MiMeDB: Showing metabocard for 3-Methylxanthine (MMDBc0000395)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:36:48 UTC

Update Date

2024-04-30 19:32:06 UTC

Metabolite ID

MMDBc0000395

Metabolite Identification

Common Name

3-Methylxanthine

Description

3-Methylxanthine, also known as 3 MX, 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. 3-Methylxanthine has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 3-methylxanthine a potential biomarker for the consumption of these foods. 3-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 3-Methylxanthine.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

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

Synonyms

Value	Source
2-oxo-3-Methylhypoxanthine	ChEBI
3 MX	ChEBI
3,9-Dihydro-3-methyl-1H-purine-2,6-dione	ChEBI
3-Methyl-3,7(9)-dihydro-purine-2,6-dione	ChEBI
3-Methyl-3,9-dihydro-2H,6H-purine-2,6-dione	ChEBI
3-Methylxanthine, methyl-(13)C-labeled	MeSH
3-Methylxanthine, monopotassium salt	MeSH
3-Methylxanthine, monosodium salt	MeSH
2,6-Dihydroxy-3-methylpurine	HMDB
3-Methyl xanthine	HMDB
3-Methyl-3,9-dihydro-purine-2,6-dione	HMDB
Purine analog	HMDB
3-Methylxanthine	ChEBI

Molecular Formula

C₆H₆N₄O₂

Average Mass

166.1374

Monoisotopic Mass

166.049075456

IUPAC Name

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

Traditional Name

3-methylxanthine

CAS Registry Number

Not Available

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

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
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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

3-methylxanthine (CHEBI:62207 )
Purine alkaloids (C16357 )
a small molecule (3-METHYLXANTHINE )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	12.7 g/L	ALOGPS
logP	-0.46	ALOGPS
logP	-0.99	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	7.86	ChemAxon
pKa (Strongest Basic)	-0.76	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	78.09 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	40.04 m³·mol⁻¹	ChemAxon
Polarizability	14.75 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-01bj-5900000000-e52c5f846a0fa5fe07ef	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-1900000000-ddc5f6a902d7bbd1fb47	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-01b9-1900000000-c8fefaf49ff542098257	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0006-9100000000-e21e77b88dfb9995efdd	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-014i-1900000000-e5e3ab4240496c2d1174	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-014i-0900000000-18cbc6f55db32d03e9fb	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-014i-0900000000-18cbc6f55db32d03e9fb	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-014i-1900000000-e5e3ab4240496c2d1174	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-00kf-9000000000-2798f94f3fae6b71fd24	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-014i-1900000000-e669f6d72e0c6f52426d	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-00xr-4900000000-c551a8b2a18860020666	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-014i-0900000000-368b9799295bcad108a6	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-00xu-5900000000-37aae7a39dc6fe95fe73	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-00r6-9300000000-8446d34de983224e406e	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-014l-9000000000-e59666cd3257a8b919c2	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-0900000000-c30c1961ecbdf271a24e	2015-04-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-1900000000-ab9e73c4012de4c80f38	2015-04-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-014i-9100000000-8c4dac19316eed77c6dc	2015-04-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0900000000-ef5279264b1ae3a9f2c0	2015-04-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01bc-5900000000-ae2f574c67e566bead1c	2015-04-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-1a0783c7fb8ec28a786f	2015-04-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-0900000000-d3632c2d43dc7c3c5d2b	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-4900000000-c71fccea6e32b15af7fa	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00kf-9200000000-9a5e9e09ea4184c6ef37	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0900000000-d5b4655ae02ddbadcfc0	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-4900000000-21e34d3a8183ecf2d209	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, 5%_DMSO, experimental)		2012-12-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2021-10-10	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2021-10-10	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2021-10-10	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, 5%_DMSO, experimental)		2012-12-05	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Feces
Kidney
Liver
Urine

Tissue Locations

Kidney
Liver

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014992	3-Methylxanthine	Formaldehyde	Methylxanthine N3-demethylase NdmB	Demethylation	RHEA	34755880
MMDBr0015484	Hydrogen Ion	3-Methylxanthine	Methylxanthine N1-demethylase NdmA	Demethylation	RHEA	34755880
MMDBr0015485	Hydrogen Ion	3-Methylxanthine	Methylxanthine N1-demethylase NdmA	Demethylation	RHEA	34755880
MMDBr0015488	3-Methylxanthine	Formaldehyde	Methylxanthine N3-demethylase NdmB	Demethylation	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Asthma	Slight Increase	Association	Human Urine	HMDB	15537072
Eosinophilic esophagitis		Association	Human Urine	HMDB	Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	2	Human feces; Human stool; Human	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Bacteroidetes	1		Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Proteobacteria	1	Human

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Urine	Detected and Quantified	8.0		5.0	14.0	umol/mmol creatinine	Adult (>18 years old)	Both	Asthma	HMDB	15537072
Human Urine	Detected and Quantified	4.0		2.3	6.3	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	15537072
Human Urine	Detected and Quantified	6.2		1.4	17.8	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Urine	Detected and Quantified	12.755	12.241			umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human Urine	Detected and Quantified	10.322	9.229			umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human Urine	Detected and Quantified	4.73				umol/mmol creatinine	Adult (>18 years old)	Male	Normal	HMDB	Shaykhutdinov RA, MacInnis GD, Dowlatabadi R, Weljie AM, Vogel HJ. Quantitative analysis of metabolite concentrations in human urine samples using 13C{1H} NMR spectroscopy. Metabolomics. 2009
Human Kidney	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Liver	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Urine	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22932811
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	21389975
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	19754154
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

HMDB0001886

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Xanthine

METLIN ID

2820

PubChem Compound

70639

PDB ID

Not Available

ChEBI ID

62207

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Desiraju RK, Sugita ET, Mayock RL: Determination of theophylline and its metabolites by liquid chromatography. J Chromatogr Sci. 1977 Dec;15(12):563-8. doi: 10.1093/chromsci/15.12.563. [PubMed:591601 ]
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. doi: 10.1038/clpt.1988.147. [PubMed:3046811 ]
Miller M, Opheim KE, Raisys VA, Motulsky AG: Theophylline metabolism: variation and genetics. Clin Pharmacol Ther. 1984 Feb;35(2):170-82. doi: 10.1038/clpt.1984.23. [PubMed:6362955 ]
Tarka SM Jr, Arnaud MJ, Dvorchik BH, Vesell ES: Theobromine kinetics and metabolic disposition. Clin Pharmacol Ther. 1983 Oct;34(4):546-55. doi: 10.1038/clpt.1983.212. [PubMed:6617078 ]
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. doi: 10.1203/00006450-199901000-00011. [PubMed:9890610 ]
Orlando R, Padrini R, Perazzi M, De Martin S, Piccoli P, Palatini P: Liver dysfunction markedly decreases the inhibition of cytochrome P450 1A2-mediated theophylline metabolism by fluvoxamine. Clin Pharmacol Ther. 2006 May;79(5):489-99. doi: 10.1016/j.clpt.2006.01.012. [PubMed:16678550 ]
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. doi: 10.1016/j.bcp.2006.06.023. Epub 2006 Jul 25. [PubMed:16870158 ]

Showing metabocard for 3-Methylxanthine (MMDBc0000395)

MOL for #<Metabolite:0x00007fa4ea1627e0>

3D MOL for #<Metabolite:0x00007fa4ea1627e0>

3D SDF for #<Metabolite:0x00007fa4ea1627e0>

3D-SDF for #<Metabolite:0x00007fa4ea1627e0>

PDB for #<Metabolite:0x00007fa4ea1627e0>

3D PDB for #<Metabolite:0x00007fa4ea1627e0>

SMILES for #<Metabolite:0x00007fa4ea1627e0>

INCHI for #<Metabolite:0x00007fa4ea1627e0>

Structure for #<Metabolite:0x00007fa4ea1627e0>

3D Structure for #<Metabolite:0x00007fa4ea1627e0>