Milk Composition Database: Showing metabocard for Xanthine (BMDB0000292)

Identification Taxonomy Physical properties Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:27:56 UTC

Update Date

2020-06-04 20:46:39 UTC

MCDB ID

BMDB0000292

Secondary Accession Numbers

BMDB00292

Metabolite Identification

Common Name

Xanthine

Description

Xanthine, also known as Xan or 2,6-dioxopurine, 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. Xanthine exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. Xanthine exists in all living species, ranging from bacteria to humans. Xanthine is a potentially toxic compound. Xanthine has been found to be associated with several diseases known as crohn's disease, colorectal cancer, degenerative disc disease, and cystic fibrosis; also xanthine has been linked to the inborn metabolic disorders including lesch-nyhan syndrome.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2,6-Dihydroxypurine	ChEBI
2,6-Dioxo-1,2,3,6-tetrahydropurine	ChEBI
9H-Purine-2,6-(1H,3H)-dione	ChEBI
Purine-2(3H),6(1H)-dione	ChEBI
Xan	ChEBI
1H-Purine-2,6-diol	HMDB
2,6(1,3)-Purinedion	HMDB
2,6-Dioxopurine	HMDB
3,7-Dihydro-1H-purine-2,6-dione	HMDB
3,7-Dihydropurine-2,6-dione	HMDB
9H-Purine-2,6(1H,3H)-dione	HMDB
9H-Purine-2,6-diol	HMDB
Dioxopurine	HMDB
Isoxanthine	HMDB
Pseudoxanthine	HMDB
Purine-2,6(1H,3H)-dione	HMDB
Purine-2,6-diol	HMDB
Xanthic oxide	HMDB
Xanthin	HMDB

Chemical Formula

C₅H₄N₄O₂

Average Molecular Weight

152.1109

Monoisotopic Molecular Weight

152.033425392

IUPAC Name

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

Traditional Name

xanthine

CAS Registry Number

69-89-6

SMILES

O=C1NC2=C(NC=N2)C(=O)N1

InChI Identifier

InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)

InChI Key

LRFVTYWOQMYALW-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
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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

xanthine (CHEBI:17712 )
Purine alkaloids (C00385 )
a small molecule (XANTHINE )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	> 300 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.069 mg/mL at 16 °C; 9.5 mg/mL (sodium salt)	MERCK INDEX (1996); Human Metabolome Project (salt)
LogP	-0.73	HANSCH,C ET AL. (1995)

Predicted Properties

Property	Value	Source
logP	-0.65	ALOGPS
logP	-0.21	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	7.95	ChemAxon
pKa (Strongest Basic)	-0.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.88 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	36.92 m³·mol⁻¹	ChemAxon
Polarizability	12.7 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	1	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
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0f6t-0924000000-9b80e0a2a60c73ca0180	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0f6t-0924000000-9b80e0a2a60c73ca0180	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0f6t-0924000000-30dc5892eecde860846a	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0kai-7900000000-2dc30b0fc4cff2239dbe	2016-09-22	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)	splash10-0udi-0900000000-a70539989d121bfacee0	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0a4i-6900000000-b047b06406308dbaeda8	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0a4i-9300000000-ed480ed920c3e9b576ec	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0zfr-0900000000-efb049914c9bce596267	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0zfr-0900000000-efb049914c9bce596267	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-0udi-0900000000-5fee91293851bb02193e	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT , positive	splash10-000i-0900000000-4568a814903ff411923a	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9000000000-e078a358156f5a04d4c1	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-3900000000-250f7dc30d6fd96a4ef6	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-0ik9-0900000000-3a6dad2473c1654789f6	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0900000000-a4e9443b51c3ac2fc58b	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9000000000-d23801a49488b1a5f0a2	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-4900000000-b177a2a36043e5e87efc	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0udi-0900000000-cb3b35c3117b7f36bf5c	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0zfr-0900000000-8d2a19e7c37d2cb7658f	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-05mo-9300000000-33d00ab2288aaa055517	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-0ik9-1900000000-3a6dad2473c1654789f6	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9000000000-37e76df2401a85967caa	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0udi-0900000000-4132da06dda895afc3ab	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0900000000-2e9e069e2df414aed037	2015-05-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0w29-0900000000-fa52193346bc456d89e8	2015-05-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a5i-9400000000-bbf70998e8b7515cb440	2015-05-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0900000000-566d663553ce4f0ec207	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0zfr-1900000000-d0a5d2c0f89f8d42d903	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-351d9f8ee3470f911829	2015-05-27	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-0udi-7900000000-2d5ab5d5db8ff4981467	2014-09-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	2012-12-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100.7 MHz, DMSO-d6, experimental)	Not Available	2014-09-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)	Not Available	2016-10-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, D₂O, experimental)	Not Available	2016-10-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)	Not Available	2012-12-04	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, 100%_DMSO, experimental)	Not Available	2012-12-05	View Spectrum

Concentrations

Status	Value		Reference	Details
Detected and Quantified	5.2 uM		PMID: 6539345	details

External Links

HMDB ID

HMDB0000292

DrugBank ID

DB02134

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

1188

PDB ID

Not Available

ChEBI ID

17712

References

Synthesis Reference

Procedure for the production of xanthine and xanthine-like materials. Fr. (1967), 4 pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Tiemeyer W, Stohrer M, Giesecke D: Metabolites of nucleic acids in bovine milk. J Dairy Sci. 1984 Apr;67(4):723-8. doi: 10.3168/jds.S0022-0302(84)81361-2. [PubMed:6539345 ]

Showing metabocard for Xanthine (BMDB0000292)

Structure for BMDB0000292 (Xanthine)