NP-MRD: Showing NP-Card for 1-β-D-Arabinofuranosylcytosine (NP0004807)

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Record Information

Version

2.0

Created at

2020-12-09 02:12:55 UTC

Updated at

2021-07-15 16:50:13 UTC

NP-MRD ID

NP0004807

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-β-D-Arabinofuranosylcytosine

Provided By

NPAtlas

Description

Arabinofuranosylcytosine, also known as cytosar or cytarabine, 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. 1-β-D-Arabinofuranosylcytosine is found in Castanopsis fissa, Morinda citrifolia, Xerocomus and Xerocomus nigromaculatus. 1-β-D-Arabinofuranosylcytosine was first documented in 1992 (PMID: 1394652). Based on a literature review very few articles have been published on Arabinofuranosylcytosine.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242121113D          

 30 31  0  0  0  0            999 V2000
    5.0256    0.9792   -0.9376 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6754    0.7619   -0.5527 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3324   -0.4425    0.0222 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0339   -0.6422    0.3884 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0553    0.2685    0.2239 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2604   -0.0642    0.6491 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1853    0.9335    0.4971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4390    0.3953    0.5172 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2128    0.9181   -0.6787 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3150    2.2944   -0.6460 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3087   -1.1037    0.3345 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2228   -1.5940   -0.5891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8780   -1.1884   -0.1948 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2978   -2.4088    0.0763 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4173    1.4394   -0.3412 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5241    2.3081   -0.5070 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7023    1.6740   -0.7190 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4384    0.4116   -1.7093 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6042    1.7036   -0.4514 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0721   -1.2132    0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7832   -1.6111    0.8453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2523   -0.4550    1.6962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9939    0.6161    1.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7639    0.5254   -1.5980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2466    0.4952   -0.6269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6453    2.6414   -0.0302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3387   -1.6528    1.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9067   -2.4037   -1.0410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8615   -0.9283   -1.2657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5355   -2.6577    1.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  5 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17  2  2  0  0  0  0
 13  6  1  0  0  0  0
  1 18  1  0  0  0  0
  1 19  1  0  0  0  0
  3 20  1  0  0  0  0
  4 21  1  0  0  0  0
  6 22  1  1  0  0  0
  8 23  1  1  0  0  0
  9 24  1  0  0  0  0
  9 25  1  0  0  0  0
 10 26  1  0  0  0  0
 11 27  1  1  0  0  0
 12 28  1  0  0  0  0
 13 29  1  6  0  0  0
 14 30  1  0  0  0  0
M  END

     RDKit          3D

 30 31  0  0  0  0  0  0  0  0999 V2000
    5.0256    0.9792   -0.9376 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6754    0.7619   -0.5527 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3324   -0.4425    0.0222 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0339   -0.6422    0.3884 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0553    0.2685    0.2239 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2604   -0.0642    0.6491 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1853    0.9335    0.4971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4390    0.3953    0.5172 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2128    0.9181   -0.6787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3150    2.2944   -0.6460 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3087   -1.1037    0.3345 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2228   -1.5940   -0.5891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8780   -1.1884   -0.1948 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2978   -2.4088    0.0763 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4173    1.4394   -0.3412 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5241    2.3081   -0.5070 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7023    1.6740   -0.7190 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4384    0.4116   -1.7093 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6042    1.7036   -0.4514 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0721   -1.2132    0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7832   -1.6111    0.8453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2523   -0.4550    1.6962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9939    0.6161    1.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7639    0.5254   -1.5980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2466    0.4952   -0.6269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6453    2.6414   -0.0302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3387   -1.6528    1.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9067   -2.4037   -1.0410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8615   -0.9283   -1.2657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5355   -2.6577    1.0000 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  1
  8 23  1  1
  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


  Mrv1652306242121113D          

 30 31  0  0  0  0            999 V2000
    5.0256    0.9792   -0.9376 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6754    0.7619   -0.5527 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3324   -0.4425    0.0222 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0339   -0.6422    0.3884 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0553    0.2685    0.2239 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2604   -0.0642    0.6491 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1853    0.9335    0.4971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4390    0.3953    0.5172 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2128    0.9181   -0.6787 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3150    2.2944   -0.6460 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3087   -1.1037    0.3345 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2228   -1.5940   -0.5891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8780   -1.1884   -0.1948 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2978   -2.4088    0.0763 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4173    1.4394   -0.3412 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5241    2.3081   -0.5070 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7023    1.6740   -0.7190 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4384    0.4116   -1.7093 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6042    1.7036   -0.4514 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0721   -1.2132    0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7832   -1.6111    0.8453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2523   -0.4550    1.6962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9939    0.6161    1.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7639    0.5254   -1.5980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2466    0.4952   -0.6269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6453    2.6414   -0.0302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3387   -1.6528    1.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9067   -2.4037   -1.0410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8615   -0.9283   -1.2657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5355   -2.6577    1.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  5 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17  2  2  0  0  0  0
 13  6  1  0  0  0  0
  1 18  1  0  0  0  0
  1 19  1  0  0  0  0
  3 20  1  0  0  0  0
  4 21  1  0  0  0  0
  6 22  1  1  0  0  0
  8 23  1  1  0  0  0
  9 24  1  0  0  0  0
  9 25  1  0  0  0  0
 10 26  1  0  0  0  0
 11 27  1  1  0  0  0
 12 28  1  0  0  0  0
 13 29  1  6  0  0  0
 14 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0004807

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@]1([H])O[C@]([H])(N2C([H])=C([H])C(=NC2=O)N([H])[H])[C@@]([H])(O[H])[C@]1([H])O[H]

> <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-/m0/s1

> <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>
22.46219907974114

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[(2S,3S,4S,5S)-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>
54.544799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.38e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 30 31  0  0  0  0  0  0  0  0999 V2000
    5.0256    0.9792   -0.9376 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6754    0.7619   -0.5527 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3324   -0.4425    0.0222 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0339   -0.6422    0.3884 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0553    0.2685    0.2239 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2604   -0.0642    0.6491 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1853    0.9335    0.4971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4390    0.3953    0.5172 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2128    0.9181   -0.6787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3150    2.2944   -0.6460 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3087   -1.1037    0.3345 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2228   -1.5940   -0.5891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8780   -1.1884   -0.1948 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2978   -2.4088    0.0763 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4173    1.4394   -0.3412 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5241    2.3081   -0.5070 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7023    1.6740   -0.7190 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4384    0.4116   -1.7093 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6042    1.7036   -0.4514 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0721   -1.2132    0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7832   -1.6111    0.8453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2523   -0.4550    1.6962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9939    0.6161    1.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7639    0.5254   -1.5980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2466    0.4952   -0.6269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6453    2.6414   -0.0302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3387   -1.6528    1.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9067   -2.4037   -1.0410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8615   -0.9283   -1.2657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5355   -2.6577    1.0000 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  1
  8 23  1  1
  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                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  N   UNK     0       5.026   0.979  -0.938  0.00  0.00           N+0
HETATM    2  C   UNK     0       3.675   0.762  -0.553  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.332  -0.443   0.022  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.034  -0.642   0.388  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.055   0.269   0.224  0.00  0.00           N+0
HETATM    6  C   UNK     0      -0.260  -0.064   0.649  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.185   0.934   0.497  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.439   0.395   0.517  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.213   0.918  -0.679  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.315   2.294  -0.646  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.309  -1.104   0.335  0.00  0.00           C+0
HETATM   12  O   UNK     0      -3.223  -1.594  -0.589  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.878  -1.188  -0.195  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.298  -2.409   0.076  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.417   1.439  -0.341  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.524   2.308  -0.507  0.00  0.00           O+0
HETATM   17  N   UNK     0       2.702   1.674  -0.719  0.00  0.00           N+0
HETATM   18  H   UNK     0       5.438   0.412  -1.709  0.00  0.00           H+0
HETATM   19  H   UNK     0       5.604   1.704  -0.451  0.00  0.00           H+0
HETATM   20  H   UNK     0       4.072  -1.213   0.181  0.00  0.00           H+0
HETATM   21  H   UNK     0       1.783  -1.611   0.845  0.00  0.00           H+0
HETATM   22  H   UNK     0      -0.252  -0.455   1.696  0.00  0.00           H+0
HETATM   23  H   UNK     0      -2.994   0.616   1.463  0.00  0.00           H+0
HETATM   24  H   UNK     0      -2.764   0.525  -1.598  0.00  0.00           H+0
HETATM   25  H   UNK     0      -4.247   0.495  -0.627  0.00  0.00           H+0
HETATM   26  H   UNK     0      -2.645   2.641  -0.030  0.00  0.00           H+0
HETATM   27  H   UNK     0      -2.339  -1.653   1.280  0.00  0.00           H+0
HETATM   28  H   UNK     0      -2.907  -2.404  -1.041  0.00  0.00           H+0
HETATM   29  H   UNK     0      -0.862  -0.928  -1.266  0.00  0.00           H+0
HETATM   30  H   UNK     0      -0.536  -2.658   1.000  0.00  0.00           H+0
CONECT    1    2   18   19                                                  
CONECT    2    1    3   17                                                  
CONECT    3    2    4   20                                                  
CONECT    4    3    5   21                                                  
CONECT    5    4    6   15                                                  
CONECT    6    5    7   13   22                                             
CONECT    7    6    8                                                       
CONECT    8    7    9   11   23                                             
CONECT    9    8   10   24   25                                             
CONECT   10    9   26                                                       
CONECT   11    8   12   13   27                                             
CONECT   12   11   28                                                       
CONECT   13   11   14    6   29                                             
CONECT   14   13   30                                                       
CONECT   15    5   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    2                                                       
CONECT   18    1                                                            
CONECT   19    1                                                            
CONECT   20    3                                                            
CONECT   21    4                                                            
CONECT   22    6                                                            
CONECT   23    8                                                            
CONECT   24    9                                                            
CONECT   25    9                                                            
CONECT   26   10                                                            
CONECT   27   11                                                            
CONECT   28   12                                                            
CONECT   29   13                                                            
CONECT   30   14                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   62    0
END

RDKit          3D

30 31  0  0  0  0  0  0  0  0999 V2000
    5.0256    0.9792   -0.9376 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6754    0.7619   -0.5527 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3324   -0.4425    0.0222 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0339   -0.6422    0.3884 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0553    0.2685    0.2239 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2604   -0.0642    0.6491 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1853    0.9335    0.4971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4390    0.3953    0.5172 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2128    0.9181   -0.6787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3150    2.2944   -0.6460 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3087   -1.1037    0.3345 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2228   -1.5940   -0.5891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8780   -1.1884   -0.1948 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2978   -2.4088    0.0763 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4173    1.4394   -0.3412 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5241    2.3081   -0.5070 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7023    1.6740   -0.7190 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4384    0.4116   -1.7093 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6042    1.7036   -0.4514 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0721   -1.2132    0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7832   -1.6111    0.8453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2523   -0.4550    1.6962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9939    0.6161    1.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7639    0.5254   -1.5980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2466    0.4952   -0.6269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6453    2.6414   -0.0302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3387   -1.6528    1.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9067   -2.4037   -1.0410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8615   -0.9283   -1.2657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5355   -2.6577    1.0000 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  1
  8 23  1  1
  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

Synonyms

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

Chemical Formula

C₉H₁₃N₃O₅

Average Mass

243.2166 Da

Monoisotopic Mass

243.08552 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)C1OC(CO)C(O)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

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Agaricus bisporus	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Castanopsis fissa	LOTUS Database	35616633
Morinda citrifolia	LOTUS Database	35616633
Pleurotus ostreatus	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Xerocomus	NPAtlas	1394652
Xerocomus nigromaculatus	LOTUS Database	35616633

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

Not Available

Substituents

Not Available

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
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	22.46 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

NPAtlas ID

NPA013353

HMDB ID

HMDB0248553

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB021809

KNApSAcK ID

Not Available

Chemspider ID

576

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

Good Scents ID

Not Available

References

General References

Takahashi A, Nunozawa T, Endo T, Nozoe S: Isolation of 1-beta-D-arabinofuranosylcytosine from the mushroom Xerocomus nigromaculatus Hongo. Chem Pharm Bull (Tokyo). 1992 May;40(5):1313-4. doi: 10.1248/cpb.40.1313. [PubMed:1394652 ]

Showing NP-Card for 1-β-D-Arabinofuranosylcytosine (NP0004807)

MOL for NP0004807 (1-β-D-Arabinofuranosylcytosine)

3D MOL for NP0004807 (1-β-D-Arabinofuranosylcytosine)

3D SDF for NP0004807 (1-β-D-Arabinofuranosylcytosine)

3D-SDF for NP0004807 (1-β-D-Arabinofuranosylcytosine)

PDB for NP0004807 (1-β-D-Arabinofuranosylcytosine)

3D PDB for NP0004807 (1-β-D-Arabinofuranosylcytosine)

SMILES for NP0004807 (1-β-D-Arabinofuranosylcytosine)

INCHI for NP0004807 (1-β-D-Arabinofuranosylcytosine)

Structure for NP0004807 (1-β-D-Arabinofuranosylcytosine)

3D Structure for NP0004807 (1-β-D-Arabinofuranosylcytosine)