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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 00:26:16 UTC

Update Date

2021-09-26 22:57:08 UTC

HMDB ID

HMDB0247431

Secondary Accession Numbers

None

Metabolite Identification

Common Name

8-Cyclopentyl-1,3-dimethylxanthine

Description

8-Cyclopentyl-1,3-dimethylxanthine, also known as 8-CPDMX or 8-cyclopentyltheophylline, belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety. Based on a literature review a significant number of articles have been published on 8-Cyclopentyl-1,3-dimethylxanthine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 8-cyclopentyl-1,3-dimethylxanthine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 8-Cyclopentyl-1,3-dimethylxanthine 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

HMDB0247431
     RDKit          3D
8-Cyclopentyl-1,3-dimethylxanthine
 34 36  0  0  0  0  0  0  0  0999 V2000
   -4.6106   -1.5585   -0.4273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4468   -0.7016   -0.2533 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2410   -1.2970   -0.2985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0877   -2.5330   -0.4806 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1171   -0.5155   -0.1375 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1853   -0.8468   -0.1389 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8553    0.3188    0.0635 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3154    0.5218    0.1493 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9924    0.0034   -1.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0966   -0.9192   -0.6525 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3692   -0.4278    0.7529 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9387   -0.2677    1.2791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0315    1.3241    0.1830 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2828    0.8384    0.0621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5015    1.4204    0.1048 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6071    2.8434    0.3171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5805    0.6258   -0.0566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7297    1.1565   -0.0191 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7466   -2.1011    0.5431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3424   -2.3104   -1.1988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4971   -0.9674   -0.7028 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6386   -1.7643   -0.2613 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5745    1.5813    0.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4523    0.8425   -1.6368 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2967   -0.5743   -1.7399 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7712   -1.9781   -0.5763 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9944   -0.8310   -1.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8083    0.5855    0.7657 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9411   -1.1598    1.3555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9408    0.2683    2.2348 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5077   -1.2798    1.3231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0317    3.1815    1.2252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1634    3.3910   -0.5404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6609    3.1306    0.4984 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
  7 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  2  0
 17  2  1  0
 14  5  2  0
 12  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  6 22  1  0
  8 23  1  0
  9 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
 11 29  1  0
 12 30  1  0
 12 31  1  0
 16 32  1  0
 16 33  1  0
 16 34  1  0
M  END


  Mrv1652309112102262D          

 18 20  0  0  0  0            999 V2000
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0945    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5795   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3641    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3641    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5795    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  7 10  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  3 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 14 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0247431

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C2=C(NC(=N2)C2CCCC2)C(=O)N(C)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H16N4O2/c1-15-10-8(11(17)16(2)12(15)18)13-9(14-10)7-5-3-4-6-7/h7H,3-6H2,1-2H3,(H,13,14)

> <INCHI_KEY>
SCVHFRLUNIOSGI-UHFFFAOYSA-N

> <FORMULA>
C12H16N4O2

> <MOLECULAR_WEIGHT>
248.286

> <EXACT_MASS>
248.127325771

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
26.687708081959546

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-cyclopentyl-1,3-dimethyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione

> <ALOGPS_LOGP>
1.29

> <JCHEM_LOGP>
1.022676626

> <ALOGPS_LOGS>
-2.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.04321140846485

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5344308118438349

> <JCHEM_POLAR_SURFACE_AREA>
69.30000000000001

> <JCHEM_REFRACTIVITY>
65.9764

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.67e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8-cyclopentyl-1,3-dimethyl-7H-purine-2,6-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0247431
     RDKit          3D
8-Cyclopentyl-1,3-dimethylxanthine
 34 36  0  0  0  0  0  0  0  0999 V2000
   -4.6106   -1.5585   -0.4273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4468   -0.7016   -0.2533 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2410   -1.2970   -0.2985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0877   -2.5330   -0.4806 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1171   -0.5155   -0.1375 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1853   -0.8468   -0.1389 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8553    0.3188    0.0635 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3154    0.5218    0.1493 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9924    0.0034   -1.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0966   -0.9192   -0.6525 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3692   -0.4278    0.7529 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9387   -0.2677    1.2791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0315    1.3241    0.1830 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2828    0.8384    0.0621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5015    1.4204    0.1048 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6071    2.8434    0.3171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5805    0.6258   -0.0566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7297    1.1565   -0.0191 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7466   -2.1011    0.5431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3424   -2.3104   -1.1988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4971   -0.9674   -0.7028 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6386   -1.7643   -0.2613 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5745    1.5813    0.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4523    0.8425   -1.6368 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2967   -0.5743   -1.7399 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7712   -1.9781   -0.5763 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9944   -0.8310   -1.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8083    0.5855    0.7657 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9411   -1.1598    1.3555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9408    0.2683    2.2348 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5077   -1.2798    1.3231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0317    3.1815    1.2252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1634    3.3910   -0.5404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6609    3.1306    0.4984 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
  7 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  2  0
 17  2  1  0
 14  5  2  0
 12  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  6 22  1  0
  8 23  1  0
  9 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
 11 29  1  0
 12 30  1  0
 12 31  1  0
 16 32  1  0
 16 33  1  0
 16 34  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       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -1.465   2.016   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -2.370   0.770   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -1.465  -0.476   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -3.910   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.815  -0.476   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -6.280   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -6.280   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.815   2.016   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4   13                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   10                                                  
CONECT    8    7    2    9                                                  
CONECT    9    8                                                            
CONECT   10    7                                                            
CONECT   11    4   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12    3                                                       
CONECT   14   12   15   18                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   14                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0247431
HETATM    1  C1  UNL     1      -4.611  -1.558  -0.427  1.00  0.00           C  
HETATM    2  N1  UNL     1      -3.447  -0.702  -0.253  1.00  0.00           N  
HETATM    3  C2  UNL     1      -2.241  -1.297  -0.299  1.00  0.00           C  
HETATM    4  O1  UNL     1      -2.088  -2.533  -0.481  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.117  -0.515  -0.137  1.00  0.00           C  
HETATM    6  N2  UNL     1       0.185  -0.847  -0.139  1.00  0.00           N  
HETATM    7  C4  UNL     1       0.855   0.319   0.064  1.00  0.00           C  
HETATM    8  C5  UNL     1       2.315   0.522   0.149  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.992   0.003  -1.104  1.00  0.00           C  
HETATM   10  C7  UNL     1       4.097  -0.919  -0.653  1.00  0.00           C  
HETATM   11  C8  UNL     1       4.369  -0.428   0.753  1.00  0.00           C  
HETATM   12  C9  UNL     1       2.939  -0.268   1.279  1.00  0.00           C  
HETATM   13  N3  UNL     1      -0.031   1.324   0.183  1.00  0.00           N  
HETATM   14  C10 UNL     1      -1.283   0.838   0.062  1.00  0.00           C  
HETATM   15  N4  UNL     1      -2.501   1.420   0.105  1.00  0.00           N  
HETATM   16  C11 UNL     1      -2.607   2.843   0.317  1.00  0.00           C  
HETATM   17  C12 UNL     1      -3.580   0.626  -0.057  1.00  0.00           C  
HETATM   18  O2  UNL     1      -4.730   1.156  -0.019  1.00  0.00           O  
HETATM   19  H1  UNL     1      -4.747  -2.101   0.543  1.00  0.00           H  
HETATM   20  H2  UNL     1      -4.342  -2.310  -1.199  1.00  0.00           H  
HETATM   21  H3  UNL     1      -5.497  -0.967  -0.703  1.00  0.00           H  
HETATM   22  H4  UNL     1       0.639  -1.764  -0.261  1.00  0.00           H  
HETATM   23  H5  UNL     1       2.574   1.581   0.320  1.00  0.00           H  
HETATM   24  H6  UNL     1       3.452   0.842  -1.637  1.00  0.00           H  
HETATM   25  H7  UNL     1       2.297  -0.574  -1.740  1.00  0.00           H  
HETATM   26  H8  UNL     1       3.771  -1.978  -0.576  1.00  0.00           H  
HETATM   27  H9  UNL     1       4.994  -0.831  -1.304  1.00  0.00           H  
HETATM   28  H10 UNL     1       4.808   0.586   0.766  1.00  0.00           H  
HETATM   29  H11 UNL     1       4.941  -1.160   1.355  1.00  0.00           H  
HETATM   30  H12 UNL     1       2.941   0.268   2.235  1.00  0.00           H  
HETATM   31  H13 UNL     1       2.508  -1.280   1.323  1.00  0.00           H  
HETATM   32  H14 UNL     1      -2.032   3.182   1.225  1.00  0.00           H  
HETATM   33  H15 UNL     1      -2.163   3.391  -0.540  1.00  0.00           H  
HETATM   34  H16 UNL     1      -3.661   3.131   0.498  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3   17
CONECT    3    4    4    5
CONECT    5    6   14   14
CONECT    6    7   22
CONECT    7    8   13   13
CONECT    8    9   12   23
CONECT    9   10   24   25
CONECT   10   11   26   27
CONECT   11   12   28   29
CONECT   12   30   31
CONECT   13   14
CONECT   14   15
CONECT   15   16   17
CONECT   16   32   33   34
CONECT   17   18   18
END

HMDB0247431
     RDKit          3D
8-Cyclopentyl-1,3-dimethylxanthine
 34 36  0  0  0  0  0  0  0  0999 V2000
   -4.6106   -1.5585   -0.4273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4468   -0.7016   -0.2533 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2410   -1.2970   -0.2985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0877   -2.5330   -0.4806 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1171   -0.5155   -0.1375 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1853   -0.8468   -0.1389 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8553    0.3188    0.0635 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3154    0.5218    0.1493 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9924    0.0034   -1.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0966   -0.9192   -0.6525 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3692   -0.4278    0.7529 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9387   -0.2677    1.2791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0315    1.3241    0.1830 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2828    0.8384    0.0621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5015    1.4204    0.1048 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6071    2.8434    0.3171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5805    0.6258   -0.0566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7297    1.1565   -0.0191 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7466   -2.1011    0.5431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3424   -2.3104   -1.1988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4971   -0.9674   -0.7028 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6386   -1.7643   -0.2613 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5745    1.5813    0.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4523    0.8425   -1.6368 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2967   -0.5743   -1.7399 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7712   -1.9781   -0.5763 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9944   -0.8310   -1.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8083    0.5855    0.7657 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9411   -1.1598    1.3555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9408    0.2683    2.2348 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5077   -1.2798    1.3231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0317    3.1815    1.2252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1634    3.3910   -0.5404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6609    3.1306    0.4984 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
  7 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  2  0
 17  2  1  0
 14  5  2  0
 12  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  6 22  1  0
  8 23  1  0
  9 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
 11 29  1  0
 12 30  1  0
 12 31  1  0
 16 32  1  0
 16 33  1  0
 16 34  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
8-CPDMX	HMDB
8-Cyclopentyltheophylline	HMDB

Chemical Formula

C₁₂H₁₆N₄O₂

Average Molecular Weight

248.286

Monoisotopic Molecular Weight

248.127325771

IUPAC Name

8-cyclopentyl-1,3-dimethyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione

Traditional Name

8-cyclopentyl-1,3-dimethyl-7H-purine-2,6-dione

CAS Registry Number

Not Available

SMILES

CN1C2=C(NC(=N2)C2CCCC2)C(=O)N(C)C1=O

InChI Identifier

InChI=1S/C12H16N4O2/c1-15-10-8(11(17)16(2)12(15)18)13-9(14-10)7-5-3-4-6-7/h7H,3-6H2,1-2H3,(H,13,14)

InChI Key

SCVHFRLUNIOSGI-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyrimidines

Sub Class

Purines and purine derivatives

Direct Parent

Xanthines

Alternative Parents

Substituents

Xanthine
6-oxopurine
Purinone
Alkaloid or derivatives
Pyrimidone
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Vinylogous amide
Lactam
Urea
Azacycle
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organopnictogen compound
Organic oxygen 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	1.29	ALOGPS
logP	1.02	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	8.04	ChemAxon
pKa (Strongest Basic)	-0.53	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	69.3 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	65.98 m³·mol⁻¹	ChemAxon
Polarizability	26.69 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]+	160.261	30932474
DeepCCS	[M-H]-	157.903	30932474
DeepCCS	[M-2H]-	190.804	30932474
DeepCCS	[M+Na]+	166.354	30932474
AllCCS	[M+H]+	156.0	32859911
AllCCS	[M+H-H2O]+	152.4	32859911
AllCCS	[M+NH4]+	159.4	32859911
AllCCS	[M+Na]+	160.4	32859911
AllCCS	[M-H]-	159.6	32859911
AllCCS	[M+Na-2H]-	159.4	32859911
AllCCS	[M+HCOO]-	159.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	10.0151 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.91 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1412.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	233.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	138.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	154.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	107.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	313.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	442.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	88.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	803.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	450.4 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1136.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	233.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	273.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	483.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	256.7 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	198.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
8-Cyclopentyl-1,3-dimethylxanthine	CN1C2=C(NC(=N2)C2CCCC2)C(=O)N(C)C1=O	2591.6	Standard polar	33892256
8-Cyclopentyl-1,3-dimethylxanthine	CN1C2=C(NC(=N2)C2CCCC2)C(=O)N(C)C1=O	2287.8	Standard non polar	33892256
8-Cyclopentyl-1,3-dimethylxanthine	CN1C2=C(NC(=N2)C2CCCC2)C(=O)N(C)C1=O	2388.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
8-Cyclopentyl-1,3-dimethylxanthine,1TMS,isomer #1	CN1C(=O)C2=C(N=C(C3CCCC3)N2[Si](C)(C)C)N(C)C1=O	2354.8	Semi standard non polar	33892256
8-Cyclopentyl-1,3-dimethylxanthine,1TMS,isomer #1	CN1C(=O)C2=C(N=C(C3CCCC3)N2[Si](C)(C)C)N(C)C1=O	2369.0	Standard non polar	33892256
8-Cyclopentyl-1,3-dimethylxanthine,1TMS,isomer #1	CN1C(=O)C2=C(N=C(C3CCCC3)N2[Si](C)(C)C)N(C)C1=O	3056.8	Standard polar	33892256
8-Cyclopentyl-1,3-dimethylxanthine,1TBDMS,isomer #1	CN1C(=O)C2=C(N=C(C3CCCC3)N2[Si](C)(C)C(C)(C)C)N(C)C1=O	2540.8	Semi standard non polar	33892256
8-Cyclopentyl-1,3-dimethylxanthine,1TBDMS,isomer #1	CN1C(=O)C2=C(N=C(C3CCCC3)N2[Si](C)(C)C(C)(C)C)N(C)C1=O	2638.8	Standard non polar	33892256
8-Cyclopentyl-1,3-dimethylxanthine,1TBDMS,isomer #1	CN1C(=O)C2=C(N=C(C3CCCC3)N2[Si](C)(C)C(C)(C)C)N(C)C1=O	3112.5	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 8-Cyclopentyl-1,3-dimethylxanthine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-0950000000-3da11ea22d59f7aab8c7	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 8-Cyclopentyl-1,3-dimethylxanthine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 8-Cyclopentyl-1,3-dimethylxanthine 10V, Positive-QTOF	splash10-0002-0090000000-2d6df444943bd8abf9e0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 8-Cyclopentyl-1,3-dimethylxanthine 20V, Positive-QTOF	splash10-0002-0090000000-2d6df444943bd8abf9e0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 8-Cyclopentyl-1,3-dimethylxanthine 40V, Positive-QTOF	splash10-01q3-3910000000-5305e9c2e9a0b29d38de	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 8-Cyclopentyl-1,3-dimethylxanthine 10V, Negative-QTOF	splash10-0002-0090000000-9825da4495af4eed0ee2	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 8-Cyclopentyl-1,3-dimethylxanthine 20V, Negative-QTOF	splash10-0002-0390000000-9d744dc00a15313fbea4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 8-Cyclopentyl-1,3-dimethylxanthine 40V, Negative-QTOF	splash10-01q9-1900000000-c24db7442700721557dd	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

1843

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

8-Cyclopentyl-1,3-dimethylxanthine

METLIN ID

Not Available

PubChem Compound

1917

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 8-Cyclopentyl-1,3-dimethylxanthine (HMDB0247431)

MOL for HMDB0247431 (8-Cyclopentyl-1,3-dimethylxanthine)

3D MOL for HMDB0247431 (8-Cyclopentyl-1,3-dimethylxanthine)

3D SDF for HMDB0247431 (8-Cyclopentyl-1,3-dimethylxanthine)

3D-SDF for HMDB0247431 (8-Cyclopentyl-1,3-dimethylxanthine)

PDB for HMDB0247431 (8-Cyclopentyl-1,3-dimethylxanthine)

3D PDB for HMDB0247431 (8-Cyclopentyl-1,3-dimethylxanthine)

SMILES for HMDB0247431 (8-Cyclopentyl-1,3-dimethylxanthine)

INCHI for HMDB0247431 (8-Cyclopentyl-1,3-dimethylxanthine)

Structure for HMDB0247431 (8-Cyclopentyl-1,3-dimethylxanthine)

3D Structure for HMDB0247431 (8-Cyclopentyl-1,3-dimethylxanthine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra