Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 18:59:13 UTC

Update Date

2021-09-26 23:14:29 UTC

HMDB ID

HMDB0257883

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-DFCR (Deoxy-5-fluorocytidine)

Description

2-(5-fluoro-2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-methyloxolane-3,4-diol 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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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. Based on a literature review very few articles have been published on 2-(5-fluoro-2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-methyloxolane-3,4-diol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-dfcr (deoxy-5-fluorocytidine) is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-DFCR (Deoxy-5-fluorocytidine) is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0257883
     RDKit          3D
5-DFCR (Deoxy-5-fluorocytidine)
 29 30  0  0  0  0  0  0  0  0999 V2000
   -3.5991    0.3726    0.9885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4109    0.6659    0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1988    0.4934    0.7688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3090    0.5553   -0.3252 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0536    0.2986    0.0820 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3830   -0.6802    0.9219 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7265   -0.8511    1.2570 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1243   -1.8252    2.1030 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.7012   -0.0274    0.7336 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0856   -0.1780    1.0582 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3132    0.9487   -0.1127 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0065    1.1016   -0.4278 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7244    2.0347   -1.2238 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8729   -0.4901   -1.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5055   -0.3739   -2.5467 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3757   -0.1970   -1.1231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0182   -1.3969   -0.9840 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4866    0.3137    0.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4720   -0.5358    1.5982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7523    1.2491    1.6464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4812    1.7357   -0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4299    1.5659   -0.7484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6289   -1.3335    1.3398 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5192    0.1928    1.9220 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6815   -0.6865    0.3886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6484   -1.5005   -0.7971 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2936    0.1765   -2.6596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6971    0.3941   -2.0014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9837   -1.3488   -0.8707 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  0
  4 22  1  0
  6 23  1  0
 10 24  1  0
 10 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
M  END


  Mrv1652309112120592D          

 17 18  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323   -4.5956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884   -3.7557    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3390   -2.3346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6377   -5.1768    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0032   -5.3493    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
  7 12  1  0  0  0  0
 12 13  2  0  0  0  0
 10 14  1  0  0  0  0
  9 15  1  0  0  0  0
  4 16  1  0  0  0  0
  3 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0257883

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1OC(C(O)C1O)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)

> <INCHI_KEY>
YSNABXSEHNLERR-UHFFFAOYSA-N

> <FORMULA>
C9H12FN3O4

> <MOLECULAR_WEIGHT>
245.21

> <EXACT_MASS>
245.081184041

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.88912026375002

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-(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>
108.38000000000001

> <JCHEM_REFRACTIVITY>
53.20399999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.16e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-amino-1-(3,4-dihydroxy-5-methyloxolan-2-yl)-5-fluoropyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0257883
     RDKit          3D
5-DFCR (Deoxy-5-fluorocytidine)
 29 30  0  0  0  0  0  0  0  0999 V2000
   -3.5991    0.3726    0.9885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4109    0.6659    0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1988    0.4934    0.7688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3090    0.5553   -0.3252 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0536    0.2986    0.0820 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3830   -0.6802    0.9219 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7265   -0.8511    1.2570 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1243   -1.8252    2.1030 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.7012   -0.0274    0.7336 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0856   -0.1780    1.0582 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3132    0.9487   -0.1127 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0065    1.1016   -0.4278 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7244    2.0347   -1.2238 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8729   -0.4901   -1.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5055   -0.3739   -2.5467 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3757   -0.1970   -1.1231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0182   -1.3969   -0.9840 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4866    0.3137    0.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4720   -0.5358    1.5982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7523    1.2491    1.6464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4812    1.7357   -0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4299    1.5659   -0.7484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6289   -1.3335    1.3398 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5192    0.1928    1.9220 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6815   -0.6865    0.3886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6484   -1.5005   -0.7971 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2936    0.1765   -2.6596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6971    0.3941   -2.0014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9837   -1.3488   -0.8707 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  0
  4 22  1  0
  6 23  1  0
 10 24  1  0
 10 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.088  -3.215   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -0.342  -5.926   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.285  -7.333   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.620  -8.578   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.152  -8.417   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -2.778  -7.011   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -1.873  -5.765   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -2.499  -4.358   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      -3.057  -9.663   0.000  0.00  0.00           N+0
HETATM   15  F   UNK     0       0.006  -9.985   0.000  0.00  0.00           F+0
HETATM   16  O   UNK     0       3.009  -5.926   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.044  -2.739   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4   17                                                  
CONECT    4    3    5   16                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    2                                                       
CONECT    7    5    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   15                                                  
CONECT   10    9   11   14                                                  
CONECT   11   10   12                                                       
CONECT   12   11    7   13                                                  
CONECT   13   12                                                            
CONECT   14   10                                                            
CONECT   15    9                                                            
CONECT   16    4                                                            
CONECT   17    3                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0257883
HETATM    1  C1  UNL     1      -3.599   0.373   0.988  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.411   0.666   0.111  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.199   0.493   0.769  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.309   0.555  -0.325  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.054   0.299   0.082  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.383  -0.680   0.922  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.726  -0.851   1.257  1.00  0.00           C  
HETATM    8  F1  UNL     1       3.124  -1.825   2.103  1.00  0.00           F  
HETATM    9  C6  UNL     1       3.701  -0.027   0.734  1.00  0.00           C  
HETATM   10  N2  UNL     1       5.086  -0.178   1.058  1.00  0.00           N  
HETATM   11  N3  UNL     1       3.313   0.949  -0.113  1.00  0.00           N  
HETATM   12  C7  UNL     1       2.006   1.102  -0.428  1.00  0.00           C  
HETATM   13  O2  UNL     1       1.724   2.035  -1.224  1.00  0.00           O  
HETATM   14  C8  UNL     1      -0.873  -0.490  -1.231  1.00  0.00           C  
HETATM   15  O3  UNL     1      -0.505  -0.374  -2.547  1.00  0.00           O  
HETATM   16  C9  UNL     1      -2.376  -0.197  -1.123  1.00  0.00           C  
HETATM   17  O4  UNL     1      -3.018  -1.397  -0.984  1.00  0.00           O  
HETATM   18  H1  UNL     1      -4.487   0.314   0.314  1.00  0.00           H  
HETATM   19  H2  UNL     1      -3.472  -0.536   1.598  1.00  0.00           H  
HETATM   20  H3  UNL     1      -3.752   1.249   1.646  1.00  0.00           H  
HETATM   21  H4  UNL     1      -2.481   1.736  -0.181  1.00  0.00           H  
HETATM   22  H5  UNL     1      -0.430   1.566  -0.748  1.00  0.00           H  
HETATM   23  H6  UNL     1       0.629  -1.334   1.340  1.00  0.00           H  
HETATM   24  H7  UNL     1       5.519   0.193   1.922  1.00  0.00           H  
HETATM   25  H8  UNL     1       5.681  -0.686   0.389  1.00  0.00           H  
HETATM   26  H9  UNL     1      -0.648  -1.501  -0.797  1.00  0.00           H  
HETATM   27  H10 UNL     1       0.294   0.176  -2.660  1.00  0.00           H  
HETATM   28  H11 UNL     1      -2.697   0.394  -2.001  1.00  0.00           H  
HETATM   29  H12 UNL     1      -3.984  -1.349  -0.871  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   25
CONECT   11   12
CONECT   12   13   13
CONECT   14   15   16   26
CONECT   15   27
CONECT   16   17   28
CONECT   17   29
END

HMDB0257883
     RDKit          3D
5-DFCR (Deoxy-5-fluorocytidine)
 29 30  0  0  0  0  0  0  0  0999 V2000
   -3.5991    0.3726    0.9885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4109    0.6659    0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1988    0.4934    0.7688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3090    0.5553   -0.3252 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0536    0.2986    0.0820 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3830   -0.6802    0.9219 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7265   -0.8511    1.2570 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1243   -1.8252    2.1030 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.7012   -0.0274    0.7336 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0856   -0.1780    1.0582 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3132    0.9487   -0.1127 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0065    1.1016   -0.4278 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7244    2.0347   -1.2238 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8729   -0.4901   -1.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5055   -0.3739   -2.5467 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3757   -0.1970   -1.1231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0182   -1.3969   -0.9840 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4866    0.3137    0.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4720   -0.5358    1.5982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7523    1.2491    1.6464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4812    1.7357   -0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4299    1.5659   -0.7484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6289   -1.3335    1.3398 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5192    0.1928    1.9220 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6815   -0.6865    0.3886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6484   -1.5005   -0.7971 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2936    0.1765   -2.6596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6971    0.3941   -2.0014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9837   -1.3488   -0.8707 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  0
  4 22  1  0
  6 23  1  0
 10 24  1  0
 10 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₉H₁₂FN₃O₄

Average Molecular Weight

245.21

Monoisotopic Molecular Weight

245.081184041

IUPAC Name

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

Traditional Name

4-amino-1-(3,4-dihydroxy-5-methyloxolan-2-yl)-5-fluoropyrimidin-2-one

CAS Registry Number

Not Available

SMILES

CC1OC(C(O)C1O)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)

InChI Key

YSNABXSEHNLERR-UHFFFAOYSA-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
Primary aromatic amine
Heteroaromatic compound
Oxolane
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

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.1	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	21.89 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]+	151.983	30932474
DeepCCS	[M-H]-	149.625	30932474
DeepCCS	[M-2H]-	182.787	30932474
DeepCCS	[M+Na]+	158.076	30932474
AllCCS	[M+H]+	155.4	32859911
AllCCS	[M+H-H2O]+	151.6	32859911
AllCCS	[M+NH4]+	159.0	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 Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-DFCR (Deoxy-5-fluorocytidine)	CC1OC(C(O)C1O)N1C=C(F)C(N)=NC1=O	3487.3	Standard polar	33892256
5-DFCR (Deoxy-5-fluorocytidine)	CC1OC(C(O)C1O)N1C=C(F)C(N)=NC1=O	1966.0	Standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine)	CC1OC(C(O)C1O)N1C=C(F)C(N)=NC1=O	2190.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-DFCR (Deoxy-5-fluorocytidine),3TMS,isomer #1	CC1OC(N2C=C(F)C(N[Si](C)(C)C)=NC2=O)C(O[Si](C)(C)C)C1O[Si](C)(C)C	2279.4	Semi standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TMS,isomer #1	CC1OC(N2C=C(F)C(N[Si](C)(C)C)=NC2=O)C(O[Si](C)(C)C)C1O[Si](C)(C)C	2090.6	Standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TMS,isomer #1	CC1OC(N2C=C(F)C(N[Si](C)(C)C)=NC2=O)C(O[Si](C)(C)C)C1O[Si](C)(C)C	2581.1	Standard polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TMS,isomer #2	CC1OC(N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(O[Si](C)(C)C)C1O	2270.4	Semi standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TMS,isomer #2	CC1OC(N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(O[Si](C)(C)C)C1O	2268.3	Standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TMS,isomer #2	CC1OC(N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(O[Si](C)(C)C)C1O	2718.2	Standard polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TMS,isomer #3	CC1OC(N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(O)C1O[Si](C)(C)C	2297.8	Semi standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TMS,isomer #3	CC1OC(N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(O)C1O[Si](C)(C)C	2272.4	Standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TMS,isomer #3	CC1OC(N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(O)C1O[Si](C)(C)C	2657.7	Standard polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),4TMS,isomer #1	CC1OC(N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(O[Si](C)(C)C)C1O[Si](C)(C)C	2292.1	Semi standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),4TMS,isomer #1	CC1OC(N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(O[Si](C)(C)C)C1O[Si](C)(C)C	2316.9	Standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),4TMS,isomer #1	CC1OC(N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(O[Si](C)(C)C)C1O[Si](C)(C)C	2390.6	Standard polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TBDMS,isomer #1	CC1OC(N2C=C(F)C(N[Si](C)(C)C(C)(C)C)=NC2=O)C(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	2899.9	Semi standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TBDMS,isomer #1	CC1OC(N2C=C(F)C(N[Si](C)(C)C(C)(C)C)=NC2=O)C(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	2661.5	Standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TBDMS,isomer #1	CC1OC(N2C=C(F)C(N[Si](C)(C)C(C)(C)C)=NC2=O)C(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	2909.6	Standard polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TBDMS,isomer #2	CC1OC(N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(O[Si](C)(C)C(C)(C)C)C1O	2916.6	Semi standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TBDMS,isomer #2	CC1OC(N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(O[Si](C)(C)C(C)(C)C)C1O	2863.8	Standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TBDMS,isomer #2	CC1OC(N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(O[Si](C)(C)C(C)(C)C)C1O	2965.2	Standard polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TBDMS,isomer #3	CC1OC(N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(O)C1O[Si](C)(C)C(C)(C)C	2933.6	Semi standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TBDMS,isomer #3	CC1OC(N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(O)C1O[Si](C)(C)C(C)(C)C	2868.1	Standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),3TBDMS,isomer #3	CC1OC(N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(O)C1O[Si](C)(C)C(C)(C)C	2911.6	Standard polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),4TBDMS,isomer #1	CC1OC(N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	3116.3	Semi standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),4TBDMS,isomer #1	CC1OC(N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	3050.9	Standard non polar	33892256
5-DFCR (Deoxy-5-fluorocytidine),4TBDMS,isomer #1	CC1OC(N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	2799.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (Non-derivatized) - 70eV, Positive	splash10-056u-9210000000-6dc94aa1eff337ff92a0	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-DFCR (Deoxy-5-fluorocytidine) GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

11222067

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12798017

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 5-DFCR (Deoxy-5-fluorocytidine) (HMDB0257883)

MOL for HMDB0257883 (5-DFCR (Deoxy-5-fluorocytidine))

3D MOL for HMDB0257883 (5-DFCR (Deoxy-5-fluorocytidine))

3D SDF for HMDB0257883 (5-DFCR (Deoxy-5-fluorocytidine))

3D-SDF for HMDB0257883 (5-DFCR (Deoxy-5-fluorocytidine))

PDB for HMDB0257883 (5-DFCR (Deoxy-5-fluorocytidine))

3D PDB for HMDB0257883 (5-DFCR (Deoxy-5-fluorocytidine))

SMILES for HMDB0257883 (5-DFCR (Deoxy-5-fluorocytidine))

INCHI for HMDB0257883 (5-DFCR (Deoxy-5-fluorocytidine))

Structure for HMDB0257883 (5-DFCR (Deoxy-5-fluorocytidine))

3D Structure for HMDB0257883 (5-DFCR (Deoxy-5-fluorocytidine))

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra