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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 19:04:15 UTC

Update Date

2021-09-26 23:14:33 UTC

HMDB ID

HMDB0257922

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine

Description

5-(6-amino-2-chloro-9H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol belongs to the class of organic compounds known as purine 2'-deoxyribonucleosides. Purine 2'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 2. Based on a literature review very few articles have been published on 5-(6-amino-2-chloro-9H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-chloro-9-(2-deoxy-beta-d-arabinofuranosyl)adenine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0257922
     RDKit          3D
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.2705    0.5888    0.8101 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1568    0.3406   -0.0373 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2773    0.2345   -1.3819 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1932   -0.0020   -2.1519 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2813   -0.1496   -3.8911 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.0124   -0.1273   -1.5604 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8175   -0.0341   -0.2337 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9140    0.2070    0.5657 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4588    0.2545    1.8285 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1203    0.0519    1.8443 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7301   -0.1248    0.5778 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5843   -0.3760    0.0283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9637    0.7450   -0.9433 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4599    0.4413   -1.0445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1778    1.5352   -1.4964 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7321    0.1206    0.4103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9408   -0.7437    0.5924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1693   -0.9067    1.9470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5822   -0.3774    0.9564 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4130    1.5391    1.1657 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9070   -0.1873    1.0475 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4718    0.0330    2.7073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5065   -1.3076   -0.5762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4492    0.6719   -1.8942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8145    1.6892   -0.3904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5454   -0.4445   -1.7020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5523    2.0854   -0.7772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9423    1.1123    0.9046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8087   -0.2511    0.1421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7837   -1.7269    0.1171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0115   -0.0420    2.4354 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  1  0
  4  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
  8  2  1  0
 19 12  1  0
 11  7  1  0
  1 20  1  0
  1 21  1  0
 10 22  1  0
 12 23  1  0
 13 24  1  0
 13 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
 17 30  1  0
 18 31  1  0
M  END


  Mrv1533004241519412D          

 19 21  0  0  0  0            999 V2000
   -1.1831    1.0091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.8341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    2.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865    1.4216    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.1271    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.8736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6955    3.4867    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505    2.3190    0.0000 O   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  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 12 16  1  0  0  0  0
  3 17  1  0  0  0  0
 17 18  1  0  0  0  0
  2 19  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0257922

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(Cl)=NC2=C1N=CN2C1CC(O)C(CO)O1

> <INCHI_IDENTIFIER>
InChI=1S/C10H12ClN5O3/c11-10-14-8(12)7-9(15-10)16(3-13-7)6-1-4(18)5(2-17)19-6/h3-6,17-18H,1-2H2,(H2,12,14,15)

> <INCHI_KEY>
PTOAARAWEBMLNO-UHFFFAOYSA-N

> <FORMULA>
C10H12ClN5O3

> <MOLECULAR_WEIGHT>
285.69

> <EXACT_MASS>
285.062867

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
26.291820159895757

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-(6-amino-2-chloro-9H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol

> <ALOGPS_LOGP>
-0.12

> <JCHEM_LOGP>
-0.2817754633333334

> <ALOGPS_LOGS>
-1.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.784914754944001

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.886716048865313

> <JCHEM_PKA_STRONGEST_BASIC>
0.7847800778953418

> <JCHEM_POLAR_SURFACE_AREA>
119.31

> <JCHEM_REFRACTIVITY>
67.1835

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.35e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cladribine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0257922
     RDKit          3D
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.2705    0.5888    0.8101 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1568    0.3406   -0.0373 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2773    0.2345   -1.3819 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1932   -0.0020   -2.1519 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2813   -0.1496   -3.8911 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.0124   -0.1273   -1.5604 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8175   -0.0341   -0.2337 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9140    0.2070    0.5657 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4588    0.2545    1.8285 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1203    0.0519    1.8443 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7301   -0.1248    0.5778 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5843   -0.3760    0.0283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9637    0.7450   -0.9433 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4599    0.4413   -1.0445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1778    1.5352   -1.4964 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7321    0.1206    0.4103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9408   -0.7437    0.5924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1693   -0.9067    1.9470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5822   -0.3774    0.9564 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4130    1.5391    1.1657 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9070   -0.1873    1.0475 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4718    0.0330    2.7073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5065   -1.3076   -0.5762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4492    0.6719   -1.8942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8145    1.6892   -0.3904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5454   -0.4445   -1.7020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5523    2.0854   -0.7772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9423    1.1123    0.9046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8087   -0.2511    0.1421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7837   -1.7269    0.1171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0115   -0.0420    2.4354 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  1  0
  4  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
  8  2  1  0
 19 12  1  0
 11  7  1  0
  1 20  1  0
  1 21  1  0
 10 22  1  0
 12 23  1  0
 13 24  1  0
 13 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
 17 30  1  0
 18 31  1  0
M  END

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0      -2.208   1.884   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.208   3.424   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.744   3.899   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.161   2.654   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -0.744   1.408   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       2.530   0.237   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       3.864  -0.533   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       3.864  -2.073   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       2.530  -4.383   0.000  0.00  0.00           N+0
HETATM   16 Cl   UNK     0       5.198   0.237   0.000  0.00  0.00          Cl+0
HETATM   17  C   UNK     0      -0.268   5.364   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.298   6.509   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -3.454   4.329   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3   19                                                  
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9    6   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13    9   15                                                  
CONECT   15   14                                                            
CONECT   16   12                                                            
CONECT   17    3   18                                                       
CONECT   18   17                                                            
CONECT   19    2                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

COMPND    HMDB0257922
HETATM    1  N1  UNL     1       5.270   0.589   0.810  1.00  0.00           N  
HETATM    2  C1  UNL     1       4.157   0.341  -0.037  1.00  0.00           C  
HETATM    3  N2  UNL     1       4.277   0.235  -1.382  1.00  0.00           N  
HETATM    4  C2  UNL     1       3.193  -0.002  -2.152  1.00  0.00           C  
HETATM    5 CL1  UNL     1       3.281  -0.150  -3.891  1.00  0.00          CL  
HETATM    6  N3  UNL     1       2.012  -0.127  -1.560  1.00  0.00           N  
HETATM    7  C3  UNL     1       1.818  -0.034  -0.234  1.00  0.00           C  
HETATM    8  C4  UNL     1       2.914   0.207   0.566  1.00  0.00           C  
HETATM    9  N4  UNL     1       2.459   0.255   1.829  1.00  0.00           N  
HETATM   10  C5  UNL     1       1.120   0.052   1.844  1.00  0.00           C  
HETATM   11  N5  UNL     1       0.730  -0.125   0.578  1.00  0.00           N  
HETATM   12  C6  UNL     1      -0.584  -0.376   0.028  1.00  0.00           C  
HETATM   13  C7  UNL     1      -0.964   0.745  -0.943  1.00  0.00           C  
HETATM   14  C8  UNL     1      -2.460   0.441  -1.044  1.00  0.00           C  
HETATM   15  O1  UNL     1      -3.178   1.535  -1.496  1.00  0.00           O  
HETATM   16  C9  UNL     1      -2.732   0.121   0.410  1.00  0.00           C  
HETATM   17  C10 UNL     1      -3.941  -0.744   0.592  1.00  0.00           C  
HETATM   18  O2  UNL     1      -4.169  -0.907   1.947  1.00  0.00           O  
HETATM   19  O3  UNL     1      -1.582  -0.377   0.956  1.00  0.00           O  
HETATM   20  H1  UNL     1       5.413   1.539   1.166  1.00  0.00           H  
HETATM   21  H2  UNL     1       5.907  -0.187   1.047  1.00  0.00           H  
HETATM   22  H3  UNL     1       0.472   0.033   2.707  1.00  0.00           H  
HETATM   23  H4  UNL     1      -0.506  -1.308  -0.576  1.00  0.00           H  
HETATM   24  H5  UNL     1      -0.449   0.672  -1.894  1.00  0.00           H  
HETATM   25  H6  UNL     1      -0.814   1.689  -0.390  1.00  0.00           H  
HETATM   26  H7  UNL     1      -2.545  -0.444  -1.702  1.00  0.00           H  
HETATM   27  H8  UNL     1      -3.552   2.085  -0.777  1.00  0.00           H  
HETATM   28  H9  UNL     1      -2.942   1.112   0.905  1.00  0.00           H  
HETATM   29  H10 UNL     1      -4.809  -0.251   0.142  1.00  0.00           H  
HETATM   30  H11 UNL     1      -3.784  -1.727   0.117  1.00  0.00           H  
HETATM   31  H12 UNL     1      -4.011  -0.042   2.435  1.00  0.00           H  
CONECT    1    2   20   21
CONECT    2    3    3    8
CONECT    3    4
CONECT    4    5    6    6
CONECT    6    7
CONECT    7    8    8   11
CONECT    8    9
CONECT    9   10   10
CONECT   10   11   22
CONECT   11   12
CONECT   12   13   19   23
CONECT   13   14   24   25
CONECT   14   15   16   26
CONECT   15   27
CONECT   16   17   19   28
CONECT   17   18   29   30
CONECT   18   31
END

HMDB0257922
     RDKit          3D
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.2705    0.5888    0.8101 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1568    0.3406   -0.0373 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2773    0.2345   -1.3819 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1932   -0.0020   -2.1519 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2813   -0.1496   -3.8911 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.0124   -0.1273   -1.5604 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8175   -0.0341   -0.2337 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9140    0.2070    0.5657 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4588    0.2545    1.8285 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1203    0.0519    1.8443 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7301   -0.1248    0.5778 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5843   -0.3760    0.0283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9637    0.7450   -0.9433 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4599    0.4413   -1.0445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1778    1.5352   -1.4964 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7321    0.1206    0.4103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9408   -0.7437    0.5924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1693   -0.9067    1.9470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5822   -0.3774    0.9564 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4130    1.5391    1.1657 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9070   -0.1873    1.0475 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4718    0.0330    2.7073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5065   -1.3076   -0.5762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4492    0.6719   -1.8942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8145    1.6892   -0.3904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5454   -0.4445   -1.7020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5523    2.0854   -0.7772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9423    1.1123    0.9046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8087   -0.2511    0.1421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7837   -1.7269    0.1171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0115   -0.0420    2.4354 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  1  0
  4  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
  8  2  1  0
 19 12  1  0
 11  7  1  0
  1 20  1  0
  1 21  1  0
 10 22  1  0
 12 23  1  0
 13 24  1  0
 13 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
 17 30  1  0
 18 31  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₀H₁₂ClN₅O₃

Average Molecular Weight

285.69

Monoisotopic Molecular Weight

285.062867

IUPAC Name

5-(6-amino-2-chloro-9H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol

Traditional Name

cladribine

CAS Registry Number

Not Available

SMILES

NC1=NC(Cl)=NC2=C1N=CN2C1CC(O)C(CO)O1

InChI Identifier

InChI=1S/C10H12ClN5O3/c11-10-14-8(12)7-9(15-10)16(3-13-7)6-1-4(18)5(2-17)19-6/h3-6,17-18H,1-2H2,(H2,12,14,15)

InChI Key

PTOAARAWEBMLNO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleosides. Purine 2'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Purine 2'-deoxyribonucleosides

Direct Parent

Purine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Purine 2'-deoxyribonucleoside
6-aminopurine
Imidazopyrimidine
Purine
Aminopyrimidine
2-halopyrimidine
Halopyrimidine
N-substituted imidazole
Aryl chloride
Aryl halide
Pyrimidine
Imidolactam
Tetrahydrofuran
Heteroaromatic compound
Imidazole
Azole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organohalogen compound
Primary alcohol
Primary amine
Amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Organochloride
Organonitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-0.12	ALOGPS
logP	-0.28	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	0.78	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	119.31 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	67.18 m³·mol⁻¹	ChemAxon
Polarizability	26.29 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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
DeepCCS	[M+H]+	158.774	30932474
DeepCCS	[M-H]-	156.416	30932474
DeepCCS	[M-2H]-	189.366	30932474
DeepCCS	[M+Na]+	164.867	30932474
AllCCS	[M+H]+	162.9	32859911
AllCCS	[M+H-H2O]+	159.4	32859911
AllCCS	[M+NH4]+	166.2	32859911
AllCCS	[M+Na]+	167.1	32859911
AllCCS	[M-H]-	160.6	32859911
AllCCS	[M+Na-2H]-	160.2	32859911
AllCCS	[M+HCOO]-	160.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine	NC1=NC(Cl)=NC2=C1N=CN2C1CC(O)C(CO)O1	3438.5	Standard polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine	NC1=NC(Cl)=NC2=C1N=CN2C1CC(O)C(CO)O1	1896.6	Standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine	NC1=NC(Cl)=NC2=C1N=CN2C1CC(O)C(CO)O1	2803.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O1	2672.0	Semi standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O1	2683.9	Standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O1	3624.4	Standard polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)OC1CO	2683.1	Semi standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)OC1CO	2832.4	Standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TMS,isomer #2	C[Si](C)(C)OC1CC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)OC1CO	3546.5	Standard polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)CC1O	2682.3	Semi standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)CC1O	2875.7	Standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TMS,isomer #3	C[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)CC1O	3583.9	Standard polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,4TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)CC1O[Si](C)(C)C	2698.2	Semi standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,4TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)CC1O[Si](C)(C)C	2848.7	Standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,4TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)CC1O[Si](C)(C)C	3163.0	Standard polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O1	3268.7	Semi standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O1	3385.3	Standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O1	3713.5	Standard polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)OC1CO	3204.3	Semi standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)OC1CO	3486.7	Standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)OC1CO	3602.2	Standard polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)CC1O	3214.8	Semi standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)CC1O	3542.1	Standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)CC1O	3641.6	Standard polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)CC1O[Si](C)(C)C(C)(C)C	3371.4	Semi standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)CC1O[Si](C)(C)C(C)(C)C	3656.2	Standard non polar	33892256
2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)CC1O[Si](C)(C)C(C)(C)C	3440.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9140000000-9e936800b2aa7b94f26b	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

1491

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine (HMDB0257922)

MOL for HMDB0257922 (2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine)

3D MOL for HMDB0257922 (2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine)

3D SDF for HMDB0257922 (2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine)

3D-SDF for HMDB0257922 (2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine)

PDB for HMDB0257922 (2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine)

3D PDB for HMDB0257922 (2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine)

SMILES for HMDB0257922 (2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine)

INCHI for HMDB0257922 (2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine)

Structure for HMDB0257922 (2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine)

3D Structure for HMDB0257922 (2-Chloro-9-(2-deoxy-beta-D-arabinofuranosyl)adenine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra