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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (6)transporters (3) Show 9 proteins XML

enzymes (6)transporters (3) Show 9 proteins

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:51 UTC

Update Date

2022-03-07 02:51:52 UTC

HMDB ID

HMDB0015122

Secondary Accession Numbers

HMDB0030167
HMDB15122
HMDB30167

Metabolite Identification

Common Name

Cytarabine

Description

Cytarabine, or cytosine arabinoside, a pyrimidine nucleoside analog, is found in mushrooms. Cytarabine is isolated from the mushroom Xerocomus nigromaculatus of unknown palatability. Cytarabine is an antineoplastic anti-metabolite used in the treatment of several forms of leukemia including acute myelogenous leukemia and meningeal leukemia. Cytarabine is an antimetabolite antineoplastic agent that inhibits the synthesis of DNA. Its actions are specific for the S phase of the cell cycle to stop normal cell development and division. Cytarabine is metabolized intracellularly into its active triphosphate form (cytosine arabinoside triphosphate). This metabolite then damages DNA by multiple mechanisms, including the inhibition of alpha-DNA polymerase, inhibition of DNA repair through an effect on beta-DNA polymerase, and incorporation into DNA. The latter mechanism is probably the most important. Cytotoxicity is highly specific for the S phase of the cell cycle. Cytarabine is a chemotherapy agent used mainly in the treatment of hematological malignancies such as acute myeloid leukemia (AML) and non-Hodgkin lymphoma. It is also known as ara C. Cytosine arabinoside is an antimetabolic agent with the chemical name of 1 -arabinofuranosylcytosine. Its mode of action is due to its rapid conversion into cytosine arabinoside triphosphate, which damages DNA when the cell cycle holds in the S phase (synthesis of DNA). Rapidly dividing cells, which require DNA replication for mitosis, are therefore most affected. Cytosine arabinoside also inhibits both DNA and RNA polymerases and nucleotide reductase enzymes needed for DNA synthesis

Structure

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

HMDB0015122
     RDKit          3D
Cytarabine
 30 31  0  0  0  0  0  0  0  0999 V2000
    4.8133    1.0268    0.8267 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5204    0.5300    0.4242 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2512   -0.8172    0.3836 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9919   -1.2377   -0.0107 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0216   -0.3783   -0.3556 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2953   -0.8078   -0.7685 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0449    0.2514   -1.2659 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2295    0.3083   -0.5952 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7807    1.6976   -0.4005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0131    2.3361   -1.5895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0329   -0.3819    0.7396 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2660   -0.9512    1.0990 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0686   -1.4891    0.3001 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3157   -1.9609    1.3540 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3034    0.9327   -0.3097 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4592    1.8144   -0.6145 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5339    1.3743    0.0745 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6533    0.4402    0.7306 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8595    1.9858    1.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0072   -1.5419    0.6542 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8108   -2.2921   -0.0328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2060   -1.5310   -1.6333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9948   -0.2675   -1.1645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1104    2.2993    0.2347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7600    1.5752    0.1363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1569    2.6991   -1.9185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6134    0.2589    1.5112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9813   -0.7277    0.4495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7129   -2.2764   -0.1404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6436   -2.8695    1.5832 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  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  2  0
 15 17  1  0
 17  2  2  0
 13  6  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  6 22  1  6
  8 23  1  6
  9 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  1
 12 28  1  0
 13 29  1  6
 14 30  1  0
M  END

      
  Mrv1652305271900072D          

 17 18  0  0  0  0            999 V2000
 9992.1384 9990.4102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.3507 9990.4184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9989.8832 9992.2669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.1685 9991.8562    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.3571 9991.0322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.7866 9993.5040    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9993.3585 9991.8543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.0729 9992.2668    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9994.0729 9993.0919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9993.3585 9993.5045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9992.6440 9993.0919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9992.6440 9992.2668    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9991.2615 9992.3505    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9991.9289 9991.8655    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9991.6741 9991.0808    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9990.8490 9991.0808    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9990.5940 9991.8655    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  3  4  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
 11 12  1  0  0  0  0
 12  7  1  0  0  0  0
  7  5  2  0  0  0  0
  9  6  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 13 14  1  0  0  0  0
 13 17  1  0  0  0  0
 15  1  1  1  0  0  0
 14 12  1  1  0  0  0
 17  3  1  1  0  0  0
 16  2  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0015122

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O

> <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)/t4-,6-,7+,8-/m1/s1

> <INCHI_KEY>
UHDGCWIWMRVCDJ-CCXZUQQUSA-N

> <FORMULA>
C9H13N3O5

> <MOLECULAR_WEIGHT>
243.2166

> <EXACT_MASS>
243.085520541

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
22.532482120749137

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.18

> <JCHEM_LOGP>
-2.7975172843333334

> <ALOGPS_LOGS>
-0.74

> <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>
4.38e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cytarabine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0015122
     RDKit          3D
Cytarabine
 30 31  0  0  0  0  0  0  0  0999 V2000
    4.8133    1.0268    0.8267 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5204    0.5300    0.4242 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2512   -0.8172    0.3836 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9919   -1.2377   -0.0107 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0216   -0.3783   -0.3556 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2953   -0.8078   -0.7685 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0449    0.2514   -1.2659 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2295    0.3083   -0.5952 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7807    1.6976   -0.4005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0131    2.3361   -1.5895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0329   -0.3819    0.7396 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2660   -0.9512    1.0990 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0686   -1.4891    0.3001 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3157   -1.9609    1.3540 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3034    0.9327   -0.3097 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4592    1.8144   -0.6145 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5339    1.3743    0.0745 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6533    0.4402    0.7306 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8595    1.9858    1.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0072   -1.5419    0.6542 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8108   -2.2921   -0.0328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2060   -1.5310   -1.6333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9948   -0.2675   -1.1645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1104    2.2993    0.2347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7600    1.5752    0.1363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1569    2.6991   -1.9185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6134    0.2589    1.5112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9813   -0.7277    0.4495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7129   -2.2764   -0.1404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6436   -2.8695    1.5832 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  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  2  0
 15 17  1  0
 17  2  2  0
 13  6  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  6 22  1  6
  8 23  1  6
  9 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  1
 12 28  1  0
 13 29  1  6
 14 30  1  0
M  END

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0    8651.9928648.766   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8648.6558648.781   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8647.7828652.232   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8646.4488651.465   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8654.2678649.927   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0    8656.9358654.541   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8654.2698651.461   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0    8655.6038652.231   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0    8655.6038653.772   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8654.2698654.542   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8652.9358653.772   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0    8652.9358652.231   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0    8650.3558652.388   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0    8651.6018651.482   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8651.1258650.017   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8649.5858650.017   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8649.1098651.482   0.000  0.00  0.00           C+0
CONECT    1   15                                                            
CONECT    2   16                                                            
CONECT    3    4   17                                                       
CONECT    4    3                                                            
CONECT    5    7                                                            
CONECT    6    9                                                            
CONECT    7    8   12    5                                                  
CONECT    8    7    9                                                       
CONECT    9   10    8    6                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    7   14                                                  
CONECT   13   14   17                                                       
CONECT   14   15   13   12                                                  
CONECT   15   14   16    1                                                  
CONECT   16   15   17    2                                                  
CONECT   17   16   13    3                                                  
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0015122
HETATM    1  N1  UNL     1       4.813   1.027   0.827  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.520   0.530   0.424  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.251  -0.817   0.384  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.992  -1.238  -0.011  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.022  -0.378  -0.356  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.295  -0.808  -0.769  1.00  0.00           C  
HETATM    7  O1  UNL     1      -1.045   0.251  -1.266  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.230   0.308  -0.595  1.00  0.00           C  
HETATM    9  C6  UNL     1      -2.781   1.698  -0.401  1.00  0.00           C  
HETATM   10  O2  UNL     1      -3.013   2.336  -1.590  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.033  -0.382   0.740  1.00  0.00           C  
HETATM   12  O3  UNL     1      -3.266  -0.951   1.099  1.00  0.00           O  
HETATM   13  C8  UNL     1      -1.069  -1.489   0.300  1.00  0.00           C  
HETATM   14  O4  UNL     1      -0.316  -1.961   1.354  1.00  0.00           O  
HETATM   15  C9  UNL     1       1.303   0.933  -0.310  1.00  0.00           C  
HETATM   16  O5  UNL     1       0.459   1.814  -0.614  1.00  0.00           O  
HETATM   17  N3  UNL     1       2.534   1.374   0.075  1.00  0.00           N  
HETATM   18  H1  UNL     1       5.653   0.440   0.731  1.00  0.00           H  
HETATM   19  H2  UNL     1       4.860   1.986   1.211  1.00  0.00           H  
HETATM   20  H3  UNL     1       4.007  -1.542   0.654  1.00  0.00           H  
HETATM   21  H4  UNL     1       1.811  -2.292  -0.033  1.00  0.00           H  
HETATM   22  H5  UNL     1      -0.206  -1.531  -1.633  1.00  0.00           H  
HETATM   23  H6  UNL     1      -2.995  -0.268  -1.165  1.00  0.00           H  
HETATM   24  H7  UNL     1      -2.110   2.299   0.235  1.00  0.00           H  
HETATM   25  H8  UNL     1      -3.760   1.575   0.136  1.00  0.00           H  
HETATM   26  H9  UNL     1      -2.157   2.699  -1.919  1.00  0.00           H  
HETATM   27  H10 UNL     1      -1.613   0.259   1.511  1.00  0.00           H  
HETATM   28  H11 UNL     1      -3.981  -0.728   0.450  1.00  0.00           H  
HETATM   29  H12 UNL     1      -1.713  -2.276  -0.140  1.00  0.00           H  
HETATM   30  H13 UNL     1      -0.644  -2.870   1.583  1.00  0.00           H  
CONECT    1    2   18   19
CONECT    2    3   17   17
CONECT    3    4    4   20
CONECT    4    5   21
CONECT    5    6   15
CONECT    6    7   13   22
CONECT    7    8
CONECT    8    9   11   23
CONECT    9   10   24   25
CONECT   10   26
CONECT   11   12   13   27
CONECT   12   28
CONECT   13   14   29
CONECT   14   30
CONECT   15   16   16   17
END

