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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 22:06:55 UTC

Update Date

2021-09-26 22:53:09 UTC

HMDB ID

HMDB0245000

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine

Description

2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine belongs to the class of organic compounds known as purine 2',3'-dideoxyribonucleosides. Purine 2',3'-dideoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at positions 2 and 3. Based on a literature review very few articles have been published on 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-amino-6-chloro-9-(2,3-dideoxy-beta-d-glycero-pentofuranosyl)-9h-purine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine 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

HMDB0245000
     RDKit          3D
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine
 30 32  0  0  0  0  0  0  0  0999 V2000
    4.4767   -1.6747    0.5712 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7343   -0.4535    0.5345 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3034    0.7070    0.9105 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6485    1.8807    0.8942 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4069    3.3746    1.3866 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.3230    1.9293    0.4750 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4234    2.9280    0.3508 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3024    2.3424   -0.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4927    1.0243   -0.2651 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4656    0.0306   -0.7390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5641   -1.1328    0.2233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0588   -1.3455    0.3474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5843   -0.4238   -0.7361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0049   -0.0354   -0.4348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7984   -1.1713   -0.4524 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7159    0.6436   -0.7410 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7528    0.7331    0.0927 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4522   -0.4140    0.1278 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9828   -2.5621    0.7716 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5055   -1.7269    0.4051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    2.8892   -0.3092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1699   -0.3481   -1.7211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1364   -2.0584   -0.2160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1008   -0.8721    1.1899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3607   -2.3785    0.0759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4470   -1.1031    1.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5405   -0.9458   -1.7015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3676    0.6672   -1.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1189    0.4444    0.5419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7670   -0.9484   -0.5368 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  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
  9 17  1  0
 17 18  2  0
 18  2  1  0
 17  6  1  0
 16 10  1  0
  1 19  1  0
  1 20  1  0
  8 21  1  0
 10 22  1  0
 11 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 15 30  1  0
M  END

  Mrv1652309112100072D          

 18 20  0  0  0  0            999 V2000
   -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 C   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
   -1.1831    1.0091    0.0000 O   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
   -1.8505    2.3190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7643    3.1395    0.0000 O   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 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.1271    0.0000 N   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
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  8 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  0  0  0  0
 14 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245000

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC2=C(N=CN2C2CCC(CO)O2)C(Cl)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H12ClN5O2/c11-8-7-9(15-10(12)14-8)16(4-13-7)6-2-1-5(3-17)18-6/h4-6,17H,1-3H2,(H2,12,14,15)

> <INCHI_KEY>
REYMCWJLONLXGP-UHFFFAOYSA-N

> <FORMULA>
C10H12ClN5O2

> <MOLECULAR_WEIGHT>
269.69

> <EXACT_MASS>
269.0679523

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
25.628954521788007

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[5-(2-amino-6-chloro-9H-purin-9-yl)oxolan-2-yl]methanol

> <ALOGPS_LOGP>
0.42

> <JCHEM_LOGP>
0.42687730166666604

> <ALOGPS_LOGS>
-1.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.29093840059439

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.662169780490675

> <JCHEM_PKA_STRONGEST_BASIC>
1.35480900512514

> <JCHEM_POLAR_SURFACE_AREA>
99.08

> <JCHEM_REFRACTIVITY>
66.38959999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.55e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[5-(2-amino-6-chloropurin-9-yl)oxolan-2-yl]methanol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0245000
     RDKit          3D
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine
 30 32  0  0  0  0  0  0  0  0999 V2000
    4.4767   -1.6747    0.5712 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7343   -0.4535    0.5345 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3034    0.7070    0.9105 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6485    1.8807    0.8942 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4069    3.3746    1.3866 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.3230    1.9293    0.4750 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4234    2.9280    0.3508 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3024    2.3424   -0.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4927    1.0243   -0.2651 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4656    0.0306   -0.7390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5641   -1.1328    0.2233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0588   -1.3455    0.3474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5843   -0.4238   -0.7361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0049   -0.0354   -0.4348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7984   -1.1713   -0.4524 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7159    0.6436   -0.7410 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7528    0.7331    0.0927 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4522   -0.4140    0.1278 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9828   -2.5621    0.7716 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5055   -1.7269    0.4051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    2.8892   -0.3092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1699   -0.3481   -1.7211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1364   -2.0584   -0.2160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1008   -0.8721    1.1899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3607   -2.3785    0.0759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4470   -1.1031    1.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5405   -0.9458   -1.7015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3676    0.6672   -1.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1189    0.4444    0.5419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7670   -0.9484   -0.5368 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  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
  9 17  1  0
 17 18  2  0
 18  2  1  0
 17  6  1  0
 16 10  1  0
  1 19  1  0
  1 20  1  0
  8 21  1  0
 10 22  1  0
 11 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 15 30  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -0.744   3.899   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.161   2.654   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.744   1.408   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.208   1.884   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -2.208   3.424   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.454   4.329   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.293   5.860   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       2.530   0.237   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       3.864  -0.533   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       3.864  -2.073   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
HETATM   17 Cl   UNK     0       2.530  -4.383   0.000  0.00  0.00          Cl+0
HETATM   18  N   UNK     0       5.198   0.237   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    3    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11    8   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14   16                                                       
CONECT   16   15   11   17                                                  
CONECT   17   16                                                            
CONECT   18   14                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0245000
HETATM    1  N1  UNL     1       4.477  -1.675   0.571  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.734  -0.454   0.535  1.00  0.00           C  
HETATM    3  N2  UNL     1       4.303   0.707   0.911  1.00  0.00           N  
HETATM    4  C2  UNL     1       3.648   1.881   0.894  1.00  0.00           C  
HETATM    5 CL1  UNL     1       4.407   3.375   1.387  1.00  0.00          CL  
HETATM    6  C3  UNL     1       2.323   1.929   0.475  1.00  0.00           C  
HETATM    7  N3  UNL     1       1.423   2.928   0.351  1.00  0.00           N  
HETATM    8  C4  UNL     1       0.302   2.342  -0.108  1.00  0.00           C  
HETATM    9  N4  UNL     1       0.493   1.024  -0.265  1.00  0.00           N  
HETATM   10  C5  UNL     1      -0.466   0.031  -0.739  1.00  0.00           C  
HETATM   11  C6  UNL     1      -0.564  -1.133   0.223  1.00  0.00           C  
HETATM   12  C7  UNL     1      -2.059  -1.345   0.347  1.00  0.00           C  
HETATM   13  C8  UNL     1      -2.584  -0.424  -0.736  1.00  0.00           C  
HETATM   14  C9  UNL     1      -4.005  -0.035  -0.435  1.00  0.00           C  
HETATM   15  O1  UNL     1      -4.798  -1.171  -0.452  1.00  0.00           O  
HETATM   16  O2  UNL     1      -1.716   0.644  -0.741  1.00  0.00           O  
HETATM   17  C10 UNL     1       1.753   0.733   0.093  1.00  0.00           C  
HETATM   18  N5  UNL     1       2.452  -0.414   0.128  1.00  0.00           N  
HETATM   19  H1  UNL     1       3.983  -2.562   0.772  1.00  0.00           H  
HETATM   20  H2  UNL     1       5.505  -1.727   0.405  1.00  0.00           H  
HETATM   21  H3  UNL     1      -0.604   2.889  -0.309  1.00  0.00           H  
HETATM   22  H4  UNL     1      -0.170  -0.348  -1.721  1.00  0.00           H  
HETATM   23  H5  UNL     1      -0.136  -2.058  -0.216  1.00  0.00           H  
HETATM   24  H6  UNL     1      -0.101  -0.872   1.190  1.00  0.00           H  
HETATM   25  H7  UNL     1      -2.361  -2.378   0.076  1.00  0.00           H  
HETATM   26  H8  UNL     1      -2.447  -1.103   1.345  1.00  0.00           H  
HETATM   27  H9  UNL     1      -2.540  -0.946  -1.702  1.00  0.00           H  
HETATM   28  H10 UNL     1      -4.368   0.667  -1.203  1.00  0.00           H  
HETATM   29  H11 UNL     1      -4.119   0.444   0.542  1.00  0.00           H  
HETATM   30  H12 UNL     1      -5.767  -0.948  -0.537  1.00  0.00           H  
CONECT    1    2   19   20
CONECT    2    3    3   18
CONECT    3    4
CONECT    4    5    6    6
CONECT    6    7   17
CONECT    7    8    8
CONECT    8    9   21
CONECT    9   10   17
CONECT   10   11   16   22
CONECT   11   12   23   24
CONECT   12   13   25   26
CONECT   13   14   16   27
CONECT   14   15   28   29
CONECT   15   30
CONECT   17   18   18
END

HMDB0245000
     RDKit          3D
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine
 30 32  0  0  0  0  0  0  0  0999 V2000
    4.4767   -1.6747    0.5712 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7343   -0.4535    0.5345 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3034    0.7070    0.9105 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6485    1.8807    0.8942 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4069    3.3746    1.3866 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.3230    1.9293    0.4750 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4234    2.9280    0.3508 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3024    2.3424   -0.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4927    1.0243   -0.2651 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4656    0.0306   -0.7390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5641   -1.1328    0.2233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0588   -1.3455    0.3474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5843   -0.4238   -0.7361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0049   -0.0354   -0.4348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7984   -1.1713   -0.4524 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7159    0.6436   -0.7410 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7528    0.7331    0.0927 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4522   -0.4140    0.1278 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9828   -2.5621    0.7716 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5055   -1.7269    0.4051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    2.8892   -0.3092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1699   -0.3481   -1.7211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1364   -2.0584   -0.2160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1008   -0.8721    1.1899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3607   -2.3785    0.0759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4470   -1.1031    1.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5405   -0.9458   -1.7015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3676    0.6672   -1.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1189    0.4444    0.5419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7670   -0.9484   -0.5368 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  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
  9 17  1  0
 17 18  2  0
 18  2  1  0
 17  6  1  0
 16 10  1  0
  1 19  1  0
  1 20  1  0
  8 21  1  0
 10 22  1  0
 11 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 15 30  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2-Amino-6-chloro-9-(2,3-dideoxy-b-D-glycero-pentofuranosyl)-9H-purine	Generator
2-Amino-6-chloro-9-(2,3-dideoxy-β-D-glycero-pentofuranosyl)-9H-purine	Generator

Chemical Formula

C₁₀H₁₂ClN₅O₂

Average Molecular Weight

269.69

Monoisotopic Molecular Weight

269.0679523

IUPAC Name

[5-(2-amino-6-chloro-9H-purin-9-yl)oxolan-2-yl]methanol

Traditional Name

[5-(2-amino-6-chloropurin-9-yl)oxolan-2-yl]methanol

CAS Registry Number

Not Available

SMILES

NC1=NC2=C(N=CN2C2CCC(CO)O2)C(Cl)=N1

InChI Identifier

InChI=1S/C10H12ClN5O2/c11-8-7-9(15-10(12)14-8)16(4-13-7)6-2-1-5(3-17)18-6/h4-6,17H,1-3H2,(H2,12,14,15)

InChI Key

REYMCWJLONLXGP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2',3'-dideoxyribonucleosides. Purine 2',3'-dideoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at positions 2 and 3.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Purine 2',3'-dideoxyribonucleosides

Direct Parent

Purine 2',3'-dideoxyribonucleosides

Alternative Parents

Substituents

Purine 2',3'-dideoxyribonucleoside
Purine
Imidazopyrimidine
Aminopyrimidine
Halopyrimidine
Aryl chloride
Aryl halide
Pyrimidine
N-substituted imidazole
Heteroaromatic compound
Azole
Imidazole
Oxolane
Oxacycle
Azacycle
Organoheterocyclic compound
Organohalogen compound
Primary alcohol
Primary amine
Organic nitrogen compound
Amine
Alcohol
Hydrocarbon derivative
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)

Source

Exogenous

Exogenous (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	0.42	ALOGPS
logP	0.43	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	14.66	ChemAxon
pKa (Strongest Basic)	1.35	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	99.08 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	66.39 m³·mol⁻¹	ChemAxon
Polarizability	25.63 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]+	167.358	30932474
DeepCCS	[M-H]-	165.0	30932474
DeepCCS	[M-2H]-	197.888	30932474
DeepCCS	[M+Na]+	173.452	30932474
AllCCS	[M+H]+	159.2	32859911
AllCCS	[M+H-H2O]+	155.6	32859911
AllCCS	[M+NH4]+	162.6	32859911
AllCCS	[M+Na]+	163.6	32859911
AllCCS	[M-H]-	158.5	32859911
AllCCS	[M+Na-2H]-	158.2	32859911
AllCCS	[M+HCOO]-	158.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine	NC1=NC2=C(N=CN2C2CCC(CO)O2)C(Cl)=N1	3356.6	Standard polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine	NC1=NC2=C(N=CN2C2CCC(CO)O2)C(Cl)=N1	2347.9	Standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine	NC1=NC2=C(N=CN2C2CCC(CO)O2)C(Cl)=N1	2620.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TMS,isomer #1	C[Si](C)(C)NC1=NC(Cl)=C2N=CN(C3CCC(CO[Si](C)(C)C)O3)C2=N1	2565.8	Semi standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TMS,isomer #1	C[Si](C)(C)NC1=NC(Cl)=C2N=CN(C3CCC(CO[Si](C)(C)C)O3)C2=N1	2580.9	Standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TMS,isomer #1	C[Si](C)(C)NC1=NC(Cl)=C2N=CN(C3CCC(CO[Si](C)(C)C)O3)C2=N1	3538.5	Standard polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(Cl)=C2N=CN(C3CCC(CO)O3)C2=N1)[Si](C)(C)C	2577.7	Semi standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(Cl)=C2N=CN(C3CCC(CO)O3)C2=N1)[Si](C)(C)C	2731.8	Standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(Cl)=C2N=CN(C3CCC(CO)O3)C2=N1)[Si](C)(C)C	3684.5	Standard polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,3TMS,isomer #1	C[Si](C)(C)OCC1CCC(N2C=NC3=C(Cl)N=C(N([Si](C)(C)C)[Si](C)(C)C)N=C32)O1	2588.8	Semi standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,3TMS,isomer #1	C[Si](C)(C)OCC1CCC(N2C=NC3=C(Cl)N=C(N([Si](C)(C)C)[Si](C)(C)C)N=C32)O1	2763.7	Standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,3TMS,isomer #1	C[Si](C)(C)OCC1CCC(N2C=NC3=C(Cl)N=C(N([Si](C)(C)C)[Si](C)(C)C)N=C32)O1	3214.9	Standard polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(Cl)=C2N=CN(C3CCC(CO[Si](C)(C)C(C)(C)C)O3)C2=N1	2947.0	Semi standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(Cl)=C2N=CN(C3CCC(CO[Si](C)(C)C(C)(C)C)O3)C2=N1	3084.3	Standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(Cl)=C2N=CN(C3CCC(CO[Si](C)(C)C(C)(C)C)O3)C2=N1	3559.9	Standard polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(Cl)=C2N=CN(C3CCC(CO)O3)C2=N1)[Si](C)(C)C(C)(C)C	2975.0	Semi standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(Cl)=C2N=CN(C3CCC(CO)O3)C2=N1)[Si](C)(C)C(C)(C)C	3204.8	Standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(Cl)=C2N=CN(C3CCC(CO)O3)C2=N1)[Si](C)(C)C(C)(C)C	3603.5	Standard polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CCC(N2C=NC3=C(Cl)N=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C32)O1	3136.1	Semi standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CCC(N2C=NC3=C(Cl)N=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C32)O1	3432.6	Standard non polar	33892256
2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CCC(N2C=NC3=C(Cl)N=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C32)O1	3369.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine GC-MS (Non-derivatized) - 70eV, Positive	splash10-004l-9240000000-67d82bbac47268f54bc5	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine 10V, Positive-QTOF	splash10-00di-0900000000-fa3ec9f7b8f59958cd43	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine 20V, Positive-QTOF	splash10-00di-0900000000-fa3ec9f7b8f59958cd43	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine 40V, Positive-QTOF	splash10-003r-0900000000-fde0405c56b2791ccc7c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine 10V, Negative-QTOF	splash10-014i-0190000000-ed9801a82f1ca3fae1d7	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine 20V, Negative-QTOF	splash10-001i-0900000000-64c2a89c8e33337b9122	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine 40V, Negative-QTOF	splash10-001i-0900000000-85fa2a8f017d9ff65c13	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	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

10440231

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14430370

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-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine (HMDB0245000)

MOL for HMDB0245000 (2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine)

3D MOL for HMDB0245000 (2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine)

3D SDF for HMDB0245000 (2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine)

3D-SDF for HMDB0245000 (2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine)

PDB for HMDB0245000 (2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine)

3D PDB for HMDB0245000 (2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine)

SMILES for HMDB0245000 (2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine)

INCHI for HMDB0245000 (2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine)

Structure for HMDB0245000 (2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine)

3D Structure for HMDB0245000 (2-Amino-6-chloro-9-(2,3-dideoxy-beta-D-glycero-pentofuranosyl)-9H-purine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra