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Showing Compound Pseudouridine 5'-phosphate (FDB022525)

Record Information
Version1.0
Creation date2011-09-21 00:15:22 UTC
Update date2019-11-26 03:21:04 UTC
Primary IDFDB022525
Secondary Accession NumbersNot Available
Chemical Information
FooDB NamePseudouridine 5'-phosphate
DescriptionPseudouridine (5-ribosyluracil) is a ubiquitous yet enigmatic constituent of structural RNAs (transfer, ribosomal, small nuclear, and small nucleolar). Although pseudouridine (psi) was the first modified nucleoside to be discovered in RNA, and is the most abundant, its biosynthesis and biological roles have remained poorly understood since its identification as a "fifth nucleoside" in RNA. Recently, a combination of biochemical, biophysical, and genetic approaches has helped to illuminate the structural consequences of psi in polyribonucleotides, the biochemical mechanism of U-->psi isomerization in RNA, and the role of modification enzymes (psi synthases) and box H/ACA snoRNAs, a class of eukaryotic small nucleolar RNAs, in the site-specific biosynthesis of psi. Through its unique ability to coordinate a structural water molecule via its free N1-H, psi exerts a subtle but significant "rigidifying" influence on the nearby sugar-phosphate backbone and also enhances base stacking. These effects may underlie the biological role of most (but perhaps not all) of the psi residues in RNA. Certain genetic mutants lacking specific psi residues in tRNA or rRNA exhibit difficulties in translation, display slow growth rates, and fail to compete effectively with wild-type strains in mixed culture. In particular, normal growth is severely compromised in an Escherichia coli mutant deficient in a pseudouridine synthase responsible for the formation of three closely spaced psi residues in the mRNA decoding region of the 23S rRNA. Such studies demonstrate that pseudouridylation of RNA confers an important selective advantage in a natural biological context. PMID: 10902565 [HMDB]. Pseudouridine 5'-phosphate is found in many foods, some of which are garland chrysanthemum, chives, broad bean, and green bell pepper.
CAS Number1157-60-4
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
SynonymSource
(1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitolChEBI
5-(5-O-Phosphono-beta-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dioneChEBI
5-(5-O-Phosphono-b-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dioneGenerator
5-(5-O-Phosphono-β-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dioneGenerator
Pseudouridine 5'-phosphoric acidGenerator
Pseudouridylic acidMeSH, HMDB
5-(5-O-Phosphono-beta-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
5-(5-O-Phosphono-β-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
Pseudouridine 5'-phosphateHMDB
Pseudouridine 5’-phosphateHMDB
Pseudouridine monophosphateHMDB
(1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-ONO-D-ribitolChEBI
5-(5-O-ONO-b-D-Ribofuranosyl)pyrimidine-2,4(1H,3H)-dioneGenerator
5-(5-O-ONO-beta-D-Ribofuranosyl)pyrimidine-2,4(1H,3H)-dioneChEBI
5-(5-O-ONO-β-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dioneGenerator
Pseudouridine 5'-ateChEBI
Pseudouridine 5'-ic acidGenerator
Pseudouridine 5'-phosphic acidhmdb
Predicted Properties
PropertyValueSource
Water Solubility7.51 g/LALOGPS
logP-1.9ALOGPS
logP-3.2ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area174.65 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity63.31 m³·mol⁻¹ChemAxon
Polarizability26.32 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC9H13N2O9P
IUPAC name{[(2R,3S,4R,5S)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
InChI IdentifierInChI=1S/C9H13N2O9P/c12-5-4(2-19-21(16,17)18)20-7(6(5)13)3-1-10-9(15)11-8(3)14/h1,4-7,12-13H,2H2,(H2,16,17,18)(H2,10,11,14,15)/t4-,5-,6-,7+/m1/s1
InChI KeyMOBMOJGXNHLLIR-GBNDHIKLSA-N
Isomeric SMILESO[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)C1=CNC(=O)NC1=O
Average Molecular Weight324.1813
Monoisotopic Molecular Weight324.035866536
Classification
Description Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentose phosphates
Alternative Parents
Substituents
  • Pentose phosphate
  • Pentose-5-phosphate
  • C-glycosyl compound
  • Glycosyl compound
  • Monosaccharide phosphate
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Tetrahydrofuran
  • Vinylogous amide
  • Heteroaromatic compound
  • Secondary alcohol
  • Urea
  • 1,2-diol
  • Lactam
  • Dialkyl ether
  • Azacycle
  • Ether
  • Organoheterocyclic compound
  • Oxacycle
  • Organonitrogen compound
  • Alcohol
  • Organic oxide
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Role

Industrial application:

Physico-Chemical Properties
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSPseudouridine 5'-phosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0092-7921000000-3b484f48c79da75d22b9Spectrum
Predicted GC-MSPseudouridine 5'-phosphate, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0zor-5984100000-c1d4654dc77f1a2defc3Spectrum
Predicted GC-MSPseudouridine 5'-phosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0669000000-0b19df9acf8df54d0c282015-09-14View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004j-4493000000-38400e5991956cb671842015-09-14View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000l-3900000000-ebfc1c181ae3a767f1d52015-09-14View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0096-9022000000-61eca04124385371e0702015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004l-9000000000-d8f1a9a373cb543c5a502015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-7662d761a5f16134b3402015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00fr-9007000000-706b8bb8bcb6e1f088ab2021-09-23View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1f2021-09-23View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1f2021-09-23View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0191000000-d8971429f6e3bcedb1b22021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-056r-0960000000-db21c37dfcf9636eeeb42021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-2900000000-8e2c2edc3141326a4fb12021-09-24View Spectrum
NMRNot Available
ChemSpider ID388535
ChEMBL IDNot Available
KEGG Compound IDC01168
Pubchem Compound ID439424
Pubchem Substance IDNot Available
ChEBI ID18116
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB01271
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG IDNot Available
KNApSAcK IDNot Available
HET IDPSU
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference