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.8145   -0.7267    0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0753   -0.9273   -0.2006 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9153   -1.6725   -0.2910 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5807   -1.5108   -0.0967 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6712   -2.4956   -0.4047 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5747    1.2215   -0.0744 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8339    2.2201    0.8612 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8604    0.8309   -0.8085 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7818    1.8423   -0.8353 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9231   -0.4545   -1.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1512   -2.0808   -0.9255 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2107   -1.2497    0.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5921    0.1107    1.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4580    0.0294    1.7648 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6814    1.5705    1.1329 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7534   -0.1742    0.0366 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7650   -2.9827   -1.2944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1862    1.4912   -0.8081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7889    2.2964    1.0807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5966    0.4009   -1.7760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3882    2.6365   -1.2286 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  2  3
  9 11  1  0
 11 12  2  0
 12 13  1  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  1
  4 22  1  1
  6 23  1  0
 10 24  1  0
 13 25  1  0
 14 26  1  6
 15 27  1  0
 16 28  1  6
 17 29  1  0
M  END

 
  Mrv1652303121903572D          

 17 18  0  0  1  0            999 V2000
   25.3205  -21.1676    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   25.9849  -20.0161    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.6522  -20.6919    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.0675  -21.9528    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   25.2752  -19.5969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.7062  -19.5969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9915  -21.1676    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   24.2407  -21.9528    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   25.2752  -18.7663    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.5616  -20.0047    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.7062  -18.7663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2099  -20.9108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.7537  -22.6174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.9849  -18.3547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.4159  -18.3547    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
   25.9849  -17.5354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   25.5588  -22.6271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  2  0  0  0  0
  7 12  1  1  0  0  0
  8 13  1  6  0  0  0
  9 14  2  0  0  0  0
 11 15  1  0  0  0  0
 14 16  1  0  0  0  0
  7  8  1  0  0  0  0
 11 14  1  0  0  0  0
  4 17  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0060405

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H12FN3O4/c1-3-5(14)6(15)8(17-3)13-2-4(10)7(11)12-9(13)16/h2-3,5-6,8,14-15H,1H3,(H2,11,12,16)/t3-,5-,6-,8-/m1/s1

> <INCHI_KEY>
YSNABXSEHNLERR-ZIYNGMLESA-N

> <FORMULA>
C9H12FN3O4

> <MOLECULAR_WEIGHT>
245.2077

> <EXACT_MASS>
245.081184092

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.561331229073716

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.11

> <JCHEM_LOGP>
-1.5511644076666666

> <ALOGPS_LOGS>
-1.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.086021273977238

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.587268795173568

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6273746204866413

> <JCHEM_POLAR_SURFACE_AREA>
108.38

> <JCHEM_REFRACTIVITY>
53.204

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.16e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5'-deoxy-5-fluorocytidine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060405
     RDKit          3D
5'-Deoxy-5-fluorocytidine
 29 30  0  0  0  0  0  0  0  0999 V2000
   -3.4202   -1.1097   -0.5148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3106   -0.3322    0.0854 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1092   -1.0349    0.1804 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2552   -0.0629    0.6635 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1378   -0.3628    0.4079 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0200    0.6201    0.7178 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3700    0.4743    0.5284 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2840    1.4322    0.8251 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.8145   -0.7267    0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0753   -0.9273   -0.2006 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9153   -1.6725   -0.2910 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5807   -1.5108   -0.0967 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6712   -2.4956   -0.4047 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5747    1.2215   -0.0744 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8339    2.2201    0.8612 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8604    0.8309   -0.8085 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7818    1.8423   -0.8353 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9231   -0.4545   -1.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1512   -2.0808   -0.9255 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2107   -1.2497    0.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5921    0.1107    1.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4580    0.0294    1.7648 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6814    1.5705    1.1329 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7534   -0.1742    0.0366 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7650   -2.9827   -1.2944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1862    1.4912   -0.8081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7889    2.2964    1.0807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5966    0.4009   -1.7760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3882    2.6365   -1.2286 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  2  3
  9 11  1  0
 11 12  2  0
 12 13  1  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  1
  4 22  1  1
  6 23  1  0
 10 24  1  0
 13 25  1  0
 14 26  1  6
 15 27  1  0
 16 28  1  6
 17 29  1  0
M  END

HEADER    PROTEIN                                 12-MAR-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-MAR-19         0                                  
HETATM    1  C   UNK     0      47.265 -39.513   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      48.505 -37.363   0.000  0.00  0.00           N+0
HETATM    3  O   UNK     0      46.017 -38.625   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      46.793 -40.979   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      47.180 -36.581   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      49.852 -36.581   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      44.784 -39.513   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      45.249 -40.979   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      47.180 -35.030   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      45.848 -37.342   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      49.852 -35.030   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      43.325 -39.034   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      44.340 -42.219   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      48.505 -34.262   0.000  0.00  0.00           C+0
HETATM   15  F   UNK     0      51.176 -34.262   0.000  0.00  0.00           F+0
HETATM   16  N   UNK     0      48.505 -32.733   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      47.710 -42.237   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8   17                                                  
CONECT    5    2    9   10                                                  
CONECT    6    2   11                                                       
CONECT    7    3   12    8                                                  
CONECT    8    4   13    7                                                  
CONECT    9    5   14                                                       
CONECT   10    5                                                            
CONECT   11    6   15   14                                                  
CONECT   12    7                                                            
CONECT   13    8                                                            
CONECT   14    9   16   11                                                  
CONECT   15   11                                                            
CONECT   16   14                                                            
CONECT   17    4                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0060405
HETATM    1  C1  UNL     1      -3.420  -1.110  -0.515  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.311  -0.332   0.085  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.109  -1.035   0.180  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.255  -0.063   0.664  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.138  -0.363   0.408  1.00  0.00           N  
HETATM    6  C4  UNL     1       2.020   0.620   0.718  1.00  0.00           C  
HETATM    7  C5  UNL     1       3.370   0.474   0.528  1.00  0.00           C  
HETATM    8  F1  UNL     1       4.284   1.432   0.825  1.00  0.00           F  
HETATM    9  C6  UNL     1       3.815  -0.727   0.002  1.00  0.00           C  
HETATM   10  N2  UNL     1       5.075  -0.927  -0.201  1.00  0.00           N  
HETATM   11  N3  UNL     1       2.915  -1.672  -0.291  1.00  0.00           N  
HETATM   12  C7  UNL     1       1.581  -1.511  -0.097  1.00  0.00           C  
HETATM   13  O2  UNL     1       0.671  -2.496  -0.405  1.00  0.00           O  
HETATM   14  C8  UNL     1      -0.575   1.221  -0.074  1.00  0.00           C  
HETATM   15  O3  UNL     1      -0.834   2.220   0.861  1.00  0.00           O  
HETATM   16  C9  UNL     1      -1.860   0.831  -0.809  1.00  0.00           C  
HETATM   17  O4  UNL     1      -2.782   1.842  -0.835  1.00  0.00           O  
HETATM   18  H1  UNL     1      -3.923  -0.454  -1.281  1.00  0.00           H  
HETATM   19  H2  UNL     1      -3.151  -2.081  -0.925  1.00  0.00           H  
HETATM   20  H3  UNL     1      -4.211  -1.250   0.277  1.00  0.00           H  
HETATM   21  H4  UNL     1      -2.592   0.111   1.079  1.00  0.00           H  
HETATM   22  H5  UNL     1      -0.458   0.029   1.765  1.00  0.00           H  
HETATM   23  H6  UNL     1       1.681   1.571   1.133  1.00  0.00           H  
HETATM   24  H7  UNL     1       5.753  -0.174   0.037  1.00  0.00           H  
HETATM   25  H8  UNL     1       0.765  -2.983  -1.294  1.00  0.00           H  
HETATM   26  H9  UNL     1       0.186   1.491  -0.808  1.00  0.00           H  
HETATM   27  H10 UNL     1      -1.789   2.296   1.081  1.00  0.00           H  
HETATM   28  H11 UNL     1      -1.597   0.401  -1.776  1.00  0.00           H  
HETATM   29  H12 UNL     1      -2.388   2.637  -1.229  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   10   11
CONECT   10   24
CONECT   11   12   12
CONECT   12   13
CONECT   13   25
CONECT   14   15   16   26
CONECT   15   27
CONECT   16   17   28
CONECT   17   29
END

HMDB0060405
     RDKit          3D
5'-Deoxy-5-fluorocytidine
 29 30  0  0  0  0  0  0  0  0999 V2000
   -3.4202   -1.1097   -0.5148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3106   -0.3322    0.0854 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1092   -1.0349    0.1804 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2552   -0.0629    0.6635 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1378   -0.3628    0.4079 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0200    0.6201    0.7178 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3700    0.4743    0.5284 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2840    1.4322    0.8251 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.8145   -0.7267    0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0753   -0.9273   -0.2006 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9153   -1.6725   -0.2910 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5807   -1.5108   -0.0967 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6712   -2.4956   -0.4047 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5747    1.2215   -0.0744 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8339    2.2201    0.8612 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8604    0.8309   -0.8085 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7818    1.8423   -0.8353 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9231   -0.4545   -1.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1512   -2.0808   -0.9255 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2107   -1.2497    0.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5921    0.1107    1.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4580    0.0294    1.7648 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6814    1.5705    1.1329 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7534   -0.1742    0.0366 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7650   -2.9827   -1.2944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1862    1.4912   -0.8081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7889    2.2964    1.0807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5966    0.4009   -1.7760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3882    2.6365   -1.2286 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  2  3
  9 11  1  0
 11 12  2  0
 12 13  1  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  1
  4 22  1  1
  6 23  1  0
 10 24  1  0
 13 25  1  0
 14 26  1  6
 15 27  1  0
 16 28  1  6
 17 29  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₉H₁₂FN₃O₄

