Showing Compound Pyrimidine (FDB023153)

Record Information

Version

1.0

Creation date

2011-09-21 00:25:26 UTC

Update date

2019-11-26 03:21:07 UTC

Primary ID

FDB023153

Secondary Accession Numbers

Not Available

Chemical Information

FooDB Name

Pyrimidine

Description

Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring. Pyrimidines are heterocyclic, six-membered, nitrogen-containing carbon ring structures, with uracil, cytosine and thymine being the basal structures of ribose-containing nucleosides (uridine, cytidine and thymidine respectively), or deoxyribose-containing deoxynucleosides, and their corresponding ribonucleotides or deoxyribonucleotides. Pyrimidines serve essential functions in human metabolism as ribonucleotide bases in RNA (uracil and cytosine), and as deoxyribonucleotide bases in DNA (cytosine and thymine), and are linked by phosphodiester bridges to purine nucleotides in double-stranded DNA, in both the nucleus and the mitochondria. Pyrimidine activated sugars are also involved in polysaccharide and phospholipid synthesis, glucuronidation in detoxification processes, glycosylation of proteins and lipids and in the recently identified novel endothelium-derived vasoactive dinucleotides. Pyrimidines are synthesized de novo from simple precursors. Synthesis occurs in six steps, with cellular compartmentalization of specific steps in the cytosol or mitochondria, enabling changes in metabolic rate with need. Pyrimidine synthesis differs from purine synthesis, in that the single pyrimidine ring is assembled first and is then linked to ribose phosphate to form UMP. The enzymes that catalyse UMP synthesis, CAD [carbamoylphosphate synthetase II (CPSII), aspartate transcarbamoylase (ATCasea) and dihydroorotase (DHOase)], dihydroorotate dehydrogenase (DHODH) and uridine monophosphate synthase (UMPS), are encoded by only three genes - CAD, DHODH and UMPS (chromosomal locations 2p21, 16q22 and 3q13, respectively). (PMID: 16098809) [HMDB]

CAS Number

25247-63-6

Structure

MOL SDF PDB SMILES InChI

Synonyms

Synonym	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
M-diazine	hmdb
pyrimidine	hmdb

Predicted Properties

Property	Value	Source
Water Solubility	470 g/L	ALOGPS
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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Chemical Formula

C4H4N2

IUPAC name

pyrimidine

InChI Identifier

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

InChI Key

CZPWVGJYEJSRLH-UHFFFAOYSA-N

Isomeric SMILES

C1=CN=CN=C1

Average Molecular Weight

80.088

Monoisotopic Molecular Weight

80.037448138

Classification

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 )

Ontology

Disposition

Biological location:

Biofluid and excreta:

Source:

Endogenous

Physico-Chemical Properties - Experimental

Property	Value	Reference
Physical state	Liquid
Physical Description	Not Available
Mass Composition	Not Available
Melting Point	Not Available
Boiling Point	Not Available
Experimental Water Solubility	Not Available
Experimental logP	Not Available
Experimental pKa	Not Available
Isoelectric point	Not Available
Charge	Not Available
Optical Rotation	Not Available
Spectroscopic UV Data	Not Available
Density	Not Available
Refractive Index	Not Available

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
Predicted GC-MS	Pyrimidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-001i-9000000000-d94930210c167d44af20	Spectrum
Predicted GC-MS	Pyrimidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyrimidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-001i-9000000000-bcbcbca1a7f4d54af095	2012-07-25	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0udi-9000000000-9589f26615aa6ffdf19f	2012-07-25	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-004i-9000000000-d6fe4ae4575881938f2c	2012-07-25	View Spectrum
MS/MS	LC-MS/MS Spectrum - , positive	splash10-001i-9000000000-036ccbc8350c743f75f4	2017-09-14	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9000000000-e6219273709c557c3698	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0f89-9000000000-f3e79d098ad4304a8384	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udr-9000000000-fcf5f26e0c97b91147ab	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-9000000000-8fe843c91e37282a20a3	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-25f44ab9caf4fde752e0	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0udi-9000000000-8f30bec7099c7d8746ab	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9000000000-a836173ec317f96549bd	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-9000000000-1371ace385ac68f9f317	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-9000000000-1573e0ce56775ede12c7	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-9000000000-90831ac2a79e645518ba	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-90831ac2a79e645518ba	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-f1f0ba91ed28b4268b72	2021-09-24	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Spectrum