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Showing metabocard for 3-Methylxanthine (HMDB0001886)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-02-28 10:47:30 UTC
Update Date2023-02-21 17:15:55 UTC
HMDB IDHMDB0001886
Secondary Accession Numbers
  • HMDB01886
Metabolite Identification
Common Name3-Methylxanthine
Description3-methyl-9H-xanthine is a 3-methylxanthine tautomer where the imidazole proton is located at the 9-position. It has a role as a metabolite. It is a tautomer of a 3-methyl-7H-xanthine. 3-Methylxanthine, also known as 3 MX or purine analog, 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.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001886 (3-Methylxanthine)

  Mrv1652305261923582D          

 12 13  0  0  0  0            999 V2000
   15.6064   -5.4176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0355   -2.9425    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0355   -5.4176    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.3209   -4.1801    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.5305   -3.9286    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.5305   -5.2565    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.0355   -6.2426    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3209   -5.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0355   -3.7676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7499   -5.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7499   -4.1801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0120   -4.5926    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  2  0  0  0  0
  2  9  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  3 10  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  1  0  0  0  0
  5 11  1  0  0  0  0
  5 12  1  0  0  0  0
  6 10  1  0  0  0  0
  6 12  2  0  0  0  0
  9 11  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
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3D MOL for HMDB0001886 (3-Methylxanthine)

HMDB0001886
     RDKit          3D
3-Methylxanthine
 18 19  0  0  0  0  0  0  0  0999 V2000
   -2.2514   -0.9636   -0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1147   -0.0612   -0.0571 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2831    1.2669   -0.1983 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4208    1.7806   -0.3115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2088    2.0826   -0.2208 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0348    1.5834   -0.1033 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0501    2.3401   -0.1232 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2609    0.2203    0.0446 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3161   -0.5670    0.1805 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9183   -1.8598    0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5765   -1.8372    0.2118 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1219   -0.5812    0.0621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9619   -1.8480   -0.6452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4053   -1.2435    1.0388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1733   -0.4969   -0.4133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3678    3.1178   -0.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3109   -0.2430    0.2025 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5977   -2.6903    0.4069 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  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12  2  1  0
 12  8  2  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  5 16  1  0
  9 17  1  0
 10 18  1  0
M  END
Download

3D SDF for HMDB0001886 (3-Methylxanthine)

  Mrv1652305261923582D          

 12 13  0  0  0  0            999 V2000
   15.6064   -5.4176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0355   -2.9425    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0355   -5.4176    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.3209   -4.1801    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.5305   -3.9286    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.5305   -5.2565    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.0355   -6.2426    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3209   -5.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0355   -3.7676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7499   -5.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7499   -4.1801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0120   -4.5926    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  2  0  0  0  0
  2  9  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  3 10  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  1  0  0  0  0
  5 11  1  0  0  0  0
  5 12  1  0  0  0  0
  6 10  1  0  0  0  0
  6 12  2  0  0  0  0
  9 11  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001886

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C2=C(NC=N2)C(=O)NC1=O

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

> <INCHI_KEY>
GMSNIKWWOQHZGF-UHFFFAOYSA-N

> <FORMULA>
C6H6N4O2

> <MOLECULAR_WEIGHT>
166.1374

> <EXACT_MASS>
166.049075456

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.751514434380411

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.46

> <JCHEM_LOGP>
-0.9929977229999999

> <ALOGPS_LOGS>
-1.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.89661498513289

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.856556089951798

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7602900334586414

> <JCHEM_POLAR_SURFACE_AREA>
78.09

> <JCHEM_REFRACTIVITY>
40.0378

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.27e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methylxanthine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001886 (3-Methylxanthine)

HMDB0001886
     RDKit          3D
3-Methylxanthine
 18 19  0  0  0  0  0  0  0  0999 V2000
   -2.2514   -0.9636   -0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1147   -0.0612   -0.0571 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2831    1.2669   -0.1983 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4208    1.7806   -0.3115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2088    2.0826   -0.2208 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0348    1.5834   -0.1033 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0501    2.3401   -0.1232 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2609    0.2203    0.0446 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3161   -0.5670    0.1805 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9183   -1.8598    0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5765   -1.8372    0.2118 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1219   -0.5812    0.0621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9619   -1.8480   -0.6452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4053   -1.2435    1.0388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1733   -0.4969   -0.4133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3678    3.1178   -0.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3109   -0.2430    0.2025 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5977   -2.6903    0.4069 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  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12  2  1  0
 12  8  2  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  5 16  1  0
  9 17  1  0
 10 18  1  0
M  END
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PDB for HMDB0001886 (3-Methylxanthine)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  O   UNK     0      29.132 -10.113   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      31.800  -5.493   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      31.800 -10.113   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0      30.466  -7.803   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      34.590  -7.333   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      34.590  -9.812   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      31.800 -11.653   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      30.466  -9.343   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      31.800  -7.033   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      33.133  -9.343   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      33.133  -7.803   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      35.489  -8.573   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3    7    8   10                                                  
CONECT    4    8    9                                                       
CONECT    5   11   12                                                       
CONECT    6   10   12                                                       
CONECT    7    3                                                            
CONECT    8    1    3    4                                                  
CONECT    9    2    4   11                                                  
CONECT   10    3    6   11                                                  
CONECT   11    5    9   10                                                  
CONECT   12    5    6                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
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3D PDB for HMDB0001886 (3-Methylxanthine)

COMPND    HMDB0001886
HETATM    1  C1  UNL     1      -2.251  -0.964  -0.029  1.00  0.00           C  
HETATM    2  N1  UNL     1      -1.115  -0.061  -0.057  1.00  0.00           N  
HETATM    3  C2  UNL     1      -1.283   1.267  -0.198  1.00  0.00           C  
HETATM    4  O1  UNL     1      -2.421   1.781  -0.312  1.00  0.00           O  
HETATM    5  N2  UNL     1      -0.209   2.083  -0.221  1.00  0.00           N  
HETATM    6  C3  UNL     1       1.035   1.583  -0.103  1.00  0.00           C  
HETATM    7  O2  UNL     1       2.050   2.340  -0.123  1.00  0.00           O  
HETATM    8  C4  UNL     1       1.261   0.220   0.045  1.00  0.00           C  
HETATM    9  N3  UNL     1       2.316  -0.567   0.180  1.00  0.00           N  
HETATM   10  C5  UNL     1       1.918  -1.860   0.287  1.00  0.00           C  
HETATM   11  N4  UNL     1       0.577  -1.837   0.212  1.00  0.00           N  
HETATM   12  C6  UNL     1       0.122  -0.581   0.062  1.00  0.00           C  
HETATM   13  H1  UNL     1      -1.962  -1.848  -0.645  1.00  0.00           H  
HETATM   14  H2  UNL     1      -2.405  -1.243   1.039  1.00  0.00           H  
HETATM   15  H3  UNL     1      -3.173  -0.497  -0.413  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.368   3.118  -0.332  1.00  0.00           H  
HETATM   17  H5  UNL     1       3.311  -0.243   0.202  1.00  0.00           H  
HETATM   18  H6  UNL     1       2.598  -2.690   0.407  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3   12
CONECT    3    4    4    5
CONECT    5    6   16
CONECT    6    7    7    8
CONECT    8    9   12   12
CONECT    9   10   17
CONECT   10   11   11   18
CONECT   11   12
END
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SMILES for HMDB0001886 (3-Methylxanthine)

CN1C2=C(NC=N2)C(=O)NC1=O
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INCHI for HMDB0001886 (3-Methylxanthine)

InChI=1S/C6H6N4O2/c1-10-4-3(7-2-8-4)5(11)9-6(10)12/h2H,1H3,(H,7,8)(H,9,11,12)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-oxo-3-MethylhypoxanthineChEBI
3 MXChEBI
3,9-Dihydro-3-methyl-1H-purine-2,6-dioneChEBI
3-Methyl-3,7(9)-dihydro-purine-2,6-dioneChEBI
3-Methyl-3,9-dihydro-2H,6H-purine-2,6-dioneChEBI
3-Methylxanthine, methyl-(13)C-labeledMeSH
3-Methylxanthine, monopotassium saltMeSH
3-Methylxanthine, monosodium saltMeSH
2,6-Dihydroxy-3-methylpurineHMDB
3-Methyl xanthineHMDB
3-Methyl-3,9-dihydro-purine-2,6-dioneHMDB
Purine analogHMDB
3-MethylxanthineChEBI
Chemical FormulaC6H6N4O2
Average Molecular Weight166.1374
Monoisotopic Molecular Weight166.049075456
IUPAC Name3-methyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione
Traditional Name3-methylxanthine
CAS Registry Number1076-22-8
SMILES
CN1C2=C(NC=N2)C(=O)NC1=O
InChI Identifier
InChI=1S/C6H6N4O2/c1-10-4-3(7-2-8-4)5(11)9-6(10)12/h2H,1H3,(H,7,8)(H,9,11,12)
InChI KeyGMSNIKWWOQHZGF-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
  • Purinone
  • Alkaloid or derivatives
  • Pyrimidone
  • Hydroxypyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility8394 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.50GASPARI,F & BONATI,M (1987)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg124.48430932474
[M-H]-Not Available124.484http://allccs.zhulab.cn/database/detail?ID=AllCCS00000346
[M+H]+Not Available127.896http://allccs.zhulab.cn/database/detail?ID=AllCCS00000346
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
UrineDetected and Quantified12.755 +/- 12.241 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Analysis of 30 no...
 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAutosomal dominant polycystic kidney disease (ADPKD) details
UrineDetected and Quantified8.0 (5.0-14.0) umol/mmol creatinineAdult (>18 years old)Both
Asthma		 details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. 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 ]
Autosomal dominant polycystic kidney disease
  1. Gronwald W, Klein MS, Zeltner R, Schulze BD, Reinhold SW, Deutschmann M, Immervoll AK, Boger CA, Banas B, Eckardt KU, Oefner PJ: Detection of autosomal dominant polycystic kidney disease by NMR spectroscopic fingerprinting of urine. Kidney Int. 2011 Jun;79(11):1244-53. doi: 10.1038/ki.2011.30. Epub 2011 Mar 9. [PubMed:21389975 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022724
KNApSAcK IDC00043196
Chemspider ID63805
KEGG Compound IDC16357
BioCyc IDRXN-11546
BiGG IDNot Available
Wikipedia LinkXanthine
METLIN ID2820
PubChem Compound70639
PDB IDNot Available
ChEBI ID62207
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00029999
Good Scents IDrw1192211
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
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  2. Knoppert DC, Spino M, Beck R, Thiessen JJ, MacLeod SM: Cystic fibrosis: enhanced theophylline metabolism may be linked to the disease. Clin Pharmacol Ther. 1988 Sep;44(3):254-64. [PubMed:3046811 ]
  3. Miller M, Opheim KE, Raisys VA, Motulsky AG: Theophylline metabolism: variation and genetics. Clin Pharmacol Ther. 1984 Feb;35(2):170-82. [PubMed:6362955 ]
  4. Desiraju RK, Sugita ET, Mayock RL: Determination of theophylline and its metabolites by liquid chromatography. J Chromatogr Sci. 1977 Dec;15(12):563-8. [PubMed:591601 ]
  5. Tarka SM Jr, Arnaud MJ, Dvorchik BH, Vesell ES: Theobromine kinetics and metabolic disposition. Clin Pharmacol Ther. 1983 Oct;34(4):546-55. [PubMed:6617078 ]
  6. Tateishi T, Asoh M, Yamaguchi A, Yoda T, Okano YJ, Koitabashi Y, Kobayashi S: Developmental changes in urinary elimination of theophylline and its metabolites in pediatric patients. Pediatr Res. 1999 Jan;45(1):66-70. [PubMed:9890610 ]
  7. Geraets L, Moonen HJ, Wouters EF, Bast A, Hageman GJ: Caffeine metabolites are inhibitors of the nuclear enzyme poly(ADP-ribose)polymerase-1 at physiological concentrations. Biochem Pharmacol. 2006 Sep 28;72(7):902-10. Epub 2006 Jul 25. [PubMed:16870158 ]