Record Information
Version2.0
Creation Date2012-07-30 14:55:41 -0600
Update Date2015-09-13 12:56:15 -0600
Secondary Accession Numbers
  • ECMDB21392
Identification
Name:Pyrimidine
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. (Wikipedia) The group of compounds called 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 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. Pyrimidines are synthesized de novo from simple precursors. (PMID 16098809)
Structure
Thumb
Synonyms:
  • 1,3-Diazabenzene
  • 1,3-Diazin
  • 1,3-Diazine
  • M-diazine
  • Metadiazine
  • Miazine
  • PY
  • PYR
  • Pyrimidin
  • PYRIMIDINE
  • Pyrimidine base
  • Pyrimidine dimer
Chemical Formula:C4H4N2
Weight:Average: 80.088
Monoisotopic: 80.037448138
InChI Key:CZPWVGJYEJSRLH-UHFFFAOYSA-N
InChI:InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H
CAS number:25247-63-6
IUPAC Name:pyrimidine
Traditional IUPAC Name:pyrimidine
SMILES:C1=CN=CN=C1
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.
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
Physical Properties
State:Liquid
Charge:0
Melting point:22 °C
Experimental Properties:
PropertyValueSource
Water Solubility:1000 mg/mL at 25 oC [MERCK INDEX (1996)]PhysProp
LogP:-0.40 [HANSCH,C ET AL. (1995)]PhysProp
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9000000000-d94930210c167d44af20View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-001i-9000000000-bcbcbca1a7f4d54af095View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0udi-9000000000-9589f26615aa6ffdf19fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-004i-9000000000-d6fe4ae4575881938f2cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-001i-9000000000-036ccbc8350c743f75f4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-9000000000-e6219273709c557c3698View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f89-9000000000-f3e79d098ad4304a8384View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udr-9000000000-fcf5f26e0c97b91147abView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-9000000000-8fe843c91e37282a20a3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-25f44ab9caf4fde752e0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0udi-9000000000-8f30bec7099c7d8746abView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-9000000000-a836173ec317f96549bdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-9000000000-1371ace385ac68f9f317View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-9000000000-1573e0ce56775ede12c7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-9000000000-90831ac2a79e645518baView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-90831ac2a79e645518baView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-f1f0ba91ed28b4268b72View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Loffler, M., Fairbanks, L. D., Zameitat, E., Marinaki, A. M., Simmonds, H. A. (2005). "Pyrimidine pathways in health and disease." Trends Mol Med 11:430-437. Pubmed: 16098809
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID16898
HMDB IDHMDB03361
Pubchem Compound ID9260
Kegg IDC00396
ChemSpider ID8903
WikipediaPyrimidine
BioCyc IDPYRIMIDINE-RING
EcoCyc IDPYRIMIDINE-RING
Ligand ExpoP1R

Transporters

General function:
Involved in transporter activity
Specific function:
Makes part of the rut operon, which is required for the utilization of pyrimidines as sole nitrogen source
Gene Name:
rutG
Uniprot ID:
P75892
Molecular weight:
45557