Pseudouridine 5'-phosphate (YMDB00780)

Identification
YMDB IDYMDB00780
NamePseudouridine 5'-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionPseudouridine 5'-phosphate 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. Pseudouridine 5'-phosphate exists in all living species, ranging from bacteria to plants to humans. Based on a literature review very few articles have been published on Pseudouridine 5'-phosphate.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (1S)-1,4-anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol
  • 5-(5-O-phosphono-beta-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione
  • Pseudouridine 5'-phosphate
  • Pseudouridine 5'-phosphic acid
  • Pseudouridylic acid
  • 5-(5-O-Phosphono-b-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione
  • 5-(5-O-Phosphono-β-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione
  • Pseudouridine 5'-phosphoric acid
  • 5-(5-O-Phosphono-beta-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 5-(5-O-Phosphono-β-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • Pseudouridine 5’-phosphate
  • Pseudouridine monophosphate
CAS number1157-60-4
WeightAverage: 324.1813
Monoisotopic: 324.035866536
InChI KeyMOBMOJGXNHLLIR-GBNDHIKLSA-N
InChIInChI=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
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 Namepseudouridine 5'-phosphate
Chemical FormulaC9H13N2O9P
SMILESO[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
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB ReactionsNot Available
KEGG Reactions
Uracil + alpha-D-ribose 5-phosphate ↔ water + Pseudouridine 5'-phosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0092-7921000000-3b484f48c79da75d22b9JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0zor-5984100000-c1d4654dc77f1a2defc3JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0669000000-0b19df9acf8df54d0c28JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004j-4493000000-38400e5991956cb67184JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000l-3900000000-ebfc1c181ae3a767f1d5JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0096-9022000000-61eca04124385371e070JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004l-9000000000-d8f1a9a373cb543c5a50JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-7662d761a5f16134b340JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00fr-9007000000-706b8bb8bcb6e1f088abJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0191000000-d8971429f6e3bcedb1b2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-056r-0960000000-db21c37dfcf9636eeeb4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-2900000000-8e2c2edc3141326a4fb1JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Preumont, A., Snoussi, K., Stroobant, V., Collet, J. F., Van Schaftingen, E. (2008). "Molecular identification of pseudouridine-metabolizing enzymes." J Biol Chem 283:25238-25246.18591240
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID18116
HMDB IDHMDB01271
Pubchem Compound ID439424
Kegg IDC01168
ChemSpider ID388535
FOODB IDFDB022525
Wikipedia IDNot Available
BioCyc IDPSEUDOURIDINE-5-P

Enzymes

Protein Details
1. tRNA pseudouridine synthase 1
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine at positions 27 and 28 in the anticodon stem and loop of transfer RNAs; at positions 34 and 36 of intron-containing precursor tRNA(Ile) and at position 35 in the intron-containing tRNA(Tyr)
Gene Name:
PUS1
Uniprot ID:
Q12211
Molecular weight:
62142.0
Reactions
tRNA uridine → tRNA pseudouridine.
Protein Details
2. tRNA pseudouridine synthase 4
General function:
Involved in RNA processing
Specific function:
Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
Gene Name:
PUS4
Uniprot ID:
P48567
Molecular weight:
45273.10156
Reactions
tRNA uridine → tRNA pseudouridine.
Protein Details
3. tRNA pseudouridine synthase 2
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS2
Uniprot ID:
P53167
Molecular weight:
41874.80078
Reactions
tRNA uridine → tRNA pseudouridine.
Protein Details
4. tRNA pseudouridine synthase 3
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridines at positions 38 and 39 in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS3
Uniprot ID:
P31115
Molecular weight:
50888.30078
Reactions
tRNA uridine → tRNA pseudouridine.