HMDB0015122
     RDKit          3D
Cytarabine
 30 31  0  0  0  0  0  0  0  0999 V2000
    4.8133    1.0268    0.8267 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5204    0.5300    0.4242 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2512   -0.8172    0.3836 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9919   -1.2377   -0.0107 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0216   -0.3783   -0.3556 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2953   -0.8078   -0.7685 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0449    0.2514   -1.2659 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2295    0.3083   -0.5952 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7807    1.6976   -0.4005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0131    2.3361   -1.5895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0329   -0.3819    0.7396 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2660   -0.9512    1.0990 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0686   -1.4891    0.3001 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3157   -1.9609    1.3540 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3034    0.9327   -0.3097 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4592    1.8144   -0.6145 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5339    1.3743    0.0745 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6533    0.4402    0.7306 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8595    1.9858    1.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0072   -1.5419    0.6542 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8108   -2.2921   -0.0328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2060   -1.5310   -1.6333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9948   -0.2675   -1.1645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1104    2.2993    0.2347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7600    1.5752    0.1363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1569    2.6991   -1.9185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6134    0.2589    1.5112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9813   -0.7277    0.4495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7129   -2.2764   -0.1404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6436   -2.8695    1.5832 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  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  2  0
 15 17  1  0
 17  2  2  0
 13  6  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  6 22  1  6
  8 23  1  6
  9 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  1
 12 28  1  0
 13 29  1  6
 14 30  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1-beta-D-Arabinofuranosylcytosine	ChEBI
4-Amino-1-beta-D-arabinofuranosyl-2(1H)-pyrimidinone	ChEBI
Ara-C	ChEBI
Arabinocytosine	ChEBI
Arabinoside C	ChEBI
Citarabina	ChEBI
Cytarabinum	ChEBI
Cytosine arabinoside	ChEBI
Cytosine-1-beta-D-arabinofuranoside	ChEBI
Cytosine-beta-D-arabinofuranoside	ChEBI
Depocyt	Kegg
1-b-D-Arabinofuranosylcytosine	Generator
1-Β-D-arabinofuranosylcytosine	Generator
4-Amino-1-b-D-arabinofuranosyl-2(1H)-pyrimidinone	Generator
4-Amino-1-β-D-arabinofuranosyl-2(1H)-pyrimidinone	Generator
Cytosine-1-b-D-arabinofuranoside	Generator
Cytosine-1-β-D-arabinofuranoside	Generator
Cytosine-b-D-arabinofuranoside	Generator
Cytosine-β-D-arabinofuranoside	Generator
(beta-D-Arabinofuranosyl)cytosine	HMDB
1-Arabinofuranosylcytosine	HMDB
1-beta -D-Arabinofaranosylcytosine	HMDB
1-beta -D-Arabinofuranosyl-4-amino-2(1H)pyrimidinone	HMDB
1-beta -D-Arabinofuranosylcytosine	HMDB
1-beta-D-Arabinofaranosylcytosine	HMDB
1-beta-D-Arabinofuranosyl-4-amino-2(1H)pyrimidinone	HMDB
1-beta-D-Arabinofuranosyl-cytosine	HMDB
1-beta-D-Arabinofuranosylcytosine, cytosine arabinoside	HMDB
1-beta-D-Arabinosyl-cytosine	HMDB
1-beta-D-Arabinosylcytosine	HMDB
1beta -Arabinofuranasylcytosine	HMDB
1beta -D-Arabinofuranosylcytosine	HMDB
1beta -D-Arabinosylcytosine	HMDB
1beta-Arabinofuranasylcytosine	HMDB
1beta-D-Arabinofuranosylcytosine	HMDB
1beta-D-Arabinosylcytosine	HMDB
2(1H)-Pyrimidinone, 4-amino-1- -D-arabinofuranosyl	HMDB
4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidin	HMDB
4-Amino-1-arabinofuranosyl-2-oxo-1,2-dihydropyrimidine	HMDB
4-Amino-1-b-D-arabinofuranosyl-2-(1H)-pyrimidinone	HMDB
4-Amino-1-beta-D-arabinofuranosylpyrimidin-2(1H)-one	HMDB
Alexan	HMDB
Arabinocytidine	HMDB
Arabinofuranosylcytosine	HMDB
Arabinosylcytosine	HMDB
Arabitin	HMDB
AraC	HMDB
Aracytidine	HMDB
Aracytin	HMDB
Aracytine	HMDB
Arafcyt	HMDB
beta -Arabinosylcytosine	HMDB
beta -Cytosine arabinoside	HMDB
beta -D-Arabinosylcytosine	HMDB
beta-Ara c	HMDB
beta-Arabinosylcytosine	HMDB
beta-Cytosine arabinoside	HMDB
beta-D-Arabinosylcytosine	HMDB
Cytarabin	HMDB
Cytarabina	HMDB
Cytarabine liposome injection	HMDB
Cytarabinoside	HMDB
Cytonal	HMDB
Cytosar	HMDB
Cytosar-u	HMDB
Cytosine 1-beta-D-arabinofuranoside	HMDB
Cytosine arabinofuranoside	HMDB
Cytosine arabinose	HMDB
Cytosine beta-D-arabinofuranoside	HMDB
Cytosine beta-D-arabinoside	HMDB
Cytosine, beta -D-arabinoside	HMDB
Cytosine, beta-D-arabinoside	HMDB
Cytosine-1-beta-D-arabinofuranoside hydrochloride	HMDB
Cytosine-beta -arabinoside	HMDB
Cytosine-beta -D-arabinofuranoside	HMDB
Cytosine-beta-arabinoside	HMDB
Cytosinearabinoside	HMDB
Depocyte	HMDB
Erpalfa	HMDB
Iretin	HMDB
Spongocytidine	HMDB
Tarabine	HMDB
Udicil	HMDB
Arabinoside, cytosine	HMDB
CytosarU	HMDB
Hydrochloride, cytarabine	HMDB
Cytarabine hydrochloride	HMDB
Cytosar u	HMDB
Ara C	HMDB
beta Ara C	HMDB
Cytarabine	MeSH

Chemical Formula

C₉H₁₃N₃O₅

Average Molecular Weight

243.2166

Monoisotopic Molecular Weight

243.085520541

IUPAC Name

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

Traditional Name

cytarabine

CAS Registry Number

147-94-4

SMILES

NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O

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)/t4-,6-,7+,8-/m1/s1

InChI Key

UHDGCWIWMRVCDJ-CCXZUQQUSA-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

monosaccharide derivative (CHEBI:28680 )
beta-D-arabinoside (CHEBI:28680 )
pyrimidine nucleoside (CHEBI:28680 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0015122)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0015122)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0015122)
Gastrointestinal (HMDB: HMDB0015122)

Source

Endogenous

Endogenous (HMDB: HMDB0015122)

Plant

Plant (HMDB: HMDB0015122)

Exogenous

Food

Food (HMDB: HMDB0015122)

Fruit

Tropical fruit

Guava (FooDB: FOOD00150)

Citrus

Sweet orange (FooDB: FOOD00057)

Pome

Pomes (FooDB: FOOD00856)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Vegetable

Root vegetable

Root vegetables (FooDB: FOOD00873)

Environmental

Wastewater (HMDB: HMDB0015122)

Process

Not Available

Role

Industrial application

Pharmaceutical industry

Antimicrobial agent

Antiviral

Antiviral (HMDB: HMDB0015122)

Antineoplastic agent

Antitumor (HMDB: HMDB0015122)

Manufacturing industry

Material processing agent

Coloring agent

Fluorescent agent

Immunosuppressive Agent (HMDB: HMDB0015122)

Environmental role

Environmental contaminant (HMDB: HMDB0015122)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	212 - 213 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	43.8 g/L	Not Available
LogP	-2.8	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	43.8 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.8	ChemAxon
logS	-0.74	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	22.53 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
DarkChem	[M+H]+	155.46	31661259
DarkChem	[M-H]-	147.657	31661259
DeepCCS	[M+H]+	153.984	30932474
DeepCCS	[M+H]+	152.797	30932474
DeepCCS	[M-H]-	151.588	30932474
DeepCCS	[M-H]-	150.439	30932474
DeepCCS	[M-2H]-	185.959	30932474
DeepCCS	[M+Na]+	160.964	30932474
DeepCCS	[M-2H]-	184.137	30932474
DeepCCS	[M+Na]+	159.232	30932474
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 Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	8.8002 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	6.49 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	218.4 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	419.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	241.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	50.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	157.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	50.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	298.5 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	236.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	731.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	540.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	40.3 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	684.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	166.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	201.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	630.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	444.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	270.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Cytarabine	NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O	3802.7	Standard polar	33892256
Cytarabine	NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O	2260.6	Standard non polar	33892256
Cytarabine	NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O	2622.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cytarabine,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@@H](O)[C@@H]1O	2449.8	Semi standard non polar	33892256
Cytarabine,1TMS,isomer #2	C[Si](C)(C)O[C@H]1[C@H](O)[C@H](N2C=CC(N)=NC2=O)O[C@@H]1CO	2447.9	Semi standard non polar	33892256
Cytarabine,1TMS,isomer #3	C[Si](C)(C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(N)=NC1=O	2442.5	Semi standard non polar	33892256
Cytarabine,1TMS,isomer #4	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)C=C1	2503.8	Semi standard non polar	33892256
Cytarabine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@@H](O[Si](C)(C)C)[C@@H]1O	2410.6	Semi standard non polar	33892256
Cytarabine,2TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@@H](O)[C@@H]1O[Si](C)(C)C	2406.7	Semi standard non polar	33892256
Cytarabine,2TMS,isomer #3	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@@H]2O)C=C1	2468.4	Semi standard non polar	33892256
Cytarabine,2TMS,isomer #4	C[Si](C)(C)O[C@H]1[C@H](O[Si](C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(N)=NC1=O	2395.5	Semi standard non polar	33892256
Cytarabine,2TMS,isomer #5	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@@H]2O)C=C1	2475.9	Semi standard non polar	33892256
Cytarabine,2TMS,isomer #6	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O[Si](C)(C)C)C=C1	2470.8	Semi standard non polar	33892256
Cytarabine,2TMS,isomer #7	C[Si](C)(C)N(C1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)C=C1)[Si](C)(C)C	2464.3	Semi standard non polar	33892256
Cytarabine,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2357.3	Semi standard non polar	33892256
Cytarabine,3TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@@H]2O[Si](C)(C)C)C=C1	2457.8	Semi standard non polar	33892256
Cytarabine,3TMS,isomer #3	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]2O)C=C1	2453.2	Semi standard non polar	33892256
Cytarabine,3TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H](O)[C@@H]1O	2420.4	Semi standard non polar	33892256
Cytarabine,3TMS,isomer #5	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@@H]2O[Si](C)(C)C)C=C1	2451.9	Semi standard non polar	33892256
Cytarabine,3TMS,isomer #6	C[Si](C)(C)O[C@H]1[C@H](O)[C@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O[C@@H]1CO	2405.7	Semi standard non polar	33892256
Cytarabine,3TMS,isomer #7	C[Si](C)(C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC1=O	2403.3	Semi standard non polar	33892256
Cytarabine,4TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]2O[Si](C)(C)C)C=C1	2469.0	Semi standard non polar	33892256
Cytarabine,4TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]2O[Si](C)(C)C)C=C1	2572.3	Standard non polar	33892256
Cytarabine,4TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]2O[Si](C)(C)C)C=C1	2969.5	Standard polar	33892256
Cytarabine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C)[C@@H]1O	2441.6	Semi standard non polar	33892256
Cytarabine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C)[C@@H]1O	2581.5	Standard non polar	33892256
Cytarabine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C)[C@@H]1O	2890.7	Standard polar	33892256
Cytarabine,4TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H](O)[C@@H]1O[Si](C)(C)C	2428.3	Semi standard non polar	33892256
Cytarabine,4TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H](O)[C@@H]1O[Si](C)(C)C	2563.6	Standard non polar	33892256
Cytarabine,4TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H](O)[C@@H]1O[Si](C)(C)C	2847.2	Standard polar	33892256
Cytarabine,4TMS,isomer #4	C[Si](C)(C)O[C@H]1[C@H](O[Si](C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC1=O	2428.4	Semi standard non polar	33892256
Cytarabine,4TMS,isomer #4	C[Si](C)(C)O[C@H]1[C@H](O[Si](C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC1=O	2576.3	Standard non polar	33892256
Cytarabine,4TMS,isomer #4	C[Si](C)(C)O[C@H]1[C@H](O[Si](C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC1=O	2820.1	Standard polar	33892256
Cytarabine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2477.5	Semi standard non polar	33892256
Cytarabine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2558.6	Standard non polar	33892256
Cytarabine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2669.6	Standard polar	33892256
Cytarabine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@@H](O)[C@@H]1O	2692.2	Semi standard non polar	33892256
Cytarabine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@H](N2C=CC(N)=NC2=O)O[C@@H]1CO	2697.4	Semi standard non polar	33892256
Cytarabine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(N)=NC1=O	2685.9	Semi standard non polar	33892256
Cytarabine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)C=C1	2782.1	Semi standard non polar	33892256
Cytarabine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2869.2	Semi standard non polar	33892256
Cytarabine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2870.8	Semi standard non polar	33892256
Cytarabine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]2O)C=C1	2940.9	Semi standard non polar	33892256
Cytarabine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(N)=NC1=O	2854.9	Semi standard non polar	33892256
Cytarabine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]2O)C=C1	2934.4	Semi standard non polar	33892256
Cytarabine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O[Si](C)(C)C(C)(C)C)C=C1	2918.1	Semi standard non polar	33892256
Cytarabine,2TBDMS,isomer #7	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)C=C1)[Si](C)(C)C(C)(C)C	2911.3	Semi standard non polar	33892256
Cytarabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3063.3	Semi standard non polar	33892256
Cytarabine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]2O[Si](C)(C)C(C)(C)C)C=C1	3137.1	Semi standard non polar	33892256
Cytarabine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]2O)C=C1	3128.6	Semi standard non polar	33892256
Cytarabine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H](O)[C@@H]1O	3081.4	Semi standard non polar	33892256
Cytarabine,3TBDMS,isomer #5	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]2O[Si](C)(C)C(C)(C)C)C=C1	3115.8	Semi standard non polar	33892256
Cytarabine,3TBDMS,isomer #6	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O[C@@H]1CO	3096.2	Semi standard non polar	33892256
Cytarabine,3TBDMS,isomer #7	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC1=O	3076.5	Semi standard non polar	33892256
Cytarabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]2O[Si](C)(C)C(C)(C)C)C=C1	3299.2	Semi standard non polar	33892256
Cytarabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]2O[Si](C)(C)C(C)(C)C)C=C1	3333.6	Standard non polar	33892256
Cytarabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]2O[Si](C)(C)C(C)(C)C)C=C1	3318.5	Standard polar	33892256
Cytarabine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3281.9	Semi standard non polar	33892256
Cytarabine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3368.3	Standard non polar	33892256
Cytarabine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3209.7	Standard polar	33892256
Cytarabine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3272.0	Semi standard non polar	33892256
Cytarabine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3355.4	Standard non polar	33892256
Cytarabine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3174.4	Standard polar	33892256
Cytarabine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC1=O	3274.3	Semi standard non polar	33892256
Cytarabine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC1=O	3358.3	Standard non polar	33892256
Cytarabine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC1=O	3156.0	Standard polar	33892256
Cytarabine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3460.3	Semi standard non polar	33892256
Cytarabine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3469.5	Standard non polar	33892256
Cytarabine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3133.2	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Cytarabine GC-MS (5 TMS)	splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2	2018-05-25	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Cytarabine GC-MS (4 TMS)	splash10-0g4j-2980000000-9337623aef7fec22dd97	2018-05-25	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Cytarabine GC-MS (Non-derivatized)	splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2	2018-05-25	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Cytarabine GC-MS (Non-derivatized)	splash10-0g4j-2980000000-9337623aef7fec22dd97	2018-05-25	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytarabine GC-MS (Non-derivatized) - 70eV, Positive	splash10-08ml-9320000000-b032ad2c3dbed3face55	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytarabine GC-MS (3 TMS) - 70eV, Positive	splash10-0fuu-3934200000-7c3baaaffddf6aacd0f3	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cytarabine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-QQ , negative-QTOF	splash10-0006-0190000000-eff861edb69ddab2c195	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-QQ , negative-QTOF	splash10-0a4i-0900000000-4b5b14f0a5467db173b6	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-QQ , negative-QTOF	splash10-0a4i-3900000000-d85ae6c771dd9206c4c2	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-QQ , negative-QTOF	splash10-06sl-9600000000-b154ca170372bcbf8a4a	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-QQ , negative-QTOF	splash10-00lu-9200000000-840df44a2d1149f4a7f7	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-QQ , positive-QTOF	splash10-01ox-0790000000-270551529aa609aa9ce8	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-QQ , positive-QTOF	splash10-03di-0900000000-855a7f8775ed4351b290	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-QQ , positive-QTOF	splash10-03di-0900000000-50671582f88f6b4d8cee	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-QQ , positive-QTOF	splash10-03di-1900000000-54269291900f80d353c3	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-QQ , positive-QTOF	splash10-03di-7900000000-ae3ff52581cbe6141064	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine LC-ESI-IT , positive-QTOF	splash10-03di-0900000000-9f3ae8e87da22e4e2e82	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine 35V, Negative-QTOF	splash10-0btc-3910000000-0c7172b1308a7ac699d4	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Cytarabine 35V, Positive-QTOF	splash10-03di-0900000000-204e273853aa2d8e09ab	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 10V, Positive-QTOF	splash10-03di-0910000000-9575881412c4c94a7eae	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 20V, Positive-QTOF	splash10-03di-5900000000-2cb5f7e3dbd7baa35b56	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 40V, Positive-QTOF	splash10-03dj-9600000000-7d281b2b2d57c8786e11	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 10V, Negative-QTOF	splash10-01ox-0960000000-db9207082a1fabf42dae	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 20V, Negative-QTOF	splash10-03xs-4910000000-c89de30dd376cbcb3b66	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 40V, Negative-QTOF	splash10-00kf-9200000000-5715839499753b91f845	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 10V, Positive-QTOF	splash10-03di-0900000000-61fe3ac4032a2baf1b89	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 20V, Positive-QTOF	splash10-03di-2900000000-230b224d4d0dd71d0a49	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 40V, Positive-QTOF	splash10-02t9-9200000000-7262e80c4fe078b890fc	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 10V, Negative-QTOF	splash10-03di-2900000000-66dec45988a096cc3483	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 20V, Negative-QTOF	splash10-01ox-9500000000-bc463e76fd8ac42ac1d0	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cytarabine 40V, Negative-QTOF	splash10-0006-9100000000-98e1626c7f485521a57f	2021-10-11	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	2018-05-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2018-05-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00987	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00987	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00987

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB001216

KNApSAcK ID

Not Available

Chemspider ID

6017

KEGG Compound ID

C02961

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Cytarabine

METLIN ID

Not Available

PubChem Compound

6253

PDB ID

Not Available

ChEBI ID

28680

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)

Download (PDF)

General References

Zaky DA, Betts RF, Douglas RG Jr, Bengali K, Neil GL: Varicella-zoster virus and subcutaneous cytarabine: correlation of in vitro sensitivities to blood levels. Antimicrob Agents Chemother. 1975 Mar;7(3):229-32. [PubMed:166610 ]
Relling MV, Mulhern RK, Fairclough D, Baker D, Pui CH: Chlorpromazine with and without lorazepam as antiemetic therapy in children receiving uniform chemotherapy. J Pediatr. 1993 Nov;123(5):811-6. [PubMed:8229497 ]
Mallick KS, Hajek AS, Parrish RK 2nd: Fluorouracil (5-FU) and cytarabine (ara-C) inhibition of corneal epithelial cell and conjunctival fibroblast proliferation. Arch Ophthalmol. 1985 Sep;103(9):1398-402. [PubMed:4038134 ]
Bursztyn J, Boccara JF, Paillassou B, Bavoux F: [Corneal toxicity of cytarabine. Apropos of a case]. Ophtalmologie. 1989 Jun-Aug;3(3):229-30. [PubMed:2641118 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

Enzyme Details

1. 5'-nucleotidase

General function:: Involved in hydrolase activity
Specific function:: Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:: NT5E
Uniprot ID:: P21589
Molecular weight:: 57948.125

References

Lamba JK: Genetic factors influencing cytarabine therapy. Pharmacogenomics. 2009 Oct;10(10):1657-74. doi: 10.2217/pgs.09.118. [PubMed:19842938 ]

Enzyme Details

2. Deoxycytidylate deaminase

General function:: Involved in zinc ion binding
Specific function:: Supplies the nucleotide substrate for thymidylate synthetase.
Gene Name:: DCTD
Uniprot ID:: P32321
Molecular weight:: 21013.96

References

Lamba JK: Genetic factors influencing cytarabine therapy. Pharmacogenomics. 2009 Oct;10(10):1657-74. doi: 10.2217/pgs.09.118. [PubMed:19842938 ]

Enzyme Details

3. Deoxycytidine kinase

General function:: Involved in ATP binding
Specific function:: Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.
Gene Name:: DCK
Uniprot ID:: P27707
Molecular weight:: 30518.315

References

Ohta T, Hori H, Ogawa M, Miyahara M, Kawasaki H, Taniguchi N, Komada Y: Impact of cytidine deaminase activity on intrinsic resistance to cytarabine in carcinoma cells. Oncol Rep. 2004 Nov;12(5):1115-20. [PubMed:15492802 ]
Lamba JK: Genetic factors influencing cytarabine therapy. Pharmacogenomics. 2009 Oct;10(10):1657-74. doi: 10.2217/pgs.09.118. [PubMed:19842938 ]

Enzyme Details

4. DNA polymerase beta

General function:: Involved in DNA binding
Specific function:: Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.
Gene Name:: POLB
Uniprot ID:: P06746
Molecular weight:: 38177.34

References

Angeli JP, Ribeiro LR, Bellini MF, Mantovanil: Anti-clastogenic effect of beta-glucan extracted from barley towards chemically induced DNA damage in rodent cells. Hum Exp Toxicol. 2006 Jun;25(6):319-24. [PubMed:16866189 ]
Miura S, Izuta S: DNA polymerases as targets of anticancer nucleosides. Curr Drug Targets. 2004 Feb;5(2):191-5. [PubMed:15011952 ]
Krynetskaia NF, Phadke MS, Jadhav SH, Krynetskiy EY: Chromatin-associated proteins HMGB1/2 and PDIA3 trigger cellular response to chemotherapy-induced DNA damage. Mol Cancer Ther. 2009 Apr;8(4):864-72. doi: 10.1158/1535-7163.MCT-08-0695. [PubMed:19372559 ]

Enzyme Details

5. Cytochrome P450 3A4

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:: CYP3A4
Uniprot ID:: P08684
Molecular weight:: 57255.585

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

6. Cytidine deaminase

General function:: Involved in zinc ion binding
Specific function:: This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
Gene Name:: CDA
Uniprot ID:: P32320
Molecular weight:: 16184.545

References

Ohta T, Hori H, Ogawa M, Miyahara M, Kawasaki H, Taniguchi N, Komada Y: Impact of cytidine deaminase activity on intrinsic resistance to cytarabine in carcinoma cells. Oncol Rep. 2004 Nov;12(5):1115-20. [PubMed:15492802 ]
Lamba JK: Genetic factors influencing cytarabine therapy. Pharmacogenomics. 2009 Oct;10(10):1657-74. doi: 10.2217/pgs.09.118. [PubMed:19842938 ]

Transporters

Enzyme Details

1. Equilibrative nucleoside transporter 1

General function:: Involved in nucleoside transmembrane transporter activity
Specific function:: Mediates both influx and efflux of nucleosides across the membrane (equilibrative transporter). It is sensitive (ES) to low concentrations of the inhibitor nitrobenzylmercaptopurine riboside (NBMPR) and is sodium-independent. It has a higher affinity for adenosine. Inhibited by dipyridamole and dilazep (anticancer chemotherapeutics drugs)
Gene Name:: SLC29A1
Uniprot ID:: Q99808
Molecular weight:: 50218.8

References

Santini D, Vincenzi B, Fratto ME, Perrone G, Lai R, Catalano V, Cass C, Ruffini PA, Spoto C, Muretto P, Rizzo S, Muda AO, Mackey JR, Russo A, Tonini G, Graziano F: Prognostic role of human equilibrative transporter 1 (hENT1) in patients with resected gastric cancer. J Cell Physiol. 2010 May;223(2):384-8. doi: 10.1002/jcp.22045. [PubMed:20082300 ]

Enzyme Details

2. Solute carrier family 22 member 1

General function:: Involved in ion transmembrane transporter activity
Specific function:: Translocates a broad array of organic cations with various structures and molecular weights including the model compounds 1-methyl-4-phenylpyridinium (MPP), tetraethylammonium (TEA), N-1-methylnicotinamide (NMN), 4-(4-(dimethylamino)styryl)- N-methylpyridinium (ASP), the endogenous compounds choline, guanidine, histamine, epinephrine, adrenaline, noradrenaline and dopamine, and the drugs quinine, and metformin. The transport of organic cations is inhibited by a broad array of compounds like tetramethylammonium (TMA), cocaine, lidocaine, NMDA receptor antagonists, atropine, prazosin, cimetidine, TEA and NMN, guanidine, cimetidine, choline, procainamide, quinine, tetrabutylammonium, and tetrapentylammonium. Translocates organic cations in an electrogenic and pH-independent manner. Translocates organic cations across the plasma membrane in both directions. Transports the polyamines spermine and spermidine. Transports pramipexole across the basolateral membrane of the proximal tubular epithelial cells. The choline transport is activated by MMTS. Regulated by various intracellular signaling pathways including inhibition by protein kinase A activation, and endogenously activation by the calmodulin complex, the calmodulin- dependent kinase II and LCK tyrosine kinase
Gene Name:: SLC22A1
Uniprot ID:: O15245
Molecular weight:: 61187.4

References

Chen R, Nelson JA: Role of organic cation transporters in the renal secretion of nucleosides. Biochem Pharmacol. 2000 Jul 15;60(2):215-9. [PubMed:10825466 ]

Enzyme Details

3. Solute carrier family 22 member 2

General function:: Involved in ion transmembrane transporter activity
Specific function:: Mediates tubular uptake of organic compounds from circulation. Mediates the influx of agmatine, dopamine, noradrenaline (norepinephrine), serotonin, choline, famotidine, ranitidine, histamin, creatinine, amantadine, memantine, acriflavine, 4-[4-(dimethylamino)-styryl]-N-methylpyridinium ASP, amiloride, metformin, N-1-methylnicotinamide (NMN), tetraethylammonium (TEA), 1-methyl-4-phenylpyridinium (MPP), cimetidine, cisplatin and oxaliplatin. Cisplatin may develop a nephrotoxic action. Transport of creatinine is inhibited by fluoroquinolones such as DX-619 and LVFX. This transporter is a major determinant of the anticancer activity of oxaliplatin and may contribute to antitumor specificity
Gene Name:: SLC22A2
Uniprot ID:: O15244
Molecular weight:: 62564.0

References

Chen R, Nelson JA: Role of organic cation transporters in the renal secretion of nucleosides. Biochem Pharmacol. 2000 Jul 15;60(2):215-9. [PubMed:10825466 ]

Showing metabocard for Cytarabine (HMDB0015122)

MOL for HMDB0015122 (Cytarabine)

3D MOL for HMDB0015122 (Cytarabine)

3D SDF for HMDB0015122 (Cytarabine)

3D-SDF for HMDB0015122 (Cytarabine)

PDB for HMDB0015122 (Cytarabine)

3D PDB for HMDB0015122 (Cytarabine)

SMILES for HMDB0015122 (Cytarabine)

INCHI for HMDB0015122 (Cytarabine)

Structure for HMDB0015122 (Cytarabine)

3D Structure for HMDB0015122 (Cytarabine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

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Transporters

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