NP-MRD: Showing NP-Card for Cytarabine (NP0000033)

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Record Information

Version

2.0

Created at

2012-09-06 15:16:51 UTC

Updated at

2021-08-19 20:22:30 UTC

NP-MRD ID

NP0000033

Secondary Accession Numbers

None

Natural Product 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>
NP0000033

> <DATABASE_NAME>
NP-MRD

> <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

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 Mass

243.2166 Da

Monoisotopic Mass

243.08552 Da

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

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Xerocomus	-	KNApSAcK
Xerocomus nigromaculatus	-	KNApSAcK

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 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	212 - 213 °C	Not Available
Boiling Point	545.68 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	43.8 g/L	Not Available
LogP	-2.8	Not Available

Predicted 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

External Links

HMDB ID

HMDB0015122

DrugBank ID

DB00987

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

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

Good Scents ID

rw1380091

References

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 ]
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 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing NP-Card for Cytarabine (NP0000033)

MOL for NP0000033 (Cytarabine)

3D MOL for NP0000033 (Cytarabine)

3D SDF for NP0000033 (Cytarabine)

3D-SDF for NP0000033 (Cytarabine)

PDB for NP0000033 (Cytarabine)

3D PDB for NP0000033 (Cytarabine)

SMILES for NP0000033 (Cytarabine)

INCHI for NP0000033 (Cytarabine)

Structure for NP0000033 (Cytarabine)

3D Structure for NP0000033 (Cytarabine)