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Showing metabocard for 1,3,9-Trimethylxanthine (HMDB0341218)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 19:45:42 UTC
Update Date2022-09-22 18:34:40 UTC
HMDB IDHMDB0341218
Secondary Accession NumbersNone
Metabolite Identification
Common Name1,3,9-Trimethylxanthine
DescriptionIsocaffeine 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. Isocaffeine is a moderately basic compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341218 (1,3,9-Trimethylxanthine)

  Mrv1533004241501192D          

 14 15  0  0  0  0            999 V2000
    4.0668    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
  8 13  1  0  0  0  0
  2 13  1  0  0  0  0
 13 14  2  0  0  0  0
M  END
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3D MOL for HMDB0341218 (1,3,9-Trimethylxanthine)

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3D SDF for HMDB0341218 (1,3,9-Trimethylxanthine)
  Mrv1533004241501192D          

 14 15  0  0  0  0            999 V2000
    4.0668    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
  8 13  1  0  0  0  0
  2 13  1  0  0  0  0
 13 14  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341218

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C=NC2=C1N(C)C(=O)N(C)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H10N4O2/c1-10-4-9-5-6(10)11(2)8(14)12(3)7(5)13/h4H,1-3H3

> <INCHI_KEY>
LPHGQDQBBGAPDZ-UHFFFAOYSA-N

> <FORMULA>
C8H10N4O2

> <MOLECULAR_WEIGHT>
194.194

> <EXACT_MASS>
194.080375578

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
18.87729533208951

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3,9-trimethyl-2,3,6,9-tetrahydro-1H-purine-2,6-dione

> <ALOGPS_LOGP>
-0.20

> <JCHEM_LOGP>
-0.5849629110000002

> <ALOGPS_LOGS>
-1.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
2.3013077702032247

> <JCHEM_POLAR_SURFACE_AREA>
58.440000000000005

> <JCHEM_REFRACTIVITY>
48.5215

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.15e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3,9-trimethylpurine-2,6-dione

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341218 (1,3,9-Trimethylxanthine)
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PDB for HMDB0341218 (1,3,9-Trimethylxanthine)
HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       7.591   4.383   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       6.258   3.613   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       7.591   1.303   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       4.924   1.303   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       4.924  -0.237   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.924   5.923   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   11                                                  
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    7   12                                                  
CONECT   12   11                                                            
CONECT   13    8    2   14                                                  
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

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3D PDB for HMDB0341218 (1,3,9-Trimethylxanthine)
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SMILES for HMDB0341218 (1,3,9-Trimethylxanthine)
CN1C=NC2=C1N(C)C(=O)N(C)C2=O
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INCHI for HMDB0341218 (1,3,9-Trimethylxanthine)
InChI=1S/C8H10N4O2/c1-10-4-9-5-6(10)11(2)8(14)12(3)7(5)13/h4H,1-3H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC8H10N4O2
Average Molecular Weight194.194
Monoisotopic Molecular Weight194.080375578
IUPAC Name1,3,9-trimethyl-2,3,6,9-tetrahydro-1H-purine-2,6-dione
Traditional Name1,3,9-trimethylpurine-2,6-dione
CAS Registry NumberNot Available
SMILES
CN1C=NC2=C1N(C)C(=O)N(C)C2=O
InChI Identifier
InChI=1S/C8H10N4O2/c1-10-4-9-5-6(10)11(2)8(14)12(3)7(5)13/h4H,1-3H3
InChI KeyLPHGQDQBBGAPDZ-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.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassImidazopyrimidines  
Sub ClassPurines and purine derivatives  
Direct ParentXanthines  
Alternative Parents
Substituents
  • Xanthine
    • 

  • 6-oxopurine
    • 

  • Purinone
    • 

  • Alkaloid or derivatives
    • 

  • Pyrimidone
    • 

  • N-substituted imidazole
    • 

  • Pyrimidine
    • 

  • Azole
    • 

  • Imidazole
    • 

  • Heteroaromatic compound
    • 

  • Vinylogous amide
    • 

  • Lactam
    • 

  • Urea
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Predicted Kovats Retention Indices
Not Available
Spectra
MS/MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3,9-Trimethylxanthine  10V, Positive-QTOFsplash10-0002-0900000000-0500d77659547c1c8a0e2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3,9-Trimethylxanthine  20V, Positive-QTOFsplash10-000b-0900000000-b7c7decd0b72915923d22019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3,9-Trimethylxanthine  40V, Positive-QTOFsplash10-001i-9400000000-bbcf7df00c2d4dd6ac4a2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3,9-Trimethylxanthine  10V, Negative-QTOFsplash10-0006-0900000000-150dd7b0f37ca02ac4dd2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3,9-Trimethylxanthine  20V, Negative-QTOFsplash10-0006-0900000000-c3e14c3d502b219ff0c52019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3,9-Trimethylxanthine  40V, Negative-QTOFsplash10-0a4i-9600000000-dbe694c32894119ed9692019-02-23Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound1326  
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920  ]