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Showing metabocard for 1-Methylxanthine (HMDB0010738)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2008-10-16 22:20:23 UTC
Update Date2023-02-21 17:17:26 UTC
HMDB IDHMDB0010738
Secondary Accession Numbers
  • HMDB10738
Metabolite Identification
Common Name1-Methylxanthine
Description1-Methylxanthine 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. 1-Methylxanthine exists in all living organisms, ranging from bacteria to humans. In humans, 1-methylxanthine is involved in the caffeine metabolism pathway. 1-Methylxanthine has been detected, but not quantified in, several different foods, such as garden tomatoes (Solanum lycopersicum), lotus (Nelumbo), okras (Abelmoschus esculentus), tamarinds (Tamarindus indica), and chestnuts (Castanea). This could make 1-methylxanthine a potential biomarker for the consumption of these foods. 1-Methylxanthine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on 1-Methylxanthine.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0010738 (1-Methylxanthine)

  Mrv1652309042000332D          

 12 13  0  0  0  0            999 V2000
    2.7845    0.6979    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    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -0.1271    0.0000 O   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    1.9354    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
    2.0701    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    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
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  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
  6 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
  5 12  1  0  0  0  0
M  END
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3D MOL for HMDB0010738 (1-Methylxanthine)

HMDB0010738
     RDKit          3D
1-Methylxanthine
 18 19  0  0  0  0  0  0  0  0999 V2000
    2.7073   -0.6362   -0.0370 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3476   -0.1314    0.0340 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1056    1.1394    0.4075 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1327    1.8439    0.6856 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1347    1.6592    0.4905 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2100    0.9054    0.1944 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5423    1.1099    0.1754 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1904   -0.0059   -0.2052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2456   -0.9366   -0.4317 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0274   -0.3914   -0.1907 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2684   -0.8801   -0.2607 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4638   -2.0759   -0.6141 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2136   -0.2562    0.8979 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7635   -1.7235    0.0112 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2715   -0.2338   -0.8962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2627    2.6564    0.7874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2793   -0.1309   -0.3100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3816   -1.9122   -0.7382 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  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11  2  1  0
 10  6  2  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  5 16  1  0
  8 17  1  0
  9 18  1  0
M  END
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3D SDF for HMDB0010738 (1-Methylxanthine)

  Mrv1652309042000332D          

 12 13  0  0  0  0            999 V2000
    2.7845    0.6979    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    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -0.1271    0.0000 O   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    1.9354    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
    2.0701    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    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
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  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
  6 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
  5 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0010738

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(=O)NC2=C(NC=N2)C1=O

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

> <INCHI_KEY>
MVOYJPOZRLFTCP-UHFFFAOYSA-N

> <FORMULA>
C6H6N4O2

> <MOLECULAR_WEIGHT>
166.1374

> <EXACT_MASS>
166.049075456

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.919572956844883

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-1-methyl-6,9-dihydro-1H-purin-6-one

> <ALOGPS_LOGP>
-0.46

> <JCHEM_LOGP>
-0.40012594174161076

> <ALOGPS_LOGS>
-1.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.732910917910083

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1098722859664147

> <JCHEM_PKA_STRONGEST_BASIC>
1.665090512988736

> <JCHEM_POLAR_SURFACE_AREA>
81.58

> <JCHEM_REFRACTIVITY>
41.264

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.17e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-methylxanthine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0010738 (1-Methylxanthine)

HMDB0010738
     RDKit          3D
1-Methylxanthine
 18 19  0  0  0  0  0  0  0  0999 V2000
    2.7073   -0.6362   -0.0370 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3476   -0.1314    0.0340 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1056    1.1394    0.4075 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1327    1.8439    0.6856 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1347    1.6592    0.4905 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2100    0.9054    0.1944 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5423    1.1099    0.1754 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1904   -0.0059   -0.2052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2456   -0.9366   -0.4317 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0274   -0.3914   -0.1907 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2684   -0.8801   -0.2607 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4638   -2.0759   -0.6141 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2136   -0.2562    0.8979 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7635   -1.7235    0.0112 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2715   -0.2338   -0.8962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2627    2.6564    0.7874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2793   -0.1309   -0.3100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3816   -1.9122   -0.7382 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  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11  2  1  0
 10  6  2  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  5 16  1  0
  8 17  1  0
  9 18  1  0
M  END
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PDB for HMDB0010738 (1-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       5.198   1.303   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       3.864   2.073   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.530  -0.237   0.000  0.00  0.00           O+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   3.613   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.530   4.383   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.864   3.613   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.198   4.383   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      -0.268   4.089   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -0.268   1.597   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   12                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    2    9                                                  
CONECT    9    8                                                            
CONECT   10    6   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    5                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
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3D PDB for HMDB0010738 (1-Methylxanthine)

COMPND    HMDB0010738
HETATM    1  C1  UNL     1       2.707  -0.636  -0.037  1.00  0.00           C  
HETATM    2  N1  UNL     1       1.348  -0.131   0.034  1.00  0.00           N  
HETATM    3  C2  UNL     1       1.106   1.139   0.408  1.00  0.00           C  
HETATM    4  O1  UNL     1       2.133   1.844   0.686  1.00  0.00           O  
HETATM    5  N2  UNL     1      -0.135   1.659   0.490  1.00  0.00           N  
HETATM    6  C3  UNL     1      -1.210   0.905   0.194  1.00  0.00           C  
HETATM    7  N3  UNL     1      -2.542   1.110   0.175  1.00  0.00           N  
HETATM    8  C4  UNL     1      -3.190  -0.006  -0.205  1.00  0.00           C  
HETATM    9  N4  UNL     1      -2.246  -0.937  -0.432  1.00  0.00           N  
HETATM   10  C5  UNL     1      -1.027  -0.391  -0.191  1.00  0.00           C  
HETATM   11  C6  UNL     1       0.268  -0.880  -0.261  1.00  0.00           C  
HETATM   12  O2  UNL     1       0.464  -2.076  -0.614  1.00  0.00           O  
HETATM   13  H1  UNL     1       3.214  -0.256   0.898  1.00  0.00           H  
HETATM   14  H2  UNL     1       2.763  -1.723   0.011  1.00  0.00           H  
HETATM   15  H3  UNL     1       3.271  -0.234  -0.896  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.263   2.656   0.787  1.00  0.00           H  
HETATM   17  H5  UNL     1      -4.279  -0.131  -0.310  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.382  -1.912  -0.738  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3   11
CONECT    3    4    4    5
CONECT    5    6   16
CONECT    6    7   10   10
CONECT    7    8    8
CONECT    8    9   17
CONECT    9   10   18
CONECT   10   11
CONECT   11   12   12
END
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SMILES for HMDB0010738 (1-Methylxanthine)

CN1C(=O)NC2=C(NC=N2)C1=O
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INCHI for HMDB0010738 (1-Methylxanthine)

InChI=1S/C6H6N4O2/c1-10-5(11)3-4(8-2-7-3)9-6(10)12/h2H,1H3,(H,7,8)(H,9,12)
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H6N4O2
Average Molecular Weight166.1374
Monoisotopic Molecular Weight166.049075456
IUPAC Name2-hydroxy-1-methyl-6,9-dihydro-1H-purin-6-one
Traditional Name1-methylxanthine
CAS Registry Number6136-37-4
SMILES
CN1C(=O)NC2=C(NC=N2)C1=O
InChI Identifier
InChI=1S/C6H6N4O2/c1-10-5(11)3-4(8-2-7-3)9-6(10)12/h2H,1H3,(H,7,8)(H,9,12)
InChI KeyMVOYJPOZRLFTCP-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
  • 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 FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility5340 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg124.23330932474
[M-H]-Not Available124.233http://allccs.zhulab.cn/database/detail?ID=AllCCS00000360
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
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal adenoma 		details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
UrineDetected and Quantified6.0 (4.0-10.0) umol/mmol creatinineAdult (>18 years old)Both
Asthma		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal adenoma 		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. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  3. 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 IDFDB027885
KNApSAcK IDNot Available
Chemspider ID72464
KEGG Compound IDC16358
BioCyc IDCPD-9025
BiGG IDNot Available
Wikipedia LinkXanthine
METLIN IDNot Available
PubChem Compound80220
PDB IDNot Available
ChEBI ID68444
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1155501
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Sims CR 3rd, Delima LR, Calimaran A, Hester R, Pruett WA: Validating the Physiologic Model HumMod as a Substitute for Clinical Trials Involving Acute Normovolemic Hemodilution. Anesth Analg. 2018 Jan;126(1):93-101. doi: 10.1213/ANE.0000000000002430. [PubMed:28863020 ]

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
1-Methylxanthine + Water + Oxygen → 1-Methyluric acid + Hydrogen peroxidedetails
Enzyme Details
2. Cytochrome P450 1A2
General function:
Involved in monooxygenase activity
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.
Gene Name:
CYP1A2
Uniprot ID:
P05177
Molecular weight:
58406.915