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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 09:58:03 UTC

Update Date

2021-09-26 23:04:36 UTC

HMDB ID

HMDB0252181

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-

Description

ACMC-20msgx belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3. Based on a literature review very few articles have been published on ACMC-20msgx. This compound has been identified in human blood as reported by (PMID: 31557052 ). Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- 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

HMDB0252181
     RDKit          3D
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-
 28 29  0  0  0  0  0  0  0  0999 V2000
    4.6705    0.2369    1.2669 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4193    0.2556    0.5958 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2997   -0.0258   -0.7194 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0686    0.0154   -1.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8941   -0.2390   -2.5078 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9910    0.3299   -0.5382 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3234    0.3595   -1.1985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7314   -1.0048   -1.6577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8327   -1.3369   -0.6399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2625   -1.7272    0.5617 F   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4038    0.0541   -0.4355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2517    0.1024    0.8233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6774    1.4009    1.0302 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2949    0.8543   -0.3665 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0720    0.6166    0.7775 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3110    0.5815    1.3684 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4860    0.9429    3.0703 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.8223   -0.1488    2.2229 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5001    0.6329    0.7803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2122    1.0761   -2.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0720   -1.7486   -1.6448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2691   -0.9630   -2.6469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5521   -2.0535   -1.0305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9940    0.3028   -1.3372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6959   -0.3308    1.6572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1643   -0.5161    0.6149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1188    1.4632    1.9232 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1777    0.8695    1.3560 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
  6 15  1  0
 15 16  2  0
 16 17  1  0
 16  2  1  0
 14  7  1  0
  1 18  1  0
  1 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 15 28  1  0
M  END


  Mrv1652309112111582D          

 17 18  0  0  0  0            999 V2000
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  2  0  0  0  0
  9 13  1  0  0  0  0
  8 14  1  0  0  0  0
  3 15  1  0  0  0  0
 15 16  1  0  0  0  0
  2 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0252181

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(=O)N(C=C1Cl)C1CC(F)C(CO)O1

> <INCHI_IDENTIFIER>
InChI=1S/C9H11ClFN3O3/c10-4-2-14(9(16)13-8(4)12)7-1-5(11)6(3-15)17-7/h2,5-7,15H,1,3H2,(H2,12,13,16)

> <INCHI_KEY>
DKTULUNJRRRNTA-UHFFFAOYSA-N

> <FORMULA>
C9H11ClFN3O3

> <MOLECULAR_WEIGHT>
263.65

> <EXACT_MASS>
263.0472971

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
23.073951405049208

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-amino-5-chloro-1-[4-fluoro-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-0.55

> <JCHEM_LOGP>
-0.34500179733333314

> <ALOGPS_LOGS>
-2.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.83457131393343

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.5777085940386

> <JCHEM_PKA_STRONGEST_BASIC>
-2.439082913497968

> <JCHEM_POLAR_SURFACE_AREA>
88.15

> <JCHEM_REFRACTIVITY>
56.133300000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.62e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-amino-5-chloro-1-[4-fluoro-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0252181
     RDKit          3D
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-
 28 29  0  0  0  0  0  0  0  0999 V2000
    4.6705    0.2369    1.2669 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4193    0.2556    0.5958 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2997   -0.0258   -0.7194 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0686    0.0154   -1.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8941   -0.2390   -2.5078 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9910    0.3299   -0.5382 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3234    0.3595   -1.1985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7314   -1.0048   -1.6577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8327   -1.3369   -0.6399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2625   -1.7272    0.5617 F   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4038    0.0541   -0.4355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2517    0.1024    0.8233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6774    1.4009    1.0302 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2949    0.8543   -0.3665 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0720    0.6166    0.7775 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3110    0.5815    1.3684 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4860    0.9429    3.0703 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.8223   -0.1488    2.2229 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5001    0.6329    0.7803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2122    1.0761   -2.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0720   -1.7486   -1.6448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2691   -0.9630   -2.6469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5521   -2.0535   -1.0305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9940    0.3028   -1.3372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6959   -0.3308    1.6572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1643   -0.5161    0.6149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1188    1.4632    1.9232 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1777    0.8695    1.3560 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
  6 15  1  0
 15 16  2  0
 16 17  1  0
 16  2  1  0
 14  7  1  0
  1 18  1  0
  1 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 15 28  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.088  -3.215   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM   14 Cl   UNK     0      -1.334   2.310   0.000  0.00  0.00          Cl+0
HETATM   15  C   UNK     0      -0.342  -5.926   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.285  -7.333   0.000  0.00  0.00           O+0
HETATM   17  F   UNK     0       3.009  -5.926   0.000  0.00  0.00           F+0
CONECT    1    2    5                                                       
CONECT    2    1    3   17                                                  
CONECT    3    2    4   15                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10    6   12                                                  
CONECT   12   11                                                            
CONECT   13    9                                                            
CONECT   14    8                                                            
CONECT   15    3   16                                                       
CONECT   16   15                                                            
CONECT   17    2                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0252181
HETATM    1  N1  UNL     1       4.671   0.237   1.267  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.419   0.256   0.596  1.00  0.00           C  
HETATM    3  N2  UNL     1       3.300  -0.026  -0.719  1.00  0.00           N  
HETATM    4  C2  UNL     1       2.069   0.015  -1.279  1.00  0.00           C  
HETATM    5  O1  UNL     1       1.894  -0.239  -2.508  1.00  0.00           O  
HETATM    6  N3  UNL     1       0.991   0.330  -0.538  1.00  0.00           N  
HETATM    7  C3  UNL     1      -0.323   0.360  -1.199  1.00  0.00           C  
HETATM    8  C4  UNL     1      -0.731  -1.005  -1.658  1.00  0.00           C  
HETATM    9  C5  UNL     1      -1.833  -1.337  -0.640  1.00  0.00           C  
HETATM   10  F1  UNL     1      -1.263  -1.727   0.562  1.00  0.00           F  
HETATM   11  C6  UNL     1      -2.404   0.054  -0.436  1.00  0.00           C  
HETATM   12  C7  UNL     1      -3.252   0.102   0.823  1.00  0.00           C  
HETATM   13  O2  UNL     1      -3.677   1.401   1.030  1.00  0.00           O  
HETATM   14  O3  UNL     1      -1.295   0.854  -0.367  1.00  0.00           O  
HETATM   15  C8  UNL     1       1.072   0.617   0.778  1.00  0.00           C  
HETATM   16  C9  UNL     1       2.311   0.581   1.368  1.00  0.00           C  
HETATM   17 CL1  UNL     1       2.486   0.943   3.070  1.00  0.00          CL  
HETATM   18  H1  UNL     1       4.822  -0.149   2.223  1.00  0.00           H  
HETATM   19  H2  UNL     1       5.500   0.633   0.780  1.00  0.00           H  
HETATM   20  H3  UNL     1      -0.212   1.076  -2.047  1.00  0.00           H  
HETATM   21  H4  UNL     1       0.072  -1.749  -1.645  1.00  0.00           H  
HETATM   22  H5  UNL     1      -1.269  -0.963  -2.647  1.00  0.00           H  
HETATM   23  H6  UNL     1      -2.552  -2.054  -1.031  1.00  0.00           H  
HETATM   24  H7  UNL     1      -2.994   0.303  -1.337  1.00  0.00           H  
HETATM   25  H8  UNL     1      -2.696  -0.331   1.657  1.00  0.00           H  
HETATM   26  H9  UNL     1      -4.164  -0.516   0.615  1.00  0.00           H  
HETATM   27  H10 UNL     1      -4.119   1.463   1.923  1.00  0.00           H  
HETATM   28  H11 UNL     1       0.178   0.869   1.356  1.00  0.00           H  
CONECT    1    2   18   19
CONECT    2    3    3   16
CONECT    3    4
CONECT    4    5    5    6
CONECT    6    7   15
CONECT    7    8   14   20
CONECT    8    9   21   22
CONECT    9   10   11   23
CONECT   11   12   14   24
CONECT   12   13   25   26
CONECT   13   27
CONECT   15   16   16   28
CONECT   16   17
END

HMDB0252181
     RDKit          3D
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-
 28 29  0  0  0  0  0  0  0  0999 V2000
    4.6705    0.2369    1.2669 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4193    0.2556    0.5958 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2997   -0.0258   -0.7194 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0686    0.0154   -1.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8941   -0.2390   -2.5078 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9910    0.3299   -0.5382 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3234    0.3595   -1.1985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7314   -1.0048   -1.6577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8327   -1.3369   -0.6399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2625   -1.7272    0.5617 F   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4038    0.0541   -0.4355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2517    0.1024    0.8233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6774    1.4009    1.0302 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2949    0.8543   -0.3665 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0720    0.6166    0.7775 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3110    0.5815    1.3684 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4860    0.9429    3.0703 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.8223   -0.1488    2.2229 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5001    0.6329    0.7803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2122    1.0761   -2.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0720   -1.7486   -1.6448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2691   -0.9630   -2.6469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5521   -2.0535   -1.0305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9940    0.3028   -1.3372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6959   -0.3308    1.6572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1643   -0.5161    0.6149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1188    1.4632    1.9232 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1777    0.8695    1.3560 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
  6 15  1  0
 15 16  2  0
 16 17  1  0
 16  2  1  0
 14  7  1  0
  1 18  1  0
  1 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 15 28  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₉H₁₁ClFN₃O₃

Average Molecular Weight

263.65

Monoisotopic Molecular Weight

263.0472971

IUPAC Name

4-amino-5-chloro-1-[4-fluoro-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

4-amino-5-chloro-1-[4-fluoro-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1Cl)C1CC(F)C(CO)O1

InChI Identifier

InChI=1S/C9H11ClFN3O3/c10-4-2-14(9(16)13-8(4)12)7-1-5(11)6(3-15)17-7/h2,5-7,15H,1,3H2,(H2,12,13,16)

InChI Key

DKTULUNJRRRNTA-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2',3'-dideoxyribonucleosides

Direct Parent

Pyrimidine 2',3'-dideoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2',3'-dideoxyribonucleoside
Aminopyrimidine
Halopyrimidine
Pyrimidone
Aryl chloride
Aryl halide
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Oxolane
Oxacycle
Organoheterocyclic compound
Azacycle
Primary amine
Alkyl fluoride
Organooxygen compound
Organonitrogen compound
Organofluoride
Organochloride
Organohalogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Amine
Alkyl halide
Primary alcohol
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	-0.55	ALOGPS
logP	-0.35	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	14.58	ChemAxon
pKa (Strongest Basic)	-2.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	88.15 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	56.13 m³·mol⁻¹	ChemAxon
Polarizability	23.07 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	157.122	30932474
DeepCCS	[M-H]-	154.764	30932474
DeepCCS	[M-2H]-	188.421	30932474
DeepCCS	[M+Na]+	163.464	30932474
AllCCS	[M+H]+	156.7	32859911
AllCCS	[M+H-H2O]+	153.1	32859911
AllCCS	[M+NH4]+	160.1	32859911
AllCCS	[M+Na]+	161.1	32859911
AllCCS	[M-H]-	153.9	32859911
AllCCS	[M+Na-2H]-	153.9	32859911
AllCCS	[M+HCOO]-	154.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-	NC1=NC(=O)N(C=C1Cl)C1CC(F)C(CO)O1	3139.1	Standard polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-	NC1=NC(=O)N(C=C1Cl)C1CC(F)C(CO)O1	2098.2	Standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-	NC1=NC(=O)N(C=C1Cl)C1CC(F)C(CO)O1	2329.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CC(F)C(CO[Si](C)(C)C)O2)C=C1Cl	2292.9	Semi standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CC(F)C(CO[Si](C)(C)C)O2)C=C1Cl	2315.9	Standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CC(F)C(CO[Si](C)(C)C)O2)C=C1Cl	2695.8	Standard polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N(C2CC(F)C(CO)O2)C=C1Cl)[Si](C)(C)C	2280.2	Semi standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N(C2CC(F)C(CO)O2)C=C1Cl)[Si](C)(C)C	2426.2	Standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N(C2CC(F)C(CO)O2)C=C1Cl)[Si](C)(C)C	2826.5	Standard polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,3TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=C(Cl)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CC1F	2256.3	Semi standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,3TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=C(Cl)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CC1F	2478.2	Standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,3TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=C(Cl)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CC1F	2465.1	Standard polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CC(F)C(CO[Si](C)(C)C(C)(C)C)O2)C=C1Cl	2727.4	Semi standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CC(F)C(CO[Si](C)(C)C(C)(C)C)O2)C=C1Cl	2775.6	Standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CC(F)C(CO[Si](C)(C)C(C)(C)C)O2)C=C1Cl	2869.2	Standard polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(C2CC(F)C(CO)O2)C=C1Cl)[Si](C)(C)C(C)(C)C	2726.5	Semi standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(C2CC(F)C(CO)O2)C=C1Cl)[Si](C)(C)C(C)(C)C	2865.8	Standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(C2CC(F)C(CO)O2)C=C1Cl)[Si](C)(C)C(C)(C)C	2911.6	Standard polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(Cl)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CC1F	2923.4	Semi standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(Cl)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CC1F	3089.0	Standard non polar	33892256
Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(Cl)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CC1F	2771.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- GC-MS (Non-derivatized) - 70eV, Positive	splash10-003s-9350000000-fd97ae749cd3582918d3	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-04	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 - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- 10V, Positive-QTOF	splash10-0002-0920000000-34064429cba4e8995cf5	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- 20V, Positive-QTOF	splash10-0002-0900000000-f1be57f22d3e65a4a274	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- 40V, Positive-QTOF	splash10-0002-2900000000-1a88229dcf0a0c321456	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- 10V, Negative-QTOF	splash10-03di-0190000000-1a6a2ba78c89bfae0108	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- 20V, Negative-QTOF	splash10-02hl-3970000000-252ae5d3a5f121760b04	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- 40V, Negative-QTOF	splash10-0006-9200000000-94d0794b7eab74534983	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	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

28680287

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14632484

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 Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro- (HMDB0252181)

MOL for HMDB0252181 (Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-)

3D MOL for HMDB0252181 (Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-)

3D SDF for HMDB0252181 (Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-)

3D-SDF for HMDB0252181 (Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-)

PDB for HMDB0252181 (Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-)

3D PDB for HMDB0252181 (Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-)

SMILES for HMDB0252181 (Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-)

INCHI for HMDB0252181 (Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-)

Structure for HMDB0252181 (Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-)

3D Structure for HMDB0252181 (Cytidine, 5-chloro-2',3'-dideoxy-3'-fluoro-)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra