Showing metabocard for Pseudouridine (BMDB0000767)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:36:17 UTC
Update Date2020-06-04 20:46:21 UTC
BMDB IDBMDB0000767
Secondary Accession Numbers
  • BMDB00767
Metabolite Identification
Common NamePseudouridine
DescriptionBeta-Pseudouridine, also known as p or 5-ribosyluracil, belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others. Beta-Pseudouridine is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Beta-Pseudouridine exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitolChEBI
5-(beta-D-Ribofuranosyl)uracilChEBI
beta-PseudouridineChEBI
pChEBI
Psi-uridineChEBI
5-(b-D-Ribofuranosyl)uracilGenerator
5-(Β-D-ribofuranosyl)uracilGenerator
b-PseudouridineGenerator
Β-pseudouridineGenerator
5-(b-delta-Ribofuranosyl)uracilHMDB
5-b-D-Ribofuranosyl-uracilHMDB
5-beta-delta-Ribofuranosyl-uracilHMDB
5-RibosyluracilHMDB
b-D-PseudouridineHMDB
beta-delta-PseudouridineHMDB
Pseudouridine CHMDB
Y-uridineHMDB
5-beta-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
5-Β-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
beta-D-PseudouridineHMDB
Β-D-pseudouridineHMDB
Ψ-uridineHMDB
PseudouridineHMDB
Chemical FormulaC9H12N2O6
Average Molecular Weight244.2014
Monoisotopic Molecular Weight244.069536126
IUPAC Name5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Nameβ-pseudouridine
CAS Registry Number1445-07-4
SMILES
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O
InChI Identifier
InChI=1S/C9H12N2O6/c12-2-4-5(13)6(14)7(17-4)3-1-10-9(16)11-8(3)15/h1,4-7,12-14H,2H2,(H2,10,11,15,16)/t4-,5-,6-,7+/m1/s1
InChI KeyPTJWIQPHWPFNBW-GBNDHIKLSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassNucleoside and nucleotide analogues
Sub ClassNot Available
Direct ParentNucleoside and nucleotide analogues
Alternative Parents
Substituents
  • C-glycosyl compound
  • Glycosyl compound
  • Pentose monosaccharide
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Vinylogous amide
  • Lactam
  • Secondary alcohol
  • Urea
  • Azacycle
  • Oxacycle
  • Ether
  • Dialkyl ether
  • Organoheterocyclic compound
  • Primary alcohol
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2ALOGPS
logP-3.1ChemAxon
logS-0.58ALOGPS
pKa (Strongest Acidic)8.66ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area128.12 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity52.44 m³·mol⁻¹ChemAxon
Polarizability21.79 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Liver
  • Milk
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
LiverDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified3.8 uMNot SpecifiedNot Specified
Normal		 details
PlacentaExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0000767
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB031139
KNApSAcK IDC00001508
Chemspider ID14319
KEGG Compound IDC02067
BioCyc IDCPD-497
BiGG IDNot Available
Wikipedia LinkPseudouridine
METLIN ID5734
PubChem Compound15047
PDB IDNot Available
ChEBI ID17802
References
Synthesis Referenceanessian, Stephen; Machaalani, Roger. A highly stereo-controlled and efficient synthesis of a- and b-pseudouridines. Tetrahedron Letters (2003), 44(45), 8321-8323.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Tiemeyer W, Stohrer M, Giesecke D: Metabolites of nucleic acids in bovine milk. J Dairy Sci. 1984 Apr;67(4):723-8. doi: 10.3168/jds.S0022-0302(84)81361-2. [PubMed:6539345 ]

Enzymes

Enzyme Details
1. tRNA pseudouridine synthase
General function:
Translation, ribosomal structure and biogenesis
Specific function:
Not Available
Gene Name:
PUSL1
Uniprot ID:
A6QP68
Molecular weight:
34022.0
Enzyme Details
2. Pseudouridylate synthase 7 homolog
General function:
Involved in pseudouridine synthase activity
Specific function:
Pseudouridylate synthase that catalyzes pseudouridylation of RNAs. Acts as a regulator of protein synthesis in embryonic stem cells by mediating pseudouridylation of RNA fragments derived from tRNAs (tRFs): pseudouridylated tRFs inhibit translation by targeting the translation initiation complex. Also catalyzes pseudouridylation of mRNAs: mediates pseudouridylation of mRNAs with the consensus sequence 5'-UGUAG-3'. In addition to mRNAs and tRNAs, binds other types of RNAs, such as snRNAs, Y RNAs and vault RNAs, suggesting that it can catalyze pseudouridylation of many RNA types.
Gene Name:
PUS7
Uniprot ID:
Q08DI8
Molecular weight:
74594.0
Enzyme Details
3. tRNA pseudouridine(38/39) synthase
General function:
Translation, ribosomal structure and biogenesis
Specific function:
Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs.
Gene Name:
PUS3
Uniprot ID:
Q3SX07
Molecular weight:
55665.0