Record Information |
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Version | 2.0 |
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Created at | 2006-08-12 19:21:07 UTC |
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Updated at | 2021-10-07 20:41:00 UTC |
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NP-MRD ID | NP0000310 |
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Secondary Accession Numbers | None |
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Natural Product Identification |
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Common Name | Pyrimidine |
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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 ). |
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Structure | InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H |
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Synonyms | Value | Source |
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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 |
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Chemical Formula | C4H4N2 |
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Average Mass | 80.0880 Da |
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Monoisotopic Mass | 80.03745 Da |
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IUPAC Name | pyrimidine |
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Traditional Name | pyrimidine |
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CAS Registry Number | 25247-63-6 |
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SMILES | C1=CN=CN=C1 |
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InChI Identifier | InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H |
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InChI Key | CZPWVGJYEJSRLH-UHFFFAOYSA-N |
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Experimental Spectra |
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| Spectrum Type | Description | Depositor Email | Depositor Organization | Depositor | Deposition Date | View |
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1D NMR | 1H NMR Spectrum (1D, 600 MHz, H2O, experimental) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | 2D NMR | [1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum |
| Predicted Spectra |
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| Not Available | Chemical Shift Submissions |
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| Not Available | Species |
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Species of Origin | |
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Species Where Detected | |
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Chemical Taxonomy |
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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. |
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Kingdom | Organic compounds |
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Super Class | Organoheterocyclic compounds |
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Class | Diazines |
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Sub Class | Pyrimidines and pyrimidine derivatives |
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Direct Parent | Pyrimidines and pyrimidine derivatives |
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Alternative Parents | |
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Substituents | - Pyrimidine
- Heteroaromatic compound
- Azacycle
- Organic nitrogen compound
- Organopnictogen compound
- Hydrocarbon derivative
- Organonitrogen compound
- Aromatic heteromonocyclic compound
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Molecular Framework | Aromatic heteromonocyclic compounds |
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External Descriptors | |
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Physical Properties |
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State | Solid |
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Experimental Properties | Property | Value | Reference |
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Melting Point | 22 °C | Not Available | Boiling Point | Not Available | Not Available | Water Solubility | 1000 mg/mL at 25 °C | Not Available | LogP | -0.40 | Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995). |
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Predicted Properties | |
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General References | - Loffler M, Fairbanks LD, Zameitat E, Marinaki AM, Simmonds HA: Pyrimidine pathways in health and disease. Trends Mol Med. 2005 Sep;11(9):430-7. [PubMed:16098809 ]
- Bhurta D, Bharate SB: Analyzing the scaffold diversity of cyclin-dependent kinase inhibitors and revisiting the clinical and preclinical pipeline. Med Res Rev. 2021 Oct 4. doi: 10.1002/med.21856. [PubMed:34605036 ]
- Tsiko U, Bezvikonnyi O, Sych G, Keruckiene R, Volyniuk D, Simokaitiene J, Danyliv I, Danyliv Y, Bucinskas A, Tan X, Grazulevicius JV: Multifunctional derivatives of pyrimidine-5-carbonitrile and differently substituted carbazoles for doping-free sky-blue OLEDs and luminescent sensors of oxygen. J Adv Res. 2021 Feb 4;33:41-51. doi: 10.1016/j.jare.2021.01.014. eCollection 2021 Nov. [PubMed:34603777 ]
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