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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2006-05-22 14:17:38 UTC

Update Date

2023-02-21 17:16:12 UTC

HMDB ID

HMDB0002144

Secondary Accession Numbers

HMDB02144

Metabolite Identification

Common Name

1,3-Dimethyluracil

Description

1,3-Dimethyluracil is a methyl derivative of uric acid, found occasionally in human urine. 1,3-Dimethyluracil is one of the purine component in urinary calculi. Methylated purines originate from the metabolism of methylxanthines (caffeine, theophylline and theobromine). Methyluric acids are indistinguishable from uric acid by simple methods routinely used in clinical laboratories, requiring the use of high-performance liquid chromatography (HPLC). 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 ).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2,4-Dihydroxy-1,3-dimethylpyrimidine	ChEBI
N,N'-dimethyluracil	ChEBI
N1,N3-Dimethyluracil	ChEBI
1, 3-Dimethyl-2,4(1H,3H)-pyrimidinedione	HMDB
1,3-Dimethyl-2,4(1H,3H)-pyrimidinedione	HMDB

Chemical Formula

C₆H₈N₂O₂

Average Molecular Weight

140.1399

Monoisotopic Molecular Weight

140.05857751

IUPAC Name

1,3-dimethyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

1,3-dimethyluracil

CAS Registry Number

874-14-6

SMILES

CN1C=CC(=O)N(C)C1=O

InChI Identifier

InChI=1S/C6H8N2O2/c1-7-4-3-5(9)8(2)6(7)10/h3-4H,1-2H3

InChI Key

JSDBKAHWADVXFU-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidones

Alternative Parents

Substituents

Pyrimidone
Hydropyrimidine
Heteroaromatic compound
Vinylogous amide
Urea
Lactam
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidone (CHEBI:74763 )

Ontology

Not Available

Endogenous (HMDB: HMDB0002144)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	120 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	-0.54	HANSCH,C ET AL. (1995)

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	270 g/L	ALOGPS
logP	-0.81	ALOGPS
logP	-0.41	ChemAxon
logS	0.28	ALOGPS
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	40.62 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	35.76 m³·mol⁻¹	ChemAxon
Polarizability	13.45 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	129.215	31661259
DarkChem	[M-H]-	124.892	31661259
DeepCCS	[M+H]+	124.685	30932474
DeepCCS	[M-H]-	121.597	30932474
DeepCCS	[M-2H]-	158.475	30932474
DeepCCS	[M+Na]+	133.361	30932474
AllCCS	[M+H]+	128.9	32859911
AllCCS	[M+H-H2O]+	124.3	32859911
AllCCS	[M+NH4]+	133.2	32859911
AllCCS	[M+Na]+	134.5	32859911
AllCCS	[M-H]-	126.5	32859911
AllCCS	[M+Na-2H]-	128.4	32859911
AllCCS	[M+HCOO]-	130.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	2.62 minutes	32390414
Predicted by Siyang on May 30, 2022	8.8035 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.51 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	874.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	307.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	94.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	189.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	57.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	242.0 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	296.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	126.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	642.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	244.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	910.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	205.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	219.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	497.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	243.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	106.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1,3-Dimethyluracil	CN1C=CC(=O)N(C)C1=O	1601.3	Standard polar	33892256
1,3-Dimethyluracil	CN1C=CC(=O)N(C)C1=O	1461.2	Standard non polar	33892256
1,3-Dimethyluracil	CN1C=CC(=O)N(C)C1=O	1421.0	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 1,3-Dimethyluracil GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-9400000000-a9a815f02af02149a613	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1,3-Dimethyluracil GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - 1,3-Dimethyluracil 40V, Positive-QTOF	splash10-0a4l-9000000000-ca5742a9937a9afd8a56	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 1,3-Dimethyluracil 20V, Positive-QTOF	splash10-052f-9400000000-d0ef20b2ceaea65fd8b9	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 1,3-Dimethyluracil 10V, Positive-QTOF	splash10-0006-0900000000-2a70f3aa2288125f17c9	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 10V, Positive-QTOF	splash10-0006-0900000000-9ebd3f5ba94fdccc6e33	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 20V, Positive-QTOF	splash10-000x-9400000000-e6cd72b3a31efdde15d3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 40V, Positive-QTOF	splash10-0pc0-9000000000-95451210d07eae69fd4d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 10V, Negative-QTOF	splash10-000i-3900000000-39bb5fe1809947bdc7b5	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 20V, Negative-QTOF	splash10-0f80-9500000000-bcce592f64dda98a70ae	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 40V, Negative-QTOF	splash10-0pb9-9000000000-041721ef1ce5ea95074d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 10V, Negative-QTOF	splash10-000i-4900000000-2116e278214869b1722f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 20V, Negative-QTOF	splash10-0a59-9200000000-61e4ad910ac68901a018	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 40V, Negative-QTOF	splash10-0zfr-9000000000-9f07ff6f0cbef9d0022f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 10V, Positive-QTOF	splash10-0006-0900000000-f6b797173fd148db8ab8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 20V, Positive-QTOF	splash10-0006-8900000000-0ea2521b5bb70098bab8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3-Dimethyluracil 40V, Positive-QTOF	splash10-0a4i-9000000000-bb90299755e9b50a8cf8	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022866

KNApSAcK ID

Not Available

Chemspider ID

63310

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70122

PDB ID

Not Available

ChEBI ID

74763

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Harada, Kaoru; Suzuki, Shinnichiro. The new synthesis of uracil and 1,3-dimethyluracil. Tetrahedron Letters (1976), (27), 2321-2.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

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 ]
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 ]
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 ]

Showing metabocard for 1,3-Dimethyluracil (HMDB0002144)

MOL for HMDB0002144 (1,3-Dimethyluracil)

3D MOL for HMDB0002144 (1,3-Dimethyluracil)

3D SDF for HMDB0002144 (1,3-Dimethyluracil)

3D-SDF for HMDB0002144 (1,3-Dimethyluracil)

PDB for HMDB0002144 (1,3-Dimethyluracil)

3D PDB for HMDB0002144 (1,3-Dimethyluracil)

SMILES for HMDB0002144 (1,3-Dimethyluracil)

INCHI for HMDB0002144 (1,3-Dimethyluracil)

Structure for HMDB0002144 (1,3-Dimethyluracil)

3D Structure for HMDB0002144 (1,3-Dimethyluracil)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra