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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:49 UTC

Update Date

2023-02-15 22:03:03 UTC

HMDB ID

HMDB0014340

Secondary Accession Numbers

HMDB14340

Metabolite Identification

Common Name

Vidarabine

Description

Vidarabine, also known as ara a or spongoadenosine, belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety. Vidarabine is a drug which is used for treatment of chickenpox - varicella, herpes zoster and herpes simplex. Vidarabine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Vidarabine.

Structure

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

HMDB0014340
     RDKit          3D
Vidarabine
 32 34  0  0  0  0  0  0  0  0999 V2000
    5.1683    0.9515    1.3869 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1791    0.4269    0.5175 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5844   -0.1944   -0.6000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6854   -0.7228   -1.4812 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3638   -0.6336   -1.2504 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8967   -0.0225   -0.1474 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8252    0.5145    0.7474 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1567    1.0627    1.7507 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8522    0.8751    1.4928 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6608    0.2211    0.3509 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5454   -0.1769   -0.2834 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5677    0.7941   -0.1862 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6501    0.1539   -0.7730 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9296    0.7244   -0.1759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9885    2.1079   -0.4354 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5594   -1.3055   -0.4169 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4369   -2.0541   -1.6026 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2298   -1.3541    0.3375 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5265   -1.1771    1.6742 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7108    0.3386    2.0608 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4112    1.9663    1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0511   -1.2230   -2.3832 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0156    1.2057    2.1221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4018   -0.3996   -1.3599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5888    0.3496   -1.8598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8977    0.6355    0.9290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8116    0.2224   -0.6074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3599    2.3941   -1.1161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3939   -1.6564    0.1989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0974   -1.4587   -2.3439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7089   -2.3086    0.2009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8675   -0.2568    1.8466 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
  7  2  1  0
 18 11  1  0
 10  6  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  9 23  1  0
 11 24  1  6
 13 25  1  6
 14 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  1
 17 30  1  0
 18 31  1  1
 19 32  1  0
M  END

32326
  Mrv0541 02231214302D          

 19 21  0  0  1  0            999 V2000
    3.6940    3.6075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6001    4.0236    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6576    5.4739    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1168    4.5794    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6526    2.5697    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6526    1.2419    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1575    2.7308    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4430    1.4933    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1575    0.2558    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4251    4.0222    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9089    3.3538    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9112    4.6888    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6954    4.4325    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3637    4.9163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8720    2.3183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1341    1.9058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8720    1.4933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1575    1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4430    2.3183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 11  1  0  0  0  0
  1 13  1  0  0  0  0
 10  2  1  1  0  0  0
 12  3  1  6  0  0  0
  4 14  1  0  0  0  0
 11  5  1  1  0  0  0
  5 15  1  0  0  0  0
  5 16  1  0  0  0  0
  6 16  2  0  0  0  0
  6 17  1  0  0  0  0
  7 15  1  0  0  0  0
  7 19  2  0  0  0  0
  8 18  2  0  0  0  0
  8 19  1  0  0  0  0
  9 18  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014340

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7+,10-/m1/s1

> <INCHI_KEY>
OIRDTQYFTABQOQ-UHTZMRCNSA-N

> <FORMULA>
C10H13N5O4

> <MOLECULAR_WEIGHT>
267.2413

> <EXACT_MASS>
267.096753929

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
24.491812595571652

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

> <ALOGPS_LOGP>
-1.21

> <JCHEM_LOGP>
-2.0909638716666668

> <ALOGPS_LOGS>
-1.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.891216627250436

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.454003289052789

> <JCHEM_PKA_STRONGEST_BASIC>
4.9884408144871495

> <JCHEM_POLAR_SURFACE_AREA>
139.54

> <JCHEM_REFRACTIVITY>
63.1956

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.40e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
armes

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0014340
     RDKit          3D
Vidarabine
 32 34  0  0  0  0  0  0  0  0999 V2000
    5.1683    0.9515    1.3869 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1791    0.4269    0.5175 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5844   -0.1944   -0.6000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6854   -0.7228   -1.4812 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3638   -0.6336   -1.2504 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8967   -0.0225   -0.1474 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8252    0.5145    0.7474 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1567    1.0627    1.7507 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8522    0.8751    1.4928 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6608    0.2211    0.3509 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5454   -0.1769   -0.2834 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5677    0.7941   -0.1862 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6501    0.1539   -0.7730 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9296    0.7244   -0.1759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9885    2.1079   -0.4354 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5594   -1.3055   -0.4169 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4369   -2.0541   -1.6026 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2298   -1.3541    0.3375 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5265   -1.1771    1.6742 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7108    0.3386    2.0608 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4112    1.9663    1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0511   -1.2230   -2.3832 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0156    1.2057    2.1221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4018   -0.3996   -1.3599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5888    0.3496   -1.8598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8977    0.6355    0.9290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8116    0.2224   -0.6074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3599    2.3941   -1.1161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3939   -1.6564    0.1989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0974   -1.4587   -2.3439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7089   -2.3086    0.2009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8675   -0.2568    1.8466 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
  7  2  1  0
 18 11  1  0
 10  6  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  9 23  1  0
 11 24  1  6
 13 25  1  6
 14 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  1
 17 30  1  0
 18 31  1  1
 19 32  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 32326                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       6.895   6.734   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       2.987   7.511   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       4.961  10.218   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       9.551   8.548   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       4.952   4.797   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       4.952   2.318   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       2.161   5.097   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       0.827   2.787   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       2.161   0.477   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       4.527   7.508   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.430   6.260   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.434   8.752   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.898   8.274   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.146   9.177   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.494   4.327   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.850   3.557   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.494   2.787   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.161   2.017   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.827   4.327   0.000  0.00  0.00           C+0
CONECT    1   11   13                                                       
CONECT    2   10                                                            
CONECT    3   12                                                            
CONECT    4   14                                                            
CONECT    5   11   15   16                                                  
CONECT    6   16   17                                                       
CONECT    7   15   19                                                       
CONECT    8   18   19                                                       
CONECT    9   18                                                            
CONECT   10    2   11   12                                                  
CONECT   11    1    5   10                                                  
CONECT   12    3   10   13                                                  
CONECT   13    1   12   14                                                  
CONECT   14    4   13                                                       
CONECT   15    5    7   17                                                  
CONECT   16    5    6                                                       
CONECT   17    6   15   18                                                  
CONECT   18    8    9   17                                                  
CONECT   19    7    8                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

COMPND    HMDB0014340
HETATM    1  N1  UNL     1       5.168   0.951   1.387  1.00  0.00           N  
HETATM    2  C1  UNL     1       4.179   0.427   0.518  1.00  0.00           C  
HETATM    3  N2  UNL     1       4.584  -0.194  -0.600  1.00  0.00           N  
HETATM    4  C2  UNL     1       3.685  -0.723  -1.481  1.00  0.00           C  
HETATM    5  N3  UNL     1       2.364  -0.634  -1.250  1.00  0.00           N  
HETATM    6  C3  UNL     1       1.897  -0.023  -0.147  1.00  0.00           C  
HETATM    7  C4  UNL     1       2.825   0.515   0.747  1.00  0.00           C  
HETATM    8  N4  UNL     1       2.157   1.063   1.751  1.00  0.00           N  
HETATM    9  C5  UNL     1       0.852   0.875   1.493  1.00  0.00           C  
HETATM   10  N5  UNL     1       0.661   0.221   0.351  1.00  0.00           N  
HETATM   11  C6  UNL     1      -0.545  -0.177  -0.283  1.00  0.00           C  
HETATM   12  O1  UNL     1      -1.568   0.794  -0.186  1.00  0.00           O  
HETATM   13  C7  UNL     1      -2.650   0.154  -0.773  1.00  0.00           C  
HETATM   14  C8  UNL     1      -3.930   0.724  -0.176  1.00  0.00           C  
HETATM   15  O2  UNL     1      -3.988   2.108  -0.435  1.00  0.00           O  
HETATM   16  C9  UNL     1      -2.559  -1.305  -0.417  1.00  0.00           C  
HETATM   17  O3  UNL     1      -2.437  -2.054  -1.603  1.00  0.00           O  
HETATM   18  C10 UNL     1      -1.230  -1.354   0.337  1.00  0.00           C  
HETATM   19  O4  UNL     1      -1.526  -1.177   1.674  1.00  0.00           O  
HETATM   20  H1  UNL     1       5.711   0.339   2.061  1.00  0.00           H  
HETATM   21  H2  UNL     1       5.411   1.966   1.407  1.00  0.00           H  
HETATM   22  H3  UNL     1       4.051  -1.223  -2.383  1.00  0.00           H  
HETATM   23  H4  UNL     1       0.016   1.206   2.122  1.00  0.00           H  
HETATM   24  H5  UNL     1      -0.402  -0.400  -1.360  1.00  0.00           H  
HETATM   25  H6  UNL     1      -2.589   0.350  -1.860  1.00  0.00           H  
HETATM   26  H7  UNL     1      -3.898   0.635   0.929  1.00  0.00           H  
HETATM   27  H8  UNL     1      -4.812   0.222  -0.607  1.00  0.00           H  
HETATM   28  H9  UNL     1      -3.360   2.394  -1.116  1.00  0.00           H  
HETATM   29  H10 UNL     1      -3.394  -1.656   0.199  1.00  0.00           H  
HETATM   30  H11 UNL     1      -2.097  -1.459  -2.344  1.00  0.00           H  
HETATM   31  H12 UNL     1      -0.709  -2.309   0.201  1.00  0.00           H  
HETATM   32  H13 UNL     1      -1.867  -0.257   1.847  1.00  0.00           H  
CONECT    1    2   20   21
CONECT    2    3    3    7
CONECT    3    4
CONECT    4    5    5   22
CONECT    5    6
CONECT    6    7    7   10
CONECT    7    8
CONECT    8    9    9
CONECT    9   10   23
CONECT   10   11
CONECT   11   12   18   24
CONECT   12   13
CONECT   13   14   16   25
CONECT   14   15   26   27
CONECT   15   28
CONECT   16   17   18   29
CONECT   17   30
CONECT   18   19   31
CONECT   19   32
END

HMDB0014340
     RDKit          3D
Vidarabine
 32 34  0  0  0  0  0  0  0  0999 V2000
    5.1683    0.9515    1.3869 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1791    0.4269    0.5175 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5844   -0.1944   -0.6000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6854   -0.7228   -1.4812 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3638   -0.6336   -1.2504 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8967   -0.0225   -0.1474 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8252    0.5145    0.7474 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1567    1.0627    1.7507 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8522    0.8751    1.4928 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6608    0.2211    0.3509 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5454   -0.1769   -0.2834 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5677    0.7941   -0.1862 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6501    0.1539   -0.7730 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9296    0.7244   -0.1759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9885    2.1079   -0.4354 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5594   -1.3055   -0.4169 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4369   -2.0541   -1.6026 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2298   -1.3541    0.3375 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5265   -1.1771    1.6742 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7108    0.3386    2.0608 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4112    1.9663    1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0511   -1.2230   -2.3832 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0156    1.2057    2.1221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4018   -0.3996   -1.3599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5888    0.3496   -1.8598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8977    0.6355    0.9290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8116    0.2224   -0.6074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3599    2.3941   -1.1161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3939   -1.6564    0.1989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0974   -1.4587   -2.3439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7089   -2.3086    0.2009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8675   -0.2568    1.8466 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
  7  2  1  0
 18 11  1  0
 10  6  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  9 23  1  0
 11 24  1  6
 13 25  1  6
 14 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  1
 17 30  1  0
 18 31  1  1
 19 32  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2-(6-AMINO-purin-9-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diol	ChEBI
9-beta-D-Arabinofuranosyl-9H-purin-6-amine	ChEBI
9-beta-D-Arabinofuranosyladenine	ChEBI
Spongoadenosine	ChEBI
Vidarabine anhydrous	Kegg
ARA-a	Kegg
Armes	Kegg
9-b-D-Arabinofuranosyl-9H-purin-6-amine	Generator
9-Β-D-arabinofuranosyl-9H-purin-6-amine	Generator
9-b-D-Arabinofuranosyladenine	Generator
9-Β-D-arabinofuranosyladenine	Generator
9-beta-D-Arabinofuranosyl-adenine	HMDB
Adenine arabinoside	HMDB
Araadenosine	HMDB
Arabinoside adenine	HMDB
Arabinosyl adenine	HMDB
Arabinosyladenine	HMDB
a, alpha-Ara	HMDB
Ara a	HMDB
Arabinofuranosyladenine	HMDB
Monarch brand OF vidarabine	HMDB
ViraA	HMDB
alpha Ara a	HMDB
alpha D Arabinofuranosyladenine	HMDB
alpha-Ara a	HMDB
9 beta Arabinofuranosyladenine	HMDB
9 beta D Arabinofuranosyladenine	HMDB
a, Ara	HMDB
beta Ara a	HMDB
Arabinoside, adenine	HMDB
alpha-D-Arabinofuranosyladenine	HMDB
9-beta-Arabinofuranosyladenine	HMDB
a, beta-Ara	HMDB
Parke davis brand OF vidarabine	HMDB
Vira a	HMDB
Vira-a	HMDB
beta-Ara a	HMDB
Vidarabine	ChEBI

Chemical Formula

C₁₀H₁₃N₅O₄

Average Molecular Weight

267.2413

Monoisotopic Molecular Weight

267.096753929

IUPAC Name

(2R,3S,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

armes

CAS Registry Number

24356-66-9

SMILES

NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7+,10-/m1/s1

InChI Key

OIRDTQYFTABQOQ-UHTZMRCNSA-N

Chemical Taxonomy

Description

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

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Not Available

Direct Parent

Purine nucleosides

Alternative Parents

Substituents

Purine nucleoside
Glycosyl compound
N-glycosyl compound
6-aminopurine
Pentose monosaccharide
Imidazopyrimidine
Purine
Aminopyrimidine
Monosaccharide
N-substituted imidazole
Pyrimidine
Imidolactam
Tetrahydrofuran
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organic oxygen compound
Organic nitrogen compound
Alcohol
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organooxygen compound
Amine
Primary alcohol
Primary amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine nucleoside (CHEBI:45327 )
beta-D-arabinoside (CHEBI:45327 )

Ontology

Not Available

Not Available

Not Available

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	257.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Boiling Point	676.27 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	14 g/L	Not Available
LogP	-2.115	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	Not Available	156.391	http://allccs.zhulab.cn/database/detail?ID=AllCCS00001496

Predicted Molecular Properties

Property	Value	Source
Water Solubility	14 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-2.1	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	12.45	ChemAxon
pKa (Strongest Basic)	4.99	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	139.54 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	63.2 m³·mol⁻¹	ChemAxon
Polarizability	24.49 Å³	ChemAxon
Number of Rings	3	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]+	161.878	31661259
DarkChem	[M-H]-	153.573	31661259
DeepCCS	[M+H]+	155.18	30932474
DeepCCS	[M-H]-	152.785	30932474
DeepCCS	[M-2H]-	187.111	30932474
DeepCCS	[M+Na]+	162.074	30932474
AllCCS	[M+H]+	160.4	32859911
AllCCS	[M+H-H2O]+	156.9	32859911
AllCCS	[M+NH4]+	163.7	32859911
AllCCS	[M+Na]+	164.6	32859911
AllCCS	[M-H]-	159.2	32859911
AllCCS	[M+Na-2H]-	158.7	32859911
AllCCS	[M+HCOO]-	158.3	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	1.89 minutes	32390414
Predicted by Siyang on May 30, 2022	9.5085 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.78 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	217.8 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1110.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	241.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	58.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	157.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	64.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	326.2 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	269.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	600.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	594.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	68.3 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	782.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	168.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	165.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	479.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	358.5 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	181.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Vidarabine	NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O	3472.6	Standard polar	33892256
Vidarabine	NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O	1712.7	Standard non polar	33892256
Vidarabine	NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O	2593.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Vidarabine,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@@H](O)[C@@H]1O	2670.2	Semi standard non polar	33892256
Vidarabine,1TMS,isomer #2	C[Si](C)(C)O[C@H]1[C@H](O)[C@H](N2C=NC3=C(N)N=CN=C32)O[C@@H]1CO	2671.0	Semi standard non polar	33892256
Vidarabine,1TMS,isomer #3	C[Si](C)(C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=NC2=C(N)N=CN=C21	2660.9	Semi standard non polar	33892256
Vidarabine,1TMS,isomer #4	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O	2711.3	Semi standard non polar	33892256
Vidarabine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@@H](O[Si](C)(C)C)[C@@H]1O	2605.5	Semi standard non polar	33892256
Vidarabine,2TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@@H](O)[C@@H]1O[Si](C)(C)C	2600.5	Semi standard non polar	33892256
Vidarabine,2TMS,isomer #3	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@@H]1O	2648.9	Semi standard non polar	33892256
Vidarabine,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=NC2=C(N)N=CN=C21	2607.3	Semi standard non polar	33892256
Vidarabine,2TMS,isomer #5	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@@H]1O	2651.8	Semi standard non polar	33892256
Vidarabine,2TMS,isomer #6	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O[Si](C)(C)C	2640.9	Semi standard non polar	33892256
Vidarabine,2TMS,isomer #7	C[Si](C)(C)N(C1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O)[Si](C)(C)C	2659.3	Semi standard non polar	33892256
Vidarabine,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2569.9	Semi standard non polar	33892256
Vidarabine,3TMS,isomer #2	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C	2621.9	Semi standard non polar	33892256
Vidarabine,3TMS,isomer #3	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O	2617.5	Semi standard non polar	33892256
Vidarabine,3TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H](O)[C@@H]1O	2631.0	Semi standard non polar	33892256
Vidarabine,3TMS,isomer #5	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2621.6	Semi standard non polar	33892256
Vidarabine,3TMS,isomer #6	C[Si](C)(C)O[C@H]1[C@H](O)[C@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)O[C@@H]1CO	2642.3	Semi standard non polar	33892256
Vidarabine,3TMS,isomer #7	C[Si](C)(C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	2633.4	Semi standard non polar	33892256
Vidarabine,4TMS,isomer #1	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2630.3	Semi standard non polar	33892256
Vidarabine,4TMS,isomer #1	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2712.2	Standard non polar	33892256
Vidarabine,4TMS,isomer #1	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	3681.5	Standard polar	33892256
Vidarabine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C)[C@@H]1O	2642.5	Semi standard non polar	33892256
Vidarabine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C)[C@@H]1O	2784.1	Standard non polar	33892256
Vidarabine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C)[C@@H]1O	3406.1	Standard polar	33892256
Vidarabine,4TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H](O)[C@@H]1O[Si](C)(C)C	2639.8	Semi standard non polar	33892256
Vidarabine,4TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H](O)[C@@H]1O[Si](C)(C)C	2771.1	Standard non polar	33892256
Vidarabine,4TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H](O)[C@@H]1O[Si](C)(C)C	3366.6	Standard polar	33892256
Vidarabine,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=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	2643.5	Semi standard non polar	33892256
Vidarabine,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=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	2795.9	Standard non polar	33892256
Vidarabine,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=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	3336.5	Standard polar	33892256
Vidarabine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2689.3	Semi standard non polar	33892256
Vidarabine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2768.0	Standard non polar	33892256
Vidarabine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	3158.7	Standard polar	33892256
Vidarabine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@@H](O)[C@@H]1O	2926.5	Semi standard non polar	33892256
Vidarabine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@H](N2C=NC3=C(N)N=CN=C32)O[C@@H]1CO	2920.6	Semi standard non polar	33892256
Vidarabine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=NC2=C(N)N=CN=C21	2911.6	Semi standard non polar	33892256
Vidarabine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O	2906.2	Semi standard non polar	33892256
Vidarabine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3078.2	Semi standard non polar	33892256
Vidarabine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3076.1	Semi standard non polar	33892256
Vidarabine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O	3062.2	Semi standard non polar	33892256
Vidarabine,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=NC2=C(N)N=CN=C21	3070.4	Semi standard non polar	33892256
Vidarabine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3042.6	Semi standard non polar	33892256
Vidarabine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3035.9	Semi standard non polar	33892256
Vidarabine,2TBDMS,isomer #7	CC(C)(C)[Si](C)(C)N(C1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O)[Si](C)(C)C(C)(C)C	3062.0	Semi standard non polar	33892256
Vidarabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3224.8	Semi standard non polar	33892256
Vidarabine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3226.4	Semi standard non polar	33892256
Vidarabine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3227.4	Semi standard non polar	33892256
Vidarabine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@@H](O)[C@@H]1O	3221.6	Semi standard non polar	33892256
Vidarabine,3TBDMS,isomer #5	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3212.1	Semi standard non polar	33892256
Vidarabine,3TBDMS,isomer #6	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)O[C@@H]1CO	3230.8	Semi standard non polar	33892256
Vidarabine,3TBDMS,isomer #7	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=NC2=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C21	3215.2	Semi standard non polar	33892256
Vidarabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3402.4	Semi standard non polar	33892256
Vidarabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3520.5	Standard non polar	33892256
Vidarabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3871.2	Standard polar	33892256
Vidarabine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3369.8	Semi standard non polar	33892256
Vidarabine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3596.8	Standard non polar	33892256
Vidarabine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3644.5	Standard polar	33892256
Vidarabine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3376.3	Semi standard non polar	33892256
Vidarabine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3592.8	Standard non polar	33892256
Vidarabine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3618.2	Standard polar	33892256
Vidarabine,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=NC2=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C21	3363.7	Semi standard non polar	33892256
Vidarabine,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=NC2=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C21	3595.8	Standard non polar	33892256
Vidarabine,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=NC2=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C21	3594.8	Standard polar	33892256
Vidarabine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3562.3	Semi standard non polar	33892256
Vidarabine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3694.1	Standard non polar	33892256
Vidarabine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3538.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Vidarabine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4l-9350000000-ed8639e5b54e46825628	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Vidarabine GC-MS (3 TMS) - 70eV, Positive	splash10-014i-1492400000-1fe7f0d7ca11fdb4800f	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Vidarabine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Vidarabine 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 - Vidarabine LC-ESI-qTof , Positive-QTOF	splash10-000i-2910000000-e18a8d00eb0e73aa6dec	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Vidarabine , positive-QTOF	splash10-000i-2910000000-e18a8d00eb0e73aa6dec	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 10V, Positive-QTOF	splash10-000i-0940000000-42bee9785f9b55b32eea	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 20V, Positive-QTOF	splash10-000i-0900000000-c8cda6a661ace060572c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 40V, Positive-QTOF	splash10-000i-2900000000-0304a85c3951aa1cb41a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 10V, Negative-QTOF	splash10-0159-0690000000-0258e5851611884483d9	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 20V, Negative-QTOF	splash10-001i-0900000000-e6b8fc6980387f646d64	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 40V, Negative-QTOF	splash10-053r-2900000000-1e0cad8d044715d90f12	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 10V, Negative-QTOF	splash10-001i-0910000000-83e24e24fe97518d665a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 20V, Negative-QTOF	splash10-001i-0900000000-291c06f7d909185dce29	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 40V, Negative-QTOF	splash10-053r-1900000000-1401974aef47ea042a5c	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 10V, Positive-QTOF	splash10-000i-0920000000-c89adfa0ec9ccc01f131	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 20V, Positive-QTOF	splash10-000i-0900000000-c1ee2199364d0258bae1	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vidarabine 40V, Positive-QTOF	splash10-000i-1900000000-fd986996dd15b2469008	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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, 900 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

Biological Properties

Cellular Locations

Cytoplasm

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 DB00194	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00194	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00194

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

20400

KEGG Compound ID

C07195

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Vidarabine

METLIN ID

Not Available

PubChem Compound

21704

PDB ID

RAB

ChEBI ID

45327

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1666791

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Feher Z, Mishra NC: An aphidicolin-resistant mutant of Chinese hamster ovary cell with altered DNA polymerase and 3' exonuclease activities. Biochim Biophys Acta. 1995 Aug 22;1263(2):141-6. [PubMed:7640304 ]
Russell RR 3rd, Bergeron R, Shulman GI, Young LH: Translocation of myocardial GLUT-4 and increased glucose uptake through activation of AMPK by AICAR. Am J Physiol. 1999 Aug;277(2 Pt 2):H643-9. [PubMed:10444490 ]
Moore CL, Chiaramonte M, Higgins T, Kuchta RD: Synthesis of nucleotide analogues that potently and selectively inhibit human DNA primase. Biochemistry. 2002 Nov 26;41(47):14066-75. [PubMed:12437364 ]
Kuchta RD, Ilsley D, Kravig KD, Schubert S, Harris B: Inhibition of DNA primase and polymerase alpha by arabinofuranosylnucleoside triphosphates and related compounds. Biochemistry. 1992 May 19;31(19):4720-8. [PubMed:1581321 ]
Chen J, Hudson E, Chi MM, Chang AS, Moley KH, Hardie DG, Downs SM: AMPK regulation of mouse oocyte meiotic resumption in vitro. Dev Biol. 2006 Mar 15;291(2):227-38. Epub 2006 Jan 26. [PubMed:16443210 ]
Thompson HC, Kuchta RD: Arabinofuranosyl nucleotides are not chain-terminators during initiation of new strands of DNA by DNA polymerase alpha-primase. Biochemistry. 1995 Sep 5;34(35):11198-203. [PubMed:7545435 ]
Feher Z, Mishra NC: Aphidicolin-resistant Chinese hamster ovary cells possess altered DNA polymerases of the alpha-family. Biochim Biophys Acta. 1994 May 17;1218(1):35-47. [PubMed:7514891 ]

Enzymes

Enzyme Details

1. Adenosine deaminase

General function:: Involved in deaminase activity
Specific function:: Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. Plays an important role in purine metabolism and in adenosine homeostasis. Modulates signaling by extracellular adenosine, and so contributes indirectly to cellular signaling events. Acts as a positive regulator of T-cell coactivation, by binding DPP4. Its interaction with DPP4 regulates lymphocyte-epithelial cell adhesion.
Gene Name:: ADA
Uniprot ID:: P00813
Molecular weight:: 40764.13

References

Agarwal RP, Blatt J, Miser J, Sallan S, Lipton JM, Reaman GH, Holcenberg J, Poplack DG: Clinical pharmacology of 9-beta-D-arabinofuranosyladenine in combination with 2'-deoxycoformycin. Cancer Res. 1982 Sep;42(9):3884-6. [PubMed:6980706 ]
Balzarini J, De Clercq E: The antiviral activity of 9-beta-D-arabinofuranosyladenine is enhanced by the 2',3'-dideoxyriboside, the 2',3'-didehydro-2',3'-dideoxyriboside and the 3'-azido-2',3'-dideoxyriboside of 2,6-diaminopurine. Biochem Biophys Res Commun. 1989 Feb 28;159(1):61-7. [PubMed:2538128 ]
Cristalli G, Franchetti P, Grifantini M, Vittori S, Lupidi G, Riva F, Bordoni T, Geroni C, Verini MA: Adenosine deaminase inhibitors. Synthesis and biological activity of deaza analogues of erythro-9-(2-hydroxy-3-nonyl)adenine. J Med Chem. 1988 Feb;31(2):390-3. [PubMed:3339608 ]

Showing metabocard for Vidarabine (HMDB0014340)

MOL for HMDB0014340 (Vidarabine)

3D MOL for HMDB0014340 (Vidarabine)

3D SDF for HMDB0014340 (Vidarabine)

3D-SDF for HMDB0014340 (Vidarabine)

PDB for HMDB0014340 (Vidarabine)

3D PDB for HMDB0014340 (Vidarabine)

SMILES for HMDB0014340 (Vidarabine)

INCHI for HMDB0014340 (Vidarabine)

Structure for HMDB0014340 (Vidarabine)

3D Structure for HMDB0014340 (Vidarabine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

References