Showing metabocard for Pyrimidine (BMDB0003361)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 23:03:58 UTC
Update Date2020-04-22 15:12:05 UTC
BMDB IDBMDB0003361
Secondary Accession Numbers
  • BMDB03361
Metabolite Identification
Common NamePyrimidine
DescriptionPyrimidine, also known as pyrimidine base or 1,3-diazin, 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. Pyrimidine exists as a solid, possibly soluble (in water), and a moderately basic compound (based on its pKa) molecule. Pyrimidine exists in all living organisms, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
1,3-DiazinChEBI
1,3-DiazineChEBI
m-DiazineChEBI
MetadiazineChEBI
PyrimidinChEBI
Pyrimidine baseChEBI
1,3-DiazabenzeneHMDB
MiazineHMDB
PYHMDB
PYRHMDB
Pyrimidine dimerHMDB
Chemical FormulaC4H4N2
Average Molecular Weight80.088
Monoisotopic Molecular Weight80.037448138
IUPAC Namepyrimidine
Traditional Namepyrimidine
CAS Registry Number25247-63-6
SMILES
C1=CN=CN=C1
InChI Identifier
InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H
InChI KeyCZPWVGJYEJSRLH-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.
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
StatusDetected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point22 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mL at 25 °CNot Available
LogP-0.4HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
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 FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
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 Spectrum (1D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Milk
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0003361
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023153
KNApSAcK IDC00007494
Chemspider ID8903
KEGG Compound IDC00396
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPyrimidine
METLIN IDNot Available
PubChem Compound9260
PDB IDNot Available
ChEBI ID16898
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]

Enzymes

Enzyme Details
1. Poly(U)-binding-splicing factor PUF60
General function:
Involved in DNA binding
Specific function:
DNA- and RNA-binding protein, involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation. In association with FUBP1 regulates MYC transcription at the P2 promoter through the core-TFIIH basal transcription factor. Acts as a transcriptional repressor through the core-TFIIH basal transcription factor. Represses FUBP1-induced transcriptional activation but not basal transcription. Decreases ERCC3 helicase activity. Is also involved in pre-mRNA splicing. Promotes splicing of an intron with weak 3'-splice site and pyrimidine tract in a cooperative manner with U2AF2. Involved in apoptosis induction when overexpressed in HeLa cells. Modulates alternative splicing of several mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is enhanced in presence of U2AF2. Binds to Y5 RNA in association with TROVE2. Binds to poly(U) RNA (By similarity).
Gene Name:
PUF60
Uniprot ID:
Q2HJG2
Molecular weight:
57087.0
Enzyme Details
2. Splicing factor U2AF 26 kDa subunit
General function:
Involved in nucleotide binding
Specific function:
RNA-binding protein that function as a pre-mRNA splicing factor. Plays a critical role in both constitutive and enhancer-dependent splicing by mediating protein-protein interactions and protein-RNA interactions required for accurate 3'-splice site selection. Acts by enhancing the binding of U2AF2 to weak pyrimidine tracts. Also participates in the regulation of alternative pre-mRNA splicing. Activates exon 5 skipping of PTPRC during T-cell activation; an event reversed by GFI1. Binds to RNA at the AG dinucleotide at the 3'-splice site (By similarity). Shows a preference for AGC or AGA (By similarity).
Gene Name:
U2AF1L4
Uniprot ID:
Q3T127
Molecular weight:
25884.0