Pseudouridine 5'-phosphate (ECMDB01271) (M2MDB000318)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)XML
Proteins (93)
Record Information
Version2.0
Creation Date2012-05-31 13:48:48 -0600
Update Date2015-06-03 15:53:53 -0600
Secondary Accession Numbers
  • ECMDB01271
Identification
Name:Pseudouridine 5'-phosphate
DescriptionPseudouridine 5'-phosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Pseudouridine 5'-phosphate is an intermediate in pseudouridine degradation pathway. In this pathway, pseudouridine is metabolised to uracil. [BiocycPWY-6019]
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • PseudoU5P
  • Pseudouridine 5'-phosphate
  • Pseudouridine 5'-phosphoric acid
Chemical Formula:C9H13N2O9P
Weight:Average: 324.1813
Monoisotopic: 324.035866536
InChI Key:MOBMOJGXNHLLIR-GBNDHIKLSA-N
InChI:InChI=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
CAS number:1157-60-4
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
Traditional IUPAC Name:pseudouridine 5'-phosphate
SMILES:O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)C1=CNC(=O)NC1=O
Chemical Taxonomy
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
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Pseudouridine + Adenosine triphosphate > Hydrogen ion + Pseudouridine 5'-phosphate + ADP
D-Ribose-5-phosphate + Uracil <> Water + Pseudouridine 5'-phosphate
Pseudouridine 5'-phosphate + Water > Uracil + D-Ribose-5-phosphate
Adenosine triphosphate + Pseudouridine > ADP + Pseudouridine 5'-phosphate
Adenosine triphosphate + Pseudouridine <> ADP + Pseudouridine 5'-phosphate
Pseudouridine + Adenosine triphosphate + Pseudouridine > Pseudouridine 5'-phosphate + Adenosine diphosphate + Hydrogen ion + ADP
Pseudouridine 5'-phosphate + Water > Uracil + D-ribofuranose 5-phosphate + D-ribofuranose 5-phosphate
SMPDB Pathways:
Purine degradationPW001887 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0092-7921000000-3b484f48c79da75d22b9View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0zor-5984100000-c1d4654dc77f1a2defc3View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0669000000-0b19df9acf8df54d0c28View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004j-4493000000-38400e5991956cb67184View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000l-3900000000-ebfc1c181ae3a767f1d5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0096-9022000000-61eca04124385371e070View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004l-9000000000-d8f1a9a373cb543c5a50View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-7662d761a5f16134b340View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00fr-9007000000-706b8bb8bcb6e1f088abView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0191000000-d8971429f6e3bcedb1b2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-056r-0960000000-db21c37dfcf9636eeeb4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-2900000000-8e2c2edc3141326a4fb1View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Charette M, Gray MW: Pseudouridine in RNA: what, where, how, and why. IUBMB Life. 2000 May;49(5):341-51. Pubmed: 10902565
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID18116
HMDB IDHMDB01271
Pubchem Compound ID439424
Kegg IDC01168
ChemSpider ID388535
Wikipedia IDNot Available
BioCyc IDPSEUDOURIDINE-5-P
EcoCyc IDPSEUDOURIDINE-5-P
Ligand ExpoPSU

Enzymes

Protein Details
1. Pseudouridine kinase
General function:
Carbohydrate transport and metabolism
Specific function:
Catalyzes the phosphorylation of pseudouridine to pseudouridine 5'-phosphate (PsiMP)
Gene Name:
psuK
Uniprot ID:
P30235
Molecular weight:
33573
Reactions
ATP + pseudouridine = ADP + pseudouridine 5'-phosphate.