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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 02:31:26 UTC

Update Date

2023-02-21 17:28:29 UTC

HMDB ID

HMDB0040911

Secondary Accession Numbers

HMDB40911

Metabolite Identification

Common Name

2-Methoxy-3,5-dimethylpyrimidine

Description

2-Methoxy-3,5-dimethylpyrimidine belongs to the class of organic compounds known as methoxypyrazines. These are pyrazines containing a methoxyl group attached to the pyrazine ring. Based on a literature review very few articles have been published on 2-Methoxy-3,5-dimethylpyrimidine.

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-Methoxy-3,5-dimethylpyrimidine, 9ci	HMDB

Chemical Formula

C₇H₁₀N₂O

Average Molecular Weight

138.1671

Monoisotopic Molecular Weight

138.079312952

IUPAC Name

2-methoxy-3,5-dimethylpyrazine

Traditional Name

2-methoxy-3,5-dimethylpyrazine

CAS Registry Number

92508-08-2

SMILES

COC1=C(C)N=C(C)C=N1

InChI Identifier

InChI=1S/C7H10N2O/c1-5-4-8-7(10-3)6(2)9-5/h4H,1-3H3

InChI Key

BXKLSVWRSUPMBO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as methoxypyrazines. These are pyrazines containing a methoxyl group attached to the pyrazine ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrazines

Direct Parent

Methoxypyrazines

Alternative Parents

Substituents

Methoxypyrazine
Alkyl aryl ether
Heteroaromatic compound
Azacycle
Ether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0040911)
Cytoplasm (HMDB: HMDB0040911)

Source

Exogenous

Exogenous (HMDB: HMDB0040911)

Food

Food (HMDB: HMDB0040911)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0040911)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	177.72 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	1633 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	1.672 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	97.4 g/L	ALOGPS
logP	1.29	ALOGPS
logP	0.24	ChemAxon
logS	-0.15	ALOGPS
pKa (Strongest Basic)	1.78	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	35.01 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	37.7 m³·mol⁻¹	ChemAxon
Polarizability	14.77 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	128.838	31661259
DarkChem	[M-H]-	128.252	31661259
DeepCCS	[M+H]+	132.315	30932474
DeepCCS	[M-H]-	128.486	30932474
DeepCCS	[M-2H]-	165.882	30932474
DeepCCS	[M+Na]+	141.24	30932474
AllCCS	[M+H]+	130.2	32859911
AllCCS	[M+H-H2O]+	125.6	32859911
AllCCS	[M+NH4]+	134.4	32859911
AllCCS	[M+Na]+	135.6	32859911
AllCCS	[M-H]-	129.7	32859911
AllCCS	[M+Na-2H]-	131.6	32859911
AllCCS	[M+HCOO]-	133.8	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.	2.38 minutes	32390414
Predicted by Siyang on May 30, 2022	9.6052 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.91 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	675.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	341.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	129.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	205.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	66.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	284.2 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	292.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	118.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	751.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	46.2 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	962.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	210.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	230.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	499.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	404.0 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	124.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Methoxy-3,5-dimethylpyrimidine	COC1=C(C)N=C(C)C=N1	1357.4	Standard polar	33892256
2-Methoxy-3,5-dimethylpyrimidine	COC1=C(C)N=C(C)C=N1	1028.5	Standard non polar	33892256
2-Methoxy-3,5-dimethylpyrimidine	COC1=C(C)N=C(C)C=N1	1052.8	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 - 2-Methoxy-3,5-dimethylpyrimidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0079-6900000000-a4f2f4c96281b957a00d	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 10V, Positive-QTOF	splash10-000i-0900000000-7724eb403262748de91a	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 20V, Positive-QTOF	splash10-000i-0900000000-2e8811d3681d9d7381c6	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 40V, Positive-QTOF	splash10-0ktf-9100000000-9d1dbc2936b68fdc58be	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 10V, Negative-QTOF	splash10-000i-0900000000-9e7bc43c391dacc2469d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 20V, Negative-QTOF	splash10-0a4r-7900000000-1dba11c3069a9044c3e3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 40V, Negative-QTOF	splash10-0006-9000000000-adb7e6801b0563aea551	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 10V, Negative-QTOF	splash10-000i-0900000000-bf618e0cda7bbb6587ee	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 20V, Negative-QTOF	splash10-00ko-9500000000-fdcb2397d5f13975b521	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 40V, Negative-QTOF	splash10-0006-9000000000-cba752d9620bde43b4c8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 10V, Positive-QTOF	splash10-000i-1900000000-f99592008b7f2664f014	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 20V, Positive-QTOF	splash10-000i-7900000000-78fbb2cf5133ecccea9d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methoxy-3,5-dimethylpyrimidine 40V, Positive-QTOF	splash10-00kf-9000000000-0f8609a78a8fac014b34	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	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]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

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

FDB020750

KNApSAcK ID

Not Available

Chemspider ID

4934595

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6429218

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1078631

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 2-Methoxy-3,5-dimethylpyrimidine (HMDB0040911)

MOL for HMDB0040911 (2-Methoxy-3,5-dimethylpyrimidine)

3D MOL for HMDB0040911 (2-Methoxy-3,5-dimethylpyrimidine)

3D SDF for HMDB0040911 (2-Methoxy-3,5-dimethylpyrimidine)

3D-SDF for HMDB0040911 (2-Methoxy-3,5-dimethylpyrimidine)

PDB for HMDB0040911 (2-Methoxy-3,5-dimethylpyrimidine)

3D PDB for HMDB0040911 (2-Methoxy-3,5-dimethylpyrimidine)

SMILES for HMDB0040911 (2-Methoxy-3,5-dimethylpyrimidine)

INCHI for HMDB0040911 (2-Methoxy-3,5-dimethylpyrimidine)

Structure for HMDB0040911 (2-Methoxy-3,5-dimethylpyrimidine)

3D Structure for HMDB0040911 (2-Methoxy-3,5-dimethylpyrimidine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra