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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 22:09:41 UTC

Update Date

2021-09-26 22:53:15 UTC

HMDB ID

HMDB0245052

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2-Chloro-3'-deoxyadenosine

Description

2-(6-amino-2-chloro-9H-purin-9-yl)-5-(hydroxymethyl)oxolan-3-ol belongs to the class of organic compounds known as purine 3'-deoxyribonucleosides. Purine 3'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 3. Based on a literature review very few articles have been published on 2-(6-amino-2-chloro-9H-purin-9-yl)-5-(hydroxymethyl)oxolan-3-ol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-chloro-3'-deoxyadenosine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Chloro-3'-deoxyadenosine 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

HMDB0245052
     RDKit          3D
2-Chloro-3'-deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.1642    0.2429    0.7582 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0185    0.7618    0.1238 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0091    1.8756   -0.6310 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9153    2.3673   -1.2341 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9939    3.8383   -2.2085 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.7601    1.7049   -1.0727 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6950    0.5681   -0.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8274    0.0810    0.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4411   -1.0234    0.9394 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1254   -1.2353    0.7567 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6667   -0.2590   -0.0165 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6901   -0.0815   -0.4725 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5345    0.3400    0.5799 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7857    0.1636   -0.0108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9133    0.4002    0.9564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7977    1.7179    1.4079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6948   -1.3048   -0.4193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3010   -1.3086   -1.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6177   -2.4712   -0.8210 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0812    0.2853    0.2836 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0784   -0.1792    1.7001 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5342   -2.0668    1.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7440    0.7238   -1.2288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8744    0.8144   -0.8775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8581    0.3424    0.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8960   -0.2932    1.8040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8384    1.9553    1.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6717   -1.9187    0.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4749   -1.5946   -1.1274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4619   -1.2369   -2.1673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1563   -3.2096   -0.4782 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
 15 16  1  0
 14 17  1  0
 17 18  1  0
 18 19  1  0
  8  2  1  0
 18 12  1  0
 11  7  1  0
  1 20  1  0
  1 21  1  0
 10 22  1  0
 12 23  1  0
 14 24  1  0
 15 25  1  0
 15 26  1  0
 16 27  1  0
 17 28  1  0
 17 29  1  0
 18 30  1  0
 19 31  1  0
M  END


  Mrv1652309112100092D          

 19 21  0  0  0  0            999 V2000
   -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
   -1.1831    1.0091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505    0.5241    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 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  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
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 13 17  1  0  0  0  0
  2 18  1  0  0  0  0
 18 19  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245052

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO)CC1O

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

> <INCHI_KEY>
HNSLUZJFGNTTEV-UHFFFAOYSA-N

> <FORMULA>
C10H12ClN5O3

> <MOLECULAR_WEIGHT>
285.69

> <EXACT_MASS>
285.062867

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
26.623407409877707

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.05

> <JCHEM_LOGP>
-0.4921188453333335

> <ALOGPS_LOGS>
-1.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.70680280673767

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.527486319788824

> <JCHEM_PKA_STRONGEST_BASIC>
1.3071669535958277

> <JCHEM_POLAR_SURFACE_AREA>
119.31

> <JCHEM_REFRACTIVITY>
67.5971

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.40e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(6-amino-2-chloropurin-9-yl)-5-(hydroxymethyl)oxolan-3-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0245052
     RDKit          3D
2-Chloro-3'-deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.1642    0.2429    0.7582 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0185    0.7618    0.1238 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0091    1.8756   -0.6310 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9153    2.3673   -1.2341 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9939    3.8383   -2.2085 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.7601    1.7049   -1.0727 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6950    0.5681   -0.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8274    0.0810    0.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4411   -1.0234    0.9394 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1254   -1.2353    0.7567 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6667   -0.2590   -0.0165 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6901   -0.0815   -0.4725 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5345    0.3400    0.5799 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7857    0.1636   -0.0108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9133    0.4002    0.9564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7977    1.7179    1.4079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6948   -1.3048   -0.4193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3010   -1.3086   -1.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6177   -2.4712   -0.8210 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0812    0.2853    0.2836 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0784   -0.1792    1.7001 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5342   -2.0668    1.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7440    0.7238   -1.2288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8744    0.8144   -0.8775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8581    0.3424    0.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8960   -0.2932    1.8040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8384    1.9553    1.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6717   -1.9187    0.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4749   -1.5946   -1.1274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4619   -1.2369   -2.1673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1563   -3.2096   -0.4782 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
 15 16  1  0
 14 17  1  0
 17 18  1  0
 18 19  1  0
  8  2  1  0
 18 12  1  0
 11  7  1  0
  1 20  1  0
  1 21  1  0
 10 22  1  0
 12 23  1  0
 14 24  1  0
 15 25  1  0
 15 26  1  0
 16 27  1  0
 17 28  1  0
 17 29  1  0
 18 30  1  0
 19 31  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      -2.208   3.424   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.744   3.899   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.161   2.654   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.744   1.408   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.208   1.884   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.454   0.978   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.530   0.237   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       3.864  -0.533   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       3.864  -2.073   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       2.530  -4.383   0.000  0.00  0.00           N+0
HETATM   17 Cl   UNK     0       5.198   0.237   0.000  0.00  0.00          Cl+0
HETATM   18  C   UNK     0      -0.268   5.364   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -1.298   6.509   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3   18                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5                                                            
CONECT    7    4    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10    7   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15                                                       
CONECT   15   14   10   16                                                  
CONECT   16   15                                                            
CONECT   17   13                                                            
CONECT   18    2   19                                                       
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

COMPND    HMDB0245052
HETATM    1  N1  UNL     1       5.164   0.243   0.758  1.00  0.00           N  
HETATM    2  C1  UNL     1       4.018   0.762   0.124  1.00  0.00           C  
HETATM    3  N2  UNL     1       4.009   1.876  -0.631  1.00  0.00           N  
HETATM    4  C2  UNL     1       2.915   2.367  -1.234  1.00  0.00           C  
HETATM    5 CL1  UNL     1       2.994   3.838  -2.209  1.00  0.00          CL  
HETATM    6  N3  UNL     1       1.760   1.705  -1.073  1.00  0.00           N  
HETATM    7  C3  UNL     1       1.695   0.568  -0.321  1.00  0.00           C  
HETATM    8  C4  UNL     1       2.827   0.081   0.289  1.00  0.00           C  
HETATM    9  N4  UNL     1       2.441  -1.023   0.939  1.00  0.00           N  
HETATM   10  C5  UNL     1       1.125  -1.235   0.757  1.00  0.00           C  
HETATM   11  N5  UNL     1       0.667  -0.259  -0.017  1.00  0.00           N  
HETATM   12  C6  UNL     1      -0.690  -0.082  -0.472  1.00  0.00           C  
HETATM   13  O1  UNL     1      -1.534   0.340   0.580  1.00  0.00           O  
HETATM   14  C7  UNL     1      -2.786   0.164  -0.011  1.00  0.00           C  
HETATM   15  C8  UNL     1      -3.913   0.400   0.956  1.00  0.00           C  
HETATM   16  O2  UNL     1      -3.798   1.718   1.408  1.00  0.00           O  
HETATM   17  C9  UNL     1      -2.695  -1.305  -0.419  1.00  0.00           C  
HETATM   18  C10 UNL     1      -1.301  -1.309  -1.054  1.00  0.00           C  
HETATM   19  O3  UNL     1      -0.618  -2.471  -0.821  1.00  0.00           O  
HETATM   20  H1  UNL     1       6.081   0.285   0.284  1.00  0.00           H  
HETATM   21  H2  UNL     1       5.078  -0.179   1.700  1.00  0.00           H  
HETATM   22  H3  UNL     1       0.534  -2.067   1.172  1.00  0.00           H  
HETATM   23  H4  UNL     1      -0.744   0.724  -1.229  1.00  0.00           H  
HETATM   24  H5  UNL     1      -2.874   0.814  -0.878  1.00  0.00           H  
HETATM   25  H6  UNL     1      -4.858   0.342   0.371  1.00  0.00           H  
HETATM   26  H7  UNL     1      -3.896  -0.293   1.804  1.00  0.00           H  
HETATM   27  H8  UNL     1      -2.838   1.955   1.612  1.00  0.00           H  
HETATM   28  H9  UNL     1      -2.672  -1.919   0.497  1.00  0.00           H  
HETATM   29  H10 UNL     1      -3.475  -1.595  -1.127  1.00  0.00           H  
HETATM   30  H11 UNL     1      -1.462  -1.237  -2.167  1.00  0.00           H  
HETATM   31  H12 UNL     1      -1.156  -3.210  -0.478  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   18   23
CONECT   13   14
CONECT   14   15   17   24
CONECT   15   16   25   26
CONECT   16   27
CONECT   17   18   28   29
CONECT   18   19   30
CONECT   19   31
END

HMDB0245052
     RDKit          3D
2-Chloro-3'-deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.1642    0.2429    0.7582 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0185    0.7618    0.1238 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0091    1.8756   -0.6310 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9153    2.3673   -1.2341 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9939    3.8383   -2.2085 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.7601    1.7049   -1.0727 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6950    0.5681   -0.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8274    0.0810    0.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4411   -1.0234    0.9394 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1254   -1.2353    0.7567 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6667   -0.2590   -0.0165 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6901   -0.0815   -0.4725 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5345    0.3400    0.5799 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7857    0.1636   -0.0108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9133    0.4002    0.9564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7977    1.7179    1.4079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6948   -1.3048   -0.4193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3010   -1.3086   -1.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6177   -2.4712   -0.8210 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0812    0.2853    0.2836 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0784   -0.1792    1.7001 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5342   -2.0668    1.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7440    0.7238   -1.2288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8744    0.8144   -0.8775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8581    0.3424    0.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8960   -0.2932    1.8040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8384    1.9553    1.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6717   -1.9187    0.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4749   -1.5946   -1.1274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4619   -1.2369   -2.1673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1563   -3.2096   -0.4782 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
 15 16  1  0
 14 17  1  0
 17 18  1  0
 18 19  1  0
  8  2  1  0
 18 12  1  0
 11  7  1  0
  1 20  1  0
  1 21  1  0
 10 22  1  0
 12 23  1  0
 14 24  1  0
 15 25  1  0
 15 26  1  0
 16 27  1  0
 17 28  1  0
 17 29  1  0
 18 30  1  0
 19 31  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₀H₁₂ClN₅O₃

Average Molecular Weight

285.69

Monoisotopic Molecular Weight

285.062867

IUPAC Name

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

Traditional Name

2-(6-amino-2-chloropurin-9-yl)-5-(hydroxymethyl)oxolan-3-ol

CAS Registry Number

Not Available

SMILES

NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO)CC1O

InChI Identifier

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

InChI Key

HNSLUZJFGNTTEV-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 3'-deoxyribonucleosides. Purine 3'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 3.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Purine 3'-deoxyribonucleosides

Direct Parent

Purine 3'-deoxyribonucleosides

Alternative Parents

Substituents

Purine 3'-deoxyribonucleoside
6-aminopurine
Imidazopyrimidine
Purine
Aminopyrimidine
2-halopyrimidine
Halopyrimidine
Aryl chloride
Aryl halide
N-substituted imidazole
Imidolactam
Pyrimidine
Heteroaromatic compound
Azole
Imidazole
Oxolane
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organic oxygen compound
Primary alcohol
Primary amine
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	-0.05	ALOGPS
logP	-0.49	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	13.53	ChemAxon
pKa (Strongest Basic)	1.31	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	67.6 m³·mol⁻¹	ChemAxon
Polarizability	26.62 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
DeepCCS	[M+H]+	159.099	30932474
DeepCCS	[M-H]-	156.741	30932474
DeepCCS	[M-2H]-	189.627	30932474
DeepCCS	[M+Na]+	165.193	30932474
AllCCS	[M+H]+	162.7	32859911
AllCCS	[M+H-H2O]+	159.2	32859911
AllCCS	[M+NH4]+	166.0	32859911
AllCCS	[M+Na]+	166.9	32859911
AllCCS	[M-H]-	160.5	32859911
AllCCS	[M+Na-2H]-	160.2	32859911
AllCCS	[M+HCOO]-	159.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Chloro-3'-deoxyadenosine	NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO)CC1O	3435.0	Standard polar	33892256
2-Chloro-3'-deoxyadenosine	NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO)CC1O	2140.2	Standard non polar	33892256
2-Chloro-3'-deoxyadenosine	NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO)CC1O	2720.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Chloro-3'-deoxyadenosine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO[Si](C)(C)C)CC1O[Si](C)(C)C	2656.2	Semi standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO[Si](C)(C)C)CC1O[Si](C)(C)C	2637.4	Standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO[Si](C)(C)C)CC1O[Si](C)(C)C	3618.8	Standard polar	33892256
2-Chloro-3'-deoxyadenosine,3TMS,isomer #2	C[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)O1	2664.0	Semi standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TMS,isomer #2	C[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)O1	2826.6	Standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TMS,isomer #2	C[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)O1	3550.4	Standard polar	33892256
2-Chloro-3'-deoxyadenosine,3TMS,isomer #3	C[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C21	2660.9	Semi standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TMS,isomer #3	C[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C21	2758.3	Standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TMS,isomer #3	C[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C21	3517.1	Standard polar	33892256
2-Chloro-3'-deoxyadenosine,4TMS,isomer #1	C[Si](C)(C)OCC1CC(O[Si](C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)O1	2675.1	Semi standard non polar	33892256
2-Chloro-3'-deoxyadenosine,4TMS,isomer #1	C[Si](C)(C)OCC1CC(O[Si](C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)O1	2761.2	Standard non polar	33892256
2-Chloro-3'-deoxyadenosine,4TMS,isomer #1	C[Si](C)(C)OCC1CC(O[Si](C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=C(Cl)N=C32)O1	3161.5	Standard polar	33892256
2-Chloro-3'-deoxyadenosine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO[Si](C)(C)C(C)(C)C)CC1O[Si](C)(C)C(C)(C)C	3252.7	Semi standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO[Si](C)(C)C(C)(C)C)CC1O[Si](C)(C)C(C)(C)C	3280.1	Standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(Cl)=NC2=C1N=CN2C1OC(CO[Si](C)(C)C(C)(C)C)CC1O[Si](C)(C)C(C)(C)C	3711.4	Standard polar	33892256
2-Chloro-3'-deoxyadenosine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)O1	3197.7	Semi standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)O1	3435.4	Standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)O1	3616.4	Standard polar	33892256
2-Chloro-3'-deoxyadenosine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C21	3174.1	Semi standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C21	3363.1	Standard non polar	33892256
2-Chloro-3'-deoxyadenosine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C21	3588.3	Standard polar	33892256
2-Chloro-3'-deoxyadenosine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CC(O[Si](C)(C)C(C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)O1	3352.5	Semi standard non polar	33892256
2-Chloro-3'-deoxyadenosine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CC(O[Si](C)(C)C(C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)O1	3528.3	Standard non polar	33892256
2-Chloro-3'-deoxyadenosine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CC(O[Si](C)(C)C(C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=C(Cl)N=C32)O1	3441.5	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-3'-deoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9120000000-ed684aa58b10350db310	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-3'-deoxyadenosine GC-MS (TBDMS_2_4) - 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-Chloro-3'-deoxyadenosine 10V, Positive-QTOF	splash10-00rj-4960000000-01f039c27e4b7d5cffab	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Chloro-3'-deoxyadenosine 20V, Positive-QTOF	splash10-00di-0900000000-fa3ec9f7b8f59958cd43	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Chloro-3'-deoxyadenosine 40V, Positive-QTOF	splash10-0089-0900000000-0586805f496ef280098e	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Chloro-3'-deoxyadenosine 10V, Negative-QTOF	splash10-001i-0390000000-95c4d37aa191fac08118	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Chloro-3'-deoxyadenosine 20V, Negative-QTOF	splash10-0159-0900000000-1d4e2e816d6ef6821b76	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Chloro-3'-deoxyadenosine 40V, Negative-QTOF	splash10-001i-1900000000-585f0f2d3388ac4de09e	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

11430963

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14485373

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-3'-deoxyadenosine (HMDB0245052)

MOL for HMDB0245052 (2-Chloro-3'-deoxyadenosine)

3D MOL for HMDB0245052 (2-Chloro-3'-deoxyadenosine)

3D SDF for HMDB0245052 (2-Chloro-3'-deoxyadenosine)

3D-SDF for HMDB0245052 (2-Chloro-3'-deoxyadenosine)

PDB for HMDB0245052 (2-Chloro-3'-deoxyadenosine)

3D PDB for HMDB0245052 (2-Chloro-3'-deoxyadenosine)

SMILES for HMDB0245052 (2-Chloro-3'-deoxyadenosine)

INCHI for HMDB0245052 (2-Chloro-3'-deoxyadenosine)

Structure for HMDB0245052 (2-Chloro-3'-deoxyadenosine)

3D Structure for HMDB0245052 (2-Chloro-3'-deoxyadenosine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra