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

2022-08-31 17:44:08 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 SDF 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

Not Available

Traditional Name

Not Available

CAS Registry Number

25247-63-6

SMILES

Not Available

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

Not Available

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	Unknown

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference

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

CMMC Knowledgebase

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:0x00007f1241723d50>

3D MOL for #<Metabolite:0x00007f1241723d50>

3D SDF for #<Metabolite:0x00007f1241723d50>

3D-SDF for #<Metabolite:0x00007f1241723d50>

PDB for #<Metabolite:0x00007f1241723d50>

3D PDB for #<Metabolite:0x00007f1241723d50>

SMILES for #<Metabolite:0x00007f1241723d50>

INCHI for #<Metabolite:0x00007f1241723d50>

Structure for #<Metabolite:0x00007f1241723d50>

3D Structure for #<Metabolite:0x00007f1241723d50>