Average Molecular Weight

245.2077

Monoisotopic Molecular Weight

245.081184092

IUPAC Name

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

Traditional Name

5'-deoxy-5-fluorocytidine

CAS Registry Number

Not Available

SMILES

C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(=N)N=C1O

InChI Identifier

InChI=1S/C9H12FN3O4/c1-3-5(14)6(15)8(17-3)13-2-4(10)7(11)12-9(13)16/h2-3,5-6,8,14-15H,1H3,(H2,11,12,16)/t3-,5-,6-,8-/m1/s1

InChI Key

YSNABXSEHNLERR-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
Aminopyrimidine
Halopyrimidine
Pyrimidone
Aryl fluoride
Aryl halide
Hydropyrimidine
Imidolactam
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
1,2-diol
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organofluoride
Organohalogen compound
Amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Primary amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

N-glycosyl compound (CHEBI:80627 )

Ontology

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	0.64 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-1.6	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	12.59	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	108.38 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	53.2 m³·mol⁻¹	ChemAxon
Polarizability	21.56 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]+	152.058	30932474
DeepCCS	[M-H]-	149.662	30932474
DeepCCS	[M-2H]-	183.78	30932474
DeepCCS	[M+Na]+	158.471	30932474
AllCCS	[M+H]+	155.4	32859911
AllCCS	[M+H-H2O]+	151.6	32859911
AllCCS	[M+NH4]+	158.9	32859911
AllCCS	[M+Na]+	160.0	32859911
AllCCS	[M-H]-	151.7	32859911
AllCCS	[M+Na-2H]-	151.7	32859911
AllCCS	[M+HCOO]-	151.8	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.	2.12 minutes	32390414
Predicted by Siyang on May 30, 2022	9.5219 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.14 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	626.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	255.6 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	56.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	161.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	50.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	288.1 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	251.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	325.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	601.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	139.4 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	786.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	154.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	174.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	482.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	450.9 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	229.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5'-Deoxy-5-fluorocytidine	C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(=N)N=C1O	3734.1	Standard polar	33892256
5'-Deoxy-5-fluorocytidine	C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(=N)N=C1O	2142.8	Standard non polar	33892256
5'-Deoxy-5-fluorocytidine	C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(=N)N=C1O	2181.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5'-Deoxy-5-fluorocytidine,1TMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O)[C@H](O[Si](C)(C)C)[C@@H]1O	2103.9	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,1TMS,isomer #2	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O)[C@H](O)[C@@H]1O[Si](C)(C)C	2132.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,1TMS,isomer #3	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O[Si](C)(C)C)[C@H](O)[C@@H]1O	2100.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,1TMS,isomer #4	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C)N=C2O)[C@H](O)[C@@H]1O	2058.4	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O	2156.9	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TMS,isomer #2	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2143.7	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TMS,isomer #3	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C)N=C2O)[C@H](O[Si](C)(C)C)[C@@H]1O	2092.4	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TMS,isomer #4	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O[Si](C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C	2175.4	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TMS,isomer #5	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C)N=C2O)[C@H](O)[C@@H]1O[Si](C)(C)C	2101.7	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TMS,isomer #6	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C)N=C2O[Si](C)(C)C)[C@H](O)[C@@H]1O	2094.7	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,3TMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2214.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,3TMS,isomer #2	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C)N=C2O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O	2132.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,3TMS,isomer #3	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C)N=C2O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2120.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,3TMS,isomer #4	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C)N=C2O[Si](C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C	2138.0	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,4TMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C)N=C2O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2183.1	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,4TMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C)N=C2O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2206.8	Standard non polar	33892256
5'-Deoxy-5-fluorocytidine,4TMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C)N=C2O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2525.0	Standard polar	33892256
5'-Deoxy-5-fluorocytidine,1TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2363.9	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,1TBDMS,isomer #2	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2380.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,1TBDMS,isomer #3	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O	2355.9	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,1TBDMS,isomer #4	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C(C)(C)C)N=C2O)[C@H](O)[C@@H]1O	2370.2	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2630.0	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TBDMS,isomer #2	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2631.0	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TBDMS,isomer #3	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C(C)(C)C)N=C2O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2596.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TBDMS,isomer #4	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2641.7	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TBDMS,isomer #5	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C(C)(C)C)N=C2O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2604.8	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,2TBDMS,isomer #6	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C(C)(C)C)N=C2O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O	2561.6	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,3TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N)N=C2O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2844.2	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,3TBDMS,isomer #2	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C(C)(C)C)N=C2O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2773.6	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,3TBDMS,isomer #3	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C(C)(C)C)N=C2O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2794.3	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,3TBDMS,isomer #4	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C(C)(C)C)N=C2O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2780.6	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,4TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C(C)(C)C)N=C2O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2961.1	Semi standard non polar	33892256
5'-Deoxy-5-fluorocytidine,4TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C(C)(C)C)N=C2O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2975.0	Standard non polar	33892256
5'-Deoxy-5-fluorocytidine,4TBDMS,isomer #1	C[C@H]1O[C@@H](N2C=C(F)C(=N[Si](C)(C)C(C)(C)C)N=C2O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2910.3	Standard 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-fluorocytidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-056u-9210000000-9e3466f322a71a8faa1f	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Deoxy-5-fluorocytidine GC-MS (3 TMS) - 70eV, Positive	splash10-00n1-6896700000-73f948f97493f63b0877	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Deoxy-5-fluorocytidine 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-fluorocytidine 10V, Positive-QTOF	splash10-001i-0910000000-032e0321a8c4aeee72f0	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 20V, Positive-QTOF	splash10-001i-0900000000-ce61dba9f0b0828ec936	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 40V, Positive-QTOF	splash10-0w3c-7900000000-2cd6e57546558d390a81	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 10V, Negative-QTOF	splash10-002f-0890000000-8f685d78656ff605ad37	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 20V, Negative-QTOF	splash10-004i-5930000000-f165a2b6eba7865e3cc9	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 40V, Negative-QTOF	splash10-0006-9300000000-68e982d847d196912136	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 10V, Positive-QTOF	splash10-001j-3910000000-841ae702c35c85b9aa37	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 20V, Positive-QTOF	splash10-001r-7900000000-359ef082095d14b594e0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 40V, Positive-QTOF	splash10-001i-8900000000-0f51da014988487d1c55	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 10V, Negative-QTOF	splash10-002f-0590000000-de6dd0c49dccdbe6d4fd	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 20V, Negative-QTOF	splash10-0f96-6900000000-0b7068a0a35a655bd649	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Deoxy-5-fluorocytidine 40V, Negative-QTOF	splash10-0006-9400000000-251361c3ec0189c629d4	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	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

Not Available

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

C16635

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10037499

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

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. Liver carboxylesterase 1

General function:: Lipid transport and metabolism
Specific function:: Involved in the detoxification of xenobiotics and in the activation of ester and amide prodrugs. Hydrolyzes aromatic and aliphatic esters, but has no catalytic activity toward amides or a fatty acyl-CoA ester. Hydrolyzes the methyl ester group of cocaine to form benzoylecgonine. Catalyzes the transesterification of cocaine to form cocaethylene. Displays fatty acid ethyl ester synthase activity, catalyzing the ethyl esterification of oleic acid to ethyloleate.
Gene Name:: CES1
Uniprot ID:: P23141
Molecular weight:: 62520.62

Reactions

Capecitabine + Water → 5'-Deoxy-5-fluorocytidine + 1-Pentanol + Carbon dioxide	details

Enzyme Details

2. Cocaine esterase

General function:: Lipid transport and metabolism
Specific function:: Involved in the detoxification of xenobiotics and in the activation of ester and amide prodrugs. Shows high catalytic efficiency for hydrolysis of cocaine, 4-methylumbelliferyl acetate, heroin and 6-monoacetylmorphine.
Gene Name:: CES2
Uniprot ID:: O00748
Molecular weight:: 68898.39

Reactions

Capecitabine + Water → 5'-Deoxy-5-fluorocytidine + 1-Pentanol + Carbon dioxide	details

Enzyme Details

3. 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-fluorocytidine (HMDB0060405)

MOL for HMDB0060405 (5'-Deoxy-5-fluorocytidine)

3D MOL for HMDB0060405 (5'-Deoxy-5-fluorocytidine)

3D SDF for HMDB0060405 (5'-Deoxy-5-fluorocytidine)

3D-SDF for HMDB0060405 (5'-Deoxy-5-fluorocytidine)

PDB for HMDB0060405 (5'-Deoxy-5-fluorocytidine)

3D PDB for HMDB0060405 (5'-Deoxy-5-fluorocytidine)

SMILES for HMDB0060405 (5'-Deoxy-5-fluorocytidine)

INCHI for HMDB0060405 (5'-Deoxy-5-fluorocytidine)

Structure for HMDB0060405 (5'-Deoxy-5-fluorocytidine)

3D Structure for HMDB0060405 (5'-Deoxy-5-fluorocytidine)

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

Reactions