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Showing metabocard for 7-Methylxanthine (HMDB0001991)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:30 UTC
Update Date2023-02-21 17:16:02 UTC
HMDB IDHMDB0001991
Secondary Accession Numbers
  • HMDB01991
Metabolite Identification
Common Name7-Methylxanthine
Description7-Methylxanthine is a methyl derivative of xanthine, found occasionally in human urine. 7-Methylxanthine is one of the purine components in urinary calculi. Methylated purines originate from the metabolism of methylxanthines (caffeine, theophylline and theobromine). Caffeine is metabolized via successive pathways mainly catalyzed by CYP1A2, xanthine oxidase or N-acetyltransferase-2 to give 14 different metabolites, including 7-methylxanthine. CYP1A2 activity shows an inter-individual variability among the population. CYP1A2, an isoform of the CYP1A cytochrome P450 super-family, is involved in the metabolism of many drugs and plays a potentially important role in the induction of chemical carcinogenesis. Purine derivatives in urinary calculi could be considered markers of abnormal purine metabolism. The content of a purine derivative in stone depends on its average urinary excretion in the general population, similarity to the chemical structure of uric acid, and content of the latter in stone. This suggests that purines in stones represent a solid solution with uric acid as solvent. It is also plausible that methylxanthines, ubiquitous components of the diet and drugs, are involved in the pathogenesis of urolithiasis. (PMID:11712316 , 15833286 , 3506820 , 15013152 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001991 (7-Methylxanthine)

  Mrv1652309042000262D          

 12 13  0  0  0  0            999 V2000
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  5 12  1  0  0  0  0
M  END
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3D MOL for HMDB0001991 (7-Methylxanthine)

HMDB0001991
     RDKit          3D
7-Methylxanthine
 18 19  0  0  0  0  0  0  0  0999 V2000
    1.6606   -0.7646    1.8170 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0569    0.2430    0.9649 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3290    1.5544    0.8866 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5313    2.1069   -0.0353 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2693    1.1579   -0.5668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2359    1.1424   -1.5045 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9021    0.0295   -1.8621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8026    0.0759   -2.7515 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5788   -1.1216   -1.2456 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6171   -1.1522   -0.3006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2951   -2.2276    0.2948 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0746   -0.0140    0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3990   -0.2553    2.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8960   -1.2740    2.4327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2097   -1.5306    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0929    2.0267    1.5071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4865    2.0207   -1.9786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0626   -2.0175   -1.4823 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
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12  2  1  0
 12  5  2  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  6 17  1  0
  9 18  1  0
M  END
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3D SDF for HMDB0001991 (7-Methylxanthine)

  Mrv1652309042000262D          

 12 13  0  0  0  0            999 V2000
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  5 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001991

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C=NC2=C1C(=O)NC(=O)N2

> <INCHI_IDENTIFIER>
InChI=1S/C6H6N4O2/c1-10-2-7-4-3(10)5(11)9-6(12)8-4/h2H,1H3,(H2,8,9,11,12)

> <INCHI_KEY>
PFWLFWPASULGAN-UHFFFAOYSA-N

> <FORMULA>
C6H6N4O2

> <MOLECULAR_WEIGHT>
166.1374

> <EXACT_MASS>
166.049075456

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.765580625668878

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7-methyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione

> <ALOGPS_LOGP>
-0.59

> <JCHEM_LOGP>
0.01661227400000012

> <ALOGPS_LOGS>
-1.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.734120976934491

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.307899146071083

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8497959946108037

> <JCHEM_POLAR_SURFACE_AREA>
76.02000000000001

> <JCHEM_REFRACTIVITY>
41.818599999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.00e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7-methylxanthine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001991 (7-Methylxanthine)

HMDB0001991
     RDKit          3D
7-Methylxanthine
 18 19  0  0  0  0  0  0  0  0999 V2000
    1.6606   -0.7646    1.8170 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0569    0.2430    0.9649 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3290    1.5544    0.8866 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5313    2.1069   -0.0353 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2693    1.1579   -0.5668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2359    1.1424   -1.5045 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9021    0.0295   -1.8621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8026    0.0759   -2.7515 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5788   -1.1216   -1.2456 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6171   -1.1522   -0.3006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2951   -2.2276    0.2948 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0746   -0.0140    0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3990   -0.2553    2.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8960   -1.2740    2.4327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2097   -1.5306    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0929    2.0267    1.5071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4865    2.0207   -1.9786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0626   -2.0175   -1.4823 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
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12  2  1  0
 12  5  2  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  6 17  1  0
  9 18  1  0
M  END
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PDB for HMDB0001991 (7-Methylxanthine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0      -0.744   1.408   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.530   0.237   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.530   1.777   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       3.864  -0.533   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.864  -2.073   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.198  -2.843   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       2.530  -2.843   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    2    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    5                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
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3D PDB for HMDB0001991 (7-Methylxanthine)

COMPND    HMDB0001991
HETATM    1  C1  UNL     1       1.661  -0.765   1.817  1.00  0.00           C  
HETATM    2  N1  UNL     1       1.057   0.243   0.965  1.00  0.00           N  
HETATM    3  C2  UNL     1       1.329   1.554   0.887  1.00  0.00           C  
HETATM    4  N2  UNL     1       0.531   2.107  -0.035  1.00  0.00           N  
HETATM    5  C3  UNL     1      -0.269   1.158  -0.567  1.00  0.00           C  
HETATM    6  N3  UNL     1      -1.236   1.142  -1.504  1.00  0.00           N  
HETATM    7  C4  UNL     1      -1.902   0.029  -1.862  1.00  0.00           C  
HETATM    8  O1  UNL     1      -2.803   0.076  -2.752  1.00  0.00           O  
HETATM    9  N4  UNL     1      -1.579  -1.122  -1.246  1.00  0.00           N  
HETATM   10  C5  UNL     1      -0.617  -1.152  -0.301  1.00  0.00           C  
HETATM   11  O2  UNL     1      -0.295  -2.228   0.295  1.00  0.00           O  
HETATM   12  C6  UNL     1       0.075  -0.014   0.075  1.00  0.00           C  
HETATM   13  H1  UNL     1       2.399  -0.255   2.500  1.00  0.00           H  
HETATM   14  H2  UNL     1       0.896  -1.274   2.433  1.00  0.00           H  
HETATM   15  H3  UNL     1       2.210  -1.531   1.249  1.00  0.00           H  
HETATM   16  H4  UNL     1       2.093   2.027   1.507  1.00  0.00           H  
HETATM   17  H5  UNL     1      -1.486   2.021  -1.979  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.063  -2.018  -1.482  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3   12
CONECT    3    4    4   16
CONECT    4    5
CONECT    5    6   12   12
CONECT    6    7   17
CONECT    7    8    8    9
CONECT    9   10   18
CONECT   10   11   11   12
END
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SMILES for HMDB0001991 (7-Methylxanthine)

CN1C=NC2=C1C(=O)NC(=O)N2
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INCHI for HMDB0001991 (7-Methylxanthine)

InChI=1S/C6H6N4O2/c1-10-2-7-4-3(10)5(11)9-6(12)8-4/h2H,1H3,(H2,8,9,11,12)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3,7-Dihydro-7-methyl-1H-purine-2,6-dioneChEBI
7-MethylxanthinChEBI
HeteroxanthinChEBI
HeteroxanthineChEBI
7-Methylxanthine, 7-(13)C-labeledMeSH
2,6-Dihydroxy-7-methylpurineHMDB
7-Methyl-3,7-dihydro-1H-purine-2,6-dioneHMDB
7-Methyl-7H-purine-2,6-diolHMDB
MethylxanthineHMDB
Chemical FormulaC6H6N4O2
Average Molecular Weight166.1374
Monoisotopic Molecular Weight166.049075456
IUPAC Name7-methyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione
Traditional Name7-methylxanthine
CAS Registry Number552-62-5
SMILES
CN1C=NC2=C1C(=O)NC(=O)N2
InChI Identifier
InChI=1S/C6H6N4O2/c1-10-2-7-4-3(10)5(11)9-6(12)8-4/h2H,1H3,(H2,8,9,11,12)
InChI KeyPFWLFWPASULGAN-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
  • Alkaloid or derivatives
  • Hydroxypyrimidine
  • Pyrimidine
  • N-substituted imidazole
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility18070 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.89GASPARI,F & BONATI,M (1987)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg128.75130932474
[M+H]+MetCCS_train_pos130.77430932474
[M-H]-Not Available128.751http://allccs.zhulab.cn/database/detail?ID=AllCCS00000350
[M+H]+Not Available131.254http://allccs.zhulab.cn/database/detail?ID=AllCCS00000350
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
UrineDetected and Quantified10.0 (2.7-17.8) umol/mmol creatinineAdult (>18 years old)Both
Asthma		 details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Asthma
  1. Zydron M, Baranowski J, Baranowska I: Separation, pre-concentration, and HPLC analysis of methylxanthines in urine samples. J Sep Sci. 2004 Oct;27(14):1166-72. [PubMed:15537072 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB001978
KNApSAcK IDC00007326
Chemspider ID61660
KEGG Compound IDC16353
BioCyc ID7-METHYLXANTHINE
BiGG IDNot Available
Wikipedia LinkXanthine
METLIN IDNot Available
PubChem Compound68374
PDB IDNot Available
ChEBI ID48991
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1214051
References
Synthesis ReferenceHutzenlaub, Wolfgang; Pfleiderer, Wolfgang. Purines. XIII. Simplified syntheses of 7-methyl- and 1,7-dimethylxanthines and -uric acids. Liebigs Annalen der Chemie (1979), (11), 1847-54.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Morris GS, Simmonds HA, Davies PM: Use of biological fluids for the rapid diagnosis of potentially lethal inherited disorders of human purine and pyrimidine metabolism. Biomed Chromatogr. 1986 Jun;1(3):109-18. [PubMed:3506820 ]
  2. Safranow K, Machoy Z: Simultaneous determination of 16 purine derivatives in urinary calculi by gradient reversed-phase high-performance liquid chromatography with UV detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 May 25;819(2):229-35. [PubMed:15833286 ]
  3. Safranow K: [Identification and quantitation of purine derivatives in urinary calculi as markers of abnormal purine metabolism by using high-performance liquid chromatography (HPLC)]. Ann Acad Med Stetin. 2000;46:35-49. [PubMed:11712316 ]
  4. Caubet MS, Comte B, Brazier JL: Determination of urinary 13C-caffeine metabolites by liquid chromatography-mass spectrometry: the use of metabolic ratios to assess CYP1A2 activity. J Pharm Biomed Anal. 2004 Feb 4;34(2):379-89. [PubMed:15013152 ]

Enzymes

Enzyme Details
1. Xanthine dehydrogenase/oxidase
General function:
Involved in oxidoreductase activity
Specific function:
Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species. Has also low oxidase activity towards aldehydes (in vitro).
Gene Name:
XDH
Uniprot ID:
P47989
Molecular weight:
146422.99
Reactions
7-Methylxanthine + Oxygen + Water → 7-Methyluric acid + Hydrogen peroxidedetails