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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 01:58:37 UTC

Update Date

2021-09-26 22:58:53 UTC

HMDB ID

HMDB0248553

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Arabinofuranosylcytosine

Description

This compound has been identified in human blood as reported by (PMID: 31557052 ). Arabinofuranosylcytosine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Arabinofuranosylcytosine 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

HMDB0248553
     RDKit          3D
Arabinofuranosylcytosine
 30 31  0  0  0  0  0  0  0  0999 V2000
    5.1385    0.1823   -0.6252 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8904    0.0234   -0.3406 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5612   -0.8723    0.6567 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2196   -1.0213    0.9391 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2953   -0.3165    0.2613 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0894   -0.5038    0.5890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6646    0.7470    0.7631 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0137    0.4693    0.8431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7643    1.7523    0.5572 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3579    2.6737    1.5436 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3064   -0.5968   -0.1839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0576   -1.5836    0.4450 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9009   -1.1087   -0.5133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8539   -2.5021   -0.4162 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6112    0.5574   -0.7112 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6297    1.2771   -1.3999 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9182    0.7067   -0.9907 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3720    0.8620   -1.3805 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3391   -1.4168    1.1745 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9290   -1.7288    1.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2348   -1.1020    1.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2235    0.1248    1.8702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8497    1.6305    0.5418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4405    2.1808   -0.4098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7606    3.5509    1.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7668   -0.2159   -1.0977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5199   -2.3691    0.6314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5463   -0.7418   -1.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -2.9377   -1.2900 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5183    2.2790   -1.2107 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  1  0
 15 17  2  0
 17  2  1  0
 13  6  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  6 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  0
 11 26  1  0
 12 27  1  0
 13 28  1  0
 14 29  1  0
 16 30  1  0
M  END


  Mrv1652310061710162D          

 17 18  0  0  0  0            999 V2000
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 11  9  2  0  0  0  0
 12  2  1  0  0  0  0
 12  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13  3  1  0  0  0  0
 14  6  1  0  0  0  0
 15  7  1  0  0  0  0
 16  9  1  0  0  0  0
 17  4  1  0  0  0  0
 17  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0248553

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1OC(C(O)C1O)N1C=CC(=N)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)

> <INCHI_KEY>
UHDGCWIWMRVCDJ-UHFFFAOYSA-N

> <FORMULA>
C9H13N3O5

> <MOLECULAR_WEIGHT>
243.2166

> <EXACT_MASS>
243.085520541

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
22.737428489554077

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-2.04

> <JCHEM_LOGP>
-2.7975172843333334

> <ALOGPS_LOGS>
-1.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.933688762534231

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.553240841265485

> <JCHEM_PKA_STRONGEST_BASIC>
-0.06234248538184939

> <JCHEM_POLAR_SURFACE_AREA>
128.61

> <JCHEM_REFRACTIVITY>
54.5448

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.80e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cytidine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0248553
     RDKit          3D
Arabinofuranosylcytosine
 30 31  0  0  0  0  0  0  0  0999 V2000
    5.1385    0.1823   -0.6252 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8904    0.0234   -0.3406 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5612   -0.8723    0.6567 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2196   -1.0213    0.9391 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2953   -0.3165    0.2613 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0894   -0.5038    0.5890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6646    0.7470    0.7631 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0137    0.4693    0.8431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7643    1.7523    0.5572 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3579    2.6737    1.5436 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3064   -0.5968   -0.1839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0576   -1.5836    0.4450 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9009   -1.1087   -0.5133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8539   -2.5021   -0.4162 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6112    0.5574   -0.7112 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6297    1.2771   -1.3999 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9182    0.7067   -0.9907 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3720    0.8620   -1.3805 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3391   -1.4168    1.1745 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9290   -1.7288    1.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2348   -1.1020    1.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2235    0.1248    1.8702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8497    1.6305    0.5418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4405    2.1808   -0.4098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7606    3.5509    1.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7668   -0.2159   -1.0977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5199   -2.3691    0.6314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5463   -0.7418   -1.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -2.9377   -1.2900 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5183    2.2790   -1.2107 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  1  0
 15 17  2  0
 17  2  1  0
 13  6  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  6 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  0
 11 26  1  0
 12 27  1  0
 13 28  1  0
 14 29  1  0
 16 30  1  0
M  END

HEADER    PROTEIN                                 06-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-OCT-17         0                                  
HETATM    1  C   UNK     0       3.182  -6.383   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.087  -5.138   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.846  -0.544   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.650  -6.222   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.366  -2.485   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.929  -3.570   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.745  -7.468   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       1.024  -4.816   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       3.460  -3.731   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       8.166   0.962   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       5.136   1.425   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.425  -0.544   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.302  -2.163   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.906  -2.485   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1   12                                                       
CONECT    3    4   13                                                       
CONECT    4    3    6   17                                                  
CONECT    5    1   10   11                                                  
CONECT    6    4    7   14                                                  
CONECT    7    6    8   15                                                  
CONECT    8    7   12   17                                                  
CONECT    9   11   12   16                                                  
CONECT   10    5                                                            
CONECT   11    5    9                                                       
CONECT   12    2    8    9                                                  
CONECT   13    3                                                            
CONECT   14    6                                                            
CONECT   15    7                                                            
CONECT   16    9                                                            
CONECT   17    4    8                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0248553
HETATM    1  N1  UNL     1       5.139   0.182  -0.625  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.890   0.023  -0.341  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.561  -0.872   0.657  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.220  -1.021   0.939  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.295  -0.316   0.261  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.089  -0.504   0.589  1.00  0.00           C  
HETATM    7  O1  UNL     1      -0.665   0.747   0.763  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.014   0.469   0.843  1.00  0.00           C  
HETATM    9  C6  UNL     1      -2.764   1.752   0.557  1.00  0.00           C  
HETATM   10  O2  UNL     1      -2.358   2.674   1.544  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.306  -0.597  -0.184  1.00  0.00           C  
HETATM   12  O3  UNL     1      -3.058  -1.584   0.445  1.00  0.00           O  
HETATM   13  C8  UNL     1      -0.901  -1.109  -0.513  1.00  0.00           C  
HETATM   14  O4  UNL     1      -0.854  -2.502  -0.416  1.00  0.00           O  
HETATM   15  C9  UNL     1       1.611   0.557  -0.711  1.00  0.00           C  
HETATM   16  O5  UNL     1       0.630   1.277  -1.400  1.00  0.00           O  
HETATM   17  N3  UNL     1       2.918   0.707  -0.991  1.00  0.00           N  
HETATM   18  H1  UNL     1       5.372   0.862  -1.381  1.00  0.00           H  
HETATM   19  H2  UNL     1       4.339  -1.417   1.174  1.00  0.00           H  
HETATM   20  H3  UNL     1       1.929  -1.729   1.730  1.00  0.00           H  
HETATM   21  H4  UNL     1      -0.235  -1.102   1.511  1.00  0.00           H  
HETATM   22  H5  UNL     1      -2.224   0.125   1.870  1.00  0.00           H  
HETATM   23  H6  UNL     1      -3.850   1.630   0.542  1.00  0.00           H  
HETATM   24  H7  UNL     1      -2.440   2.181  -0.410  1.00  0.00           H  
HETATM   25  H8  UNL     1      -2.761   3.551   1.402  1.00  0.00           H  
HETATM   26  H9  UNL     1      -2.767  -0.216  -1.098  1.00  0.00           H  
HETATM   27  H10 UNL     1      -2.520  -2.369   0.631  1.00  0.00           H  
HETATM   28  H11 UNL     1      -0.546  -0.742  -1.480  1.00  0.00           H  
HETATM   29  H12 UNL     1      -1.072  -2.938  -1.290  1.00  0.00           H  
HETATM   30  H13 UNL     1       0.518   2.279  -1.211  1.00  0.00           H  
CONECT    1    2    2   18
CONECT    2    3   17
CONECT    3    4    4   19
CONECT    4    5   20
CONECT    5    6   15
CONECT    6    7   13   21
CONECT    7    8
CONECT    8    9   11   22
CONECT    9   10   23   24
CONECT   10   25
CONECT   11   12   13   26
CONECT   12   27
CONECT   13   14   28
CONECT   14   29
CONECT   15   16   17   17
CONECT   16   30
END

HMDB0248553
     RDKit          3D
Arabinofuranosylcytosine
 30 31  0  0  0  0  0  0  0  0999 V2000
    5.1385    0.1823   -0.6252 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8904    0.0234   -0.3406 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5612   -0.8723    0.6567 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2196   -1.0213    0.9391 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2953   -0.3165    0.2613 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0894   -0.5038    0.5890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6646    0.7470    0.7631 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0137    0.4693    0.8431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7643    1.7523    0.5572 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3579    2.6737    1.5436 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3064   -0.5968   -0.1839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0576   -1.5836    0.4450 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9009   -1.1087   -0.5133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8539   -2.5021   -0.4162 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6112    0.5574   -0.7112 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6297    1.2771   -1.3999 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9182    0.7067   -0.9907 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3720    0.8620   -1.3805 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3391   -1.4168    1.1745 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9290   -1.7288    1.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2348   -1.1020    1.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2235    0.1248    1.8702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8497    1.6305    0.5418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4405    2.1808   -0.4098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7606    3.5509    1.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7668   -0.2159   -1.0977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5199   -2.3691    0.6314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5463   -0.7418   -1.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -2.9377   -1.2900 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5183    2.2790   -1.2107 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  1  0
 15 17  2  0
 17  2  1  0
 13  6  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  6 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  0
 11 26  1  0
 12 27  1  0
 13 28  1  0
 14 29  1  0
 16 30  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Arabinosylcytosine	MeSH
Aracytidine	MeSH
Cytarabine	MeSH
Cytosar	MeSH
Cytosar-u	MeSH
CytosarU	MeSH
Cytosine arabinoside	MeSH
Hydrochloride, cytarabine	MeSH
beta-Ara C	MeSH
Ara-C	MeSH
Aracytine	MeSH
Cytarabine hydrochloride	MeSH
Cytosar u	MeSH
Arabinofuranosylcytosine	MeSH
Arabinoside, cytosine	MeSH
Cytonal	MeSH

Chemical Formula

C₉H₁₃N₃O₅

Average Molecular Weight

243.2166

Monoisotopic Molecular Weight

243.085520541

IUPAC Name

4-amino-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

cytidine

CAS Registry Number

Not Available

SMILES

OCC1OC(C(O)C1O)N1C=CC(=N)N=C1O

InChI Identifier

InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)

InChI Key

UHDGCWIWMRVCDJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Imidolactam
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Primary alcohol
Organic oxide
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organopnictogen compound
Organic oxygen compound
Primary amine
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a pyrimidine ribonucleoside (CYTIDINE )

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	-2	ALOGPS
logP	-2.8	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	-0.062	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	128.61 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	54.54 m³·mol⁻¹	ChemAxon
Polarizability	22.74 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
AllCCS	[M+H]+	155.5	32859911
AllCCS	[M+H-H2O]+	151.7	32859911
AllCCS	[M+NH4]+	159.0	32859911
AllCCS	[M+Na]+	160.0	32859911
AllCCS	[M-H]-	152.5	32859911
AllCCS	[M+Na-2H]-	152.5	32859911
AllCCS	[M+HCOO]-	152.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Arabinofuranosylcytosine	OCC1OC(C(O)C1O)N1C=CC(=N)N=C1O	4119.4	Standard polar	33892256
Arabinofuranosylcytosine	OCC1OC(C(O)C1O)N1C=CC(=N)N=C1O	2563.7	Standard non polar	33892256
Arabinofuranosylcytosine	OCC1OC(C(O)C1O)N1C=CC(=N)N=C1O	2580.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Arabinofuranosylcytosine,5TMS,isomer #1	C[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C)C(O[Si](C)(C)C)C2O[Si](C)(C)C)C(O[Si](C)(C)C)=N1	2369.8	Semi standard non polar	33892256
Arabinofuranosylcytosine,5TMS,isomer #1	C[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C)C(O[Si](C)(C)C)C2O[Si](C)(C)C)C(O[Si](C)(C)C)=N1	2580.8	Standard non polar	33892256
Arabinofuranosylcytosine,5TMS,isomer #1	C[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C)C(O[Si](C)(C)C)C2O[Si](C)(C)C)C(O[Si](C)(C)C)=N1	2802.6	Standard polar	33892256
Arabinofuranosylcytosine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C2O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)=N1	3319.6	Semi standard non polar	33892256
Arabinofuranosylcytosine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C2O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)=N1	3484.7	Standard non polar	33892256
Arabinofuranosylcytosine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N=C1C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C2O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)=N1	3214.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (Non-derivatized) - 70eV, Positive	splash10-05dl-9310000000-baa27af3867d7b2962e5	2018-04-09	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_9) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_2_10) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_5) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_6) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol GC-MS (TMS_3_8) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Arabinofuranosylcytosine 40V, Positive-QTOF	splash10-03di-0900000000-4d7ac7a2020f3bcdb8af	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Negative-QTOF	splash10-0a4l-0950000000-9d2635dbd5dba4335642	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Arabinofuranosylcytosine 20V, Positive-QTOF	splash10-03di-0900000000-0beed630d191c3ddf484	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Positive-QTOF	splash10-03di-0900000000-b5174fb5250877fc4322	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Positive-QTOF	splash10-03di-0910000000-36ec7f4bb0f43c1bea01	2015-05-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 20V, Positive-QTOF	splash10-03di-4900000000-9df78eed4f14088c8271	2015-05-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 40V, Positive-QTOF	splash10-03dj-9600000000-73e430a902e254bcf1a5	2015-05-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Negative-QTOF	splash10-0btd-0930000000-7dddc27b279db10b55f1	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 20V, Negative-QTOF	splash10-03dl-5920000000-ba0a861002b9566db684	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 40V, Negative-QTOF	splash10-0006-9200000000-1a8e142cab2f41210227	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Positive-QTOF	splash10-03di-0910000000-ebba965cb6de7bb5887e	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 20V, Positive-QTOF	splash10-03di-1910000000-c30c0903bd3816dc1da4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 40V, Positive-QTOF	splash10-03di-5900000000-8cae3c9126ea35107cde	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 10V, Negative-QTOF	splash10-006x-0590000000-34c91e737fe5299bafd8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 20V, Negative-QTOF	splash10-03dl-4910000000-751c4dfb7474605dd469	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arabinofuranosylcytosine 40V, Negative-QTOF	splash10-00kf-9200000000-284eea506bf71a5900d1	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)	2021-10-13	Wishart Lab	View Spectrum
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, 1000 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	¹H NMR Spectrum (1D, 200 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, 300 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	¹³C NMR Spectrum (1D, 400 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	¹H NMR Spectrum (1D, 500 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, 600 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	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	¹H NMR Spectrum (1D, 900 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

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

FDB001979

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Cytarabine

METLIN ID

Not Available

PubChem Compound

596

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

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VMH ID

Not Available

MarkerDB ID

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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 Arabinofuranosylcytosine (HMDB0248553)

MOL for HMDB0248553 (Arabinofuranosylcytosine)

3D MOL for HMDB0248553 (Arabinofuranosylcytosine)

3D SDF for HMDB0248553 (Arabinofuranosylcytosine)

3D-SDF for HMDB0248553 (Arabinofuranosylcytosine)

PDB for HMDB0248553 (Arabinofuranosylcytosine)

3D PDB for HMDB0248553 (Arabinofuranosylcytosine)

SMILES for HMDB0248553 (Arabinofuranosylcytosine)

INCHI for HMDB0248553 (Arabinofuranosylcytosine)

Structure for HMDB0248553 (Arabinofuranosylcytosine)

3D Structure for HMDB0248553 (Arabinofuranosylcytosine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra