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Pseudouridine (M2MDB001783)

Record Information
Version2.0
Creation Date2012-07-30 14:55:41 -0600
Update Date2015-09-13 15:15:32 -0600
Secondary Accession Numbers
  • ECMDB21388
Identification
Name:Pseudouridine
DescriptionPseudouridine is the C-glycoside isomer of the nucleoside uridine, and it is the most prevalent of the over one hundred different modified nucleosides found in RNA. Pseudouridine is found in all species and in all classes of RNA except mRNA. It is formed by enzymes called pseudouridine synthases, which post-transcriptionally isomerize specific uridine residues in RNA (Wikipedia).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • (1S)-1,4-anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol
  • 5-(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl-1H-pyrimidine-2,4-dione
  • 5-(b-D-Ribofuranosyl)uracil
  • 5-(b-delta-Ribofuranosyl)uracil
  • 5-(b-δ-Ribofuranosyl)uracil
  • 5-(beta-D-ribofuranosyl)uracil
  • 5-(β-D-Ribofuranosyl)uracil
  • 5-b-D-ribofuranosyl-Uracil
  • 5-b-delta-Ribofuranosyl-uracil
  • 5-b-δ-Ribofuranosyl-uracil
  • 5-beta-delta-ribofuranosyl-Uracil
  • 5-Ribosyluracil
  • 5-β-δ-Ribofuranosyl-uracil
  • B-D-Pseudouridine
  • b-delta-Pseudouridine
  • B-Pseudouridine
  • b-δ-Pseudouridine
  • Beta-delta-Pseudouridine
  • Beta-Pseudouridine
  • P
  • Pseudouridine C
  • Psi-uridine
  • Y-Uridine
  • β-Pseudouridine
  • β-δ-Pseudouridine
Chemical Formula:C9H12N2O6
Weight:Average: 244.2014
Monoisotopic: 244.069536126
InChI Key:PTJWIQPHWPFNBW-GBNDHIKLSA-N
InChI: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
CAS number:1445-07-4
IUPAC Name:5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name:β-pseudouridine
SMILES:OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O
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
Physical Properties
State:Solid
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility63.8 g/LALOGPS
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
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
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
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, Positivesplash10-0unc-7930000000-a1e7f343c88a63ac1976View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0fi0-3494100000-8d726ed412554c1f92f0View 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
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_6) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , negativesplash10-0udi-0900000000-6ade42aaa885371e176cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 10V, positivesplash10-0a4i-0190000000-129f123affa0ecbf7a59View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 20V, positivesplash10-052f-0910000000-302fbdef606070bd5a67View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 40V, positivesplash10-001i-9300000000-11f5761be16d1b061df5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-0006-9600000000-7585746143c62ab3f832View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-010da2c57a936868eeccView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0kai-9200000000-12f986238bdf05dc39b9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-001i-9400000000-b6dbdfa2d4643fc13e70View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0190000000-129f123affa0ecbf7a59View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-052f-0910000000-302fbdef606070bd5a67View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 0V, Positivesplash10-0bta-0890000000-2b3810ae2bbe68268b17View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-001i-9300000000-7e64dc8404ac65411358View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 0V, Positivesplash10-052b-0290000000-7cf7d5be6f7a84299cabView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0950000000-de2a45f204636756b9c4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-00l6-9000000000-b4060d47530bdf70d6ccView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-3920000000-15bb158a77906d0f87b5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0udi-2900000000-600643d24abd3ba9b5f1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0920000000-a73049fd7001db7f72d5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0udi-0900000000-46e1b064445ad43a60fdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-0490000000-226d044c24dd80a7c2caView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0h0s-2980000000-add34ee37b95c102114dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-06rm-5900000000-8d66d80928e84e9c93fdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-9360000000-3bd8fcdd66c5d245778eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9210000000-f551740a13c90ff1d324View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-bf4e4234a47d8aa03828View in MoNA
1D NMR1H 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
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Bernert JT Jr, Bell CJ, Guntupalli J, Hannon WH: Pseudouridine is unsuitable as an endogenous renal clearance marker. Clin Chem. 1988 Jun;34(6):1011-7. Pubmed: 3378317
  • Colonna A, Russo T, Esposito F, Salvatore F, Cimino F: Determination of pseudouridine and other nucleosides in human blood serum by high-performance liquid chromatography. Anal Biochem. 1983 Apr 1;130(1):19-26. Pubmed: 6869800
  • Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. Pubmed: 15116424
  • Mak TW, Ho SS, Ho CS, Jones MG, Lai CK, Lam CW: Pleural fluid pseudouridine in malignant and benign pleural effusions. Ann Clin Biochem. 1998 Jan;35 ( Pt 1):94-8. Pubmed: 9463745
  • Shoemaker JD, Elliott WH: Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease. J Chromatogr. 1991 Jan 2;562(1-2):125-38. Pubmed: 2026685
  • Uziel M, Smith LH, Taylor SA: Modified nucleosides in urine: selective removal and analysis. Clin Chem. 1976 Sep;22(9):1451-5. Pubmed: 954194
  • Woodcock TM, Chou TC, Tan CT, Sternberg SS, Philips FS, Young CW, Burchenal JH: Biochemical, pharmacological, and phase I clinical evaluation of pseudoisocytidine. Cancer Res. 1980 Nov;40(11):4243-9. Pubmed: 7471064
Synthesis Reference:anessian, 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
External Links:
ResourceLink
CHEBI ID17802
HMDB IDHMDB00767
Pubchem Compound ID15047
Kegg IDC02067
ChemSpider ID14319
WikipediaPseudouridine
BioCyc IDCPD-497
EcoCyc IDCPD-497

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.

Transporters

Protein Details
1. Putative pseudouridine transporter
General function:
Involved in nucleoside:sodium symporter activity
Specific function:
Could be involved in pseudouridine transport
Gene Name:
psuT
Uniprot ID:
P33024
Molecular weight:
43431