Milk Composition Database: Showing metabocard for Pyrimidine (BMDB0003361)

Identification Taxonomy Physical properties Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 23:03:58 UTC

Update Date

2020-04-22 15:12:05 UTC

MCDB ID

BMDB0003361

Secondary Accession Numbers

BMDB03361

Metabolite Identification

Common Name

Pyrimidine

Description

Pyrimidine, also known as pyrimidine base or 1,3-diazin, belongs to the class of organic compounds known as pyrimidines and pyrimidine derivatives. Pyrimidines and pyrimidine derivatives are compounds containing a pyrimidne ring, which is a six-member aromatic heterocycle which consists of two nitrogen atoms (at positions 1 and 3) and four carbon atoms. Pyrimidine exists as a solid, possibly soluble (in water), and a moderately basic compound (based on its pKa) molecule. Pyrimidine exists in all living organisms, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
1,3-Diazin	ChEBI
1,3-Diazine	ChEBI
m-Diazine	ChEBI
Metadiazine	ChEBI
Pyrimidin	ChEBI
Pyrimidine base	ChEBI
1,3-Diazabenzene	HMDB
Miazine	HMDB
PY	HMDB
PYR	HMDB
Pyrimidine dimer	HMDB

Chemical Formula

C₄H₄N₂

Average Molecular Weight

80.088

Monoisotopic Molecular Weight

80.037448138

IUPAC Name

pyrimidine

Traditional Name

pyrimidine

CAS Registry Number

25247-63-6

SMILES

C1=CN=CN=C1

InChI Identifier

InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H

InChI Key

CZPWVGJYEJSRLH-UHFFFAOYSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidines and pyrimidine derivatives. Pyrimidines and pyrimidine derivatives are compounds containing a pyrimidne ring, which is a six-member aromatic heterocycle which consists of two nitrogen atoms (at positions 1 and 3) and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidines and pyrimidine derivatives

Alternative Parents

Substituents

Pyrimidine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidines (CHEBI:16898 )
diazine (CHEBI:16898 )
a ring (PYRIMIDINE-RING )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	22 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	1000 mg/mL at 25 °C	Not Available
LogP	-0.4	HANSCH,C ET AL. (1995)

Predicted Properties

Property	Value	Source
logP	-0.21	ALOGPS
logP	0.05	ChemAxon
logS	0.77	ALOGPS
pKa (Strongest Basic)	1.58	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	25.78 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	22.72 m³·mol⁻¹	ChemAxon
Polarizability	7.62 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	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	splash10-001i-9000000000-d94930210c167d44af20	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
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)	splash10-001i-9000000000-bcbcbca1a7f4d54af095	2012-07-25	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0udi-9000000000-9589f26615aa6ffdf19f	2012-07-25	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-004i-9000000000-d6fe4ae4575881938f2c	2012-07-25	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , positive	splash10-001i-9000000000-036ccbc8350c743f75f4	2017-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9000000000-e6219273709c557c3698	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0f89-9000000000-f3e79d098ad4304a8384	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udr-9000000000-fcf5f26e0c97b91147ab	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-9000000000-8fe843c91e37282a20a3	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-25f44ab9caf4fde752e0	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0udi-9000000000-8f30bec7099c7d8746ab	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9000000000-a836173ec317f96549bd	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-9000000000-1371ace385ac68f9f317	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-9000000000-1573e0ce56775ede12c7	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-9000000000-90831ac2a79e645518ba	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-90831ac2a79e645518ba	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-f1f0ba91ed28b4268b72	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Not Available	2012-12-05	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-25	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	2012-12-05	View Spectrum

Concentrations

Status	Value		Reference	Details
Detected but not Quantified	Not Applicable		PMID: 29565828	details

External Links

HMDB ID

HMDB0003361

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pyrimidine

METLIN ID

Not Available

PubChem Compound

9260

PDB ID

Not Available

ChEBI ID

16898

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]

Showing metabocard for Pyrimidine (BMDB0003361)

Structure for BMDB0003361 (Pyrimidine)