Record Information
Version1.0
Creation date2011-09-21 00:25:26 UTC
Update date2019-11-26 03:21:07 UTC
Primary IDFDB023153
Secondary Accession NumbersNot Available
Chemical Information
FooDB NamePyrimidine
DescriptionPyrimidine 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 Number25247-63-6
Structure
Thumb
Synonyms
SynonymSource
1,3-DiazinChEBI
1,3-DiazineChEBI
m-DiazineChEBI
MetadiazineChEBI
PyrimidinChEBI
Pyrimidine baseChEBI
1,3-DiazabenzeneHMDB
MiazineHMDB
PYHMDB
PYRHMDB
Pyrimidine dimerHMDB
M-diazinehmdb
pyrimidinehmdb
Predicted Properties
PropertyValueSource
Water Solubility470 g/LALOGPS
logP-0.21ALOGPS
logP0.05ChemAxon
logS0.77ALOGPS
pKa (Strongest Basic)1.58ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area25.78 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity22.72 m³·mol⁻¹ChemAxon
Polarizability7.62 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC4H4N2
IUPAC namepyrimidine
InChI IdentifierInChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H
InChI KeyCZPWVGJYEJSRLH-UHFFFAOYSA-N
Isomeric SMILESC1=CN=CN=C1
Average Molecular Weight80.088
Monoisotopic Molecular Weight80.037448138
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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidines and pyrimidine derivatives
Alternative Parents
Substituents
  • Pyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Biological location:

Source:

Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateLiquid
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSPyrimidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-001i-9000000000-d94930210c167d44af20Spectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-001i-9000000000-bcbcbca1a7f4d54af095Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0udi-9000000000-9589f26615aa6ffdf19fSpectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-004i-9000000000-d6fe4ae4575881938f2cSpectrum
MS/MSLC-MS/MS Spectrum - , positivesplash10-001i-9000000000-036ccbc8350c743f75f4Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-9000000000-e6219273709c557c3698Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f89-9000000000-f3e79d098ad4304a8384Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udr-9000000000-fcf5f26e0c97b91147abSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-9000000000-8fe843c91e37282a20a3Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-25f44ab9caf4fde752e0Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0udi-9000000000-8f30bec7099c7d8746abSpectrum
NMR
TypeDescriptionView
1D NMR1H NMR SpectrumSpectrum
2D NMR[1H,13C] 2D NMR SpectrumSpectrum
ChemSpider ID8903
ChEMBL IDCHEMBL15562
KEGG Compound IDC00396
Pubchem Compound ID9260
Pubchem Substance IDNot Available
ChEBI ID16898
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB03361
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG IDNot Available
KNApSAcK IDNot Available
HET IDP1R
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDPyrimidine
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSshow
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference