MiMeDB: Showing metabocard for Pyrimidine (MMDBc0030352)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 00:04:52 UTC

Update Date

2024-04-30 19:45:30 UTC

Metabolite ID

MMDBc0030352

Metabolite Identification

Common 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. (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

MOL 3D MOL SDF 3D SDF PDB 3D 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

Molecular Formula

C₄H₄N₂

Average Mass

80.088

Monoisotopic Mass

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 )

Functional Ontology

Not Available

Physical Properties

State

Liquid

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

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)		2012-12-05	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-05	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0196449	DNA damage-binding protein 2	Unknown	Q92466	Homo sapiens
MMDBp0196450	DNA damage-binding protein 1	Unknown	Q16531	Homo sapiens
MMDBp0196451	Poly(U)-binding-splicing factor PUF60	Unknown	Q9UHX1	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference
Animal	Milk	Bos taurus	FooDB	31437929

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0003361

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB 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

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

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. doi: 10.1016/j.molmed.2005.07.003. [PubMed:16098809 ]

Showing metabocard for Pyrimidine (MMDBc0030352)

MOL for #<Metabolite:0x00007f46f80ac738>

3D MOL for #<Metabolite:0x00007f46f80ac738>

3D SDF for #<Metabolite:0x00007f46f80ac738>

3D-SDF for #<Metabolite:0x00007f46f80ac738>

PDB for #<Metabolite:0x00007f46f80ac738>

3D PDB for #<Metabolite:0x00007f46f80ac738>

SMILES for #<Metabolite:0x00007f46f80ac738>

INCHI for #<Metabolite:0x00007f46f80ac738>

Structure for #<Metabolite:0x00007f46f80ac738>

3D Structure for #<Metabolite:0x00007f46f80ac738>