Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2013-02-09 00:09:17 UTC
HMDB IDHMDB00767
Secondary Accession Numbers
  • HMDB06075
Metabolite Identification
Common NamePseudouridine
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
Synonyms
  1. 5-(b-D-Ribofuranosyl)uracil
  2. 5-(b-delta-Ribofuranosyl)uracil
  3. 5-b-D-Ribofuranosyl-Uracil
  4. 5-beta-delta-Ribofuranosyl-Uracil
  5. 5-Ribosyluracil
  6. b-D-Pseudouridine
  7. b-Pseudouridine
  8. beta-delta-Pseudouridine
  9. beta-Pseudouridine
  10. Pseudouridine
  11. Pseudouridine C
  12. y-Uridine
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 IUPAC Namepseudouridine
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
KingdomOrganic Compounds
Super ClassCarbohydrates and Carbohydrate Conjugates
ClassGlycosyl Compounds
Sub ClassC-glycosyl Compounds
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • Carbohydrates and Carbohydrate Conjugates
  • a small molecule(Cyc)
Substituents
  • 1,2 Diol
  • Dialkyl Ether
  • Hydropyrimidine
  • Oxolane
  • Pentose Monosaccharide
  • Primary Alcohol
  • Pyrimidine
  • Pyrimidone
  • Secondary Alcohol
Direct ParentC-glycosyl Compounds
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
ApplicationNot Available
Cellular locations
  • Cytoplasm (predicted from logP)
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
water solubility63.8 g/LALOGPS
logP-2ALOGPS
logP-3.1ChemAxon
logS-0.58ALOGPS
pKa (strongest acidic)9.55ChemAxon
pKa (strongest basic)-3ChemAxon
physiological charge0ChemAxon
hydrogen acceptor count6ChemAxon
hydrogen donor count5ChemAxon
polar surface area128.12ChemAxon
rotatable bond count2ChemAxon
refractivity52.44ChemAxon
polarizability21.81ChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations
  • Amniotic Fluid
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReference
Amniotic FluidDetected and Quantified1.29 +/- 1.07 uMAdult (>18 years old)FemaleNormal
BloodDetected and Quantified3.18 +/- 0.99 uMAdult (>18 years old)BothNormal
UrineDetected and Quantified63.47 +/- 32.76 umol/mmol creatinineInfant (0-1 year old)BothNormal
UrineDetected and Quantified29.8 (21.8-47.3) umol/mmol creatinineAdult (>18 years old)BothCommentNormal
UrineDetected and Quantified12.5 (6.5-20.4) umol/mmol creatinineAdult (>18 years old)BothNormal
  • Geigy Scient...
UrineDetected and Quantified26.02 +/- 4.62 umol/mmol creatinineAdult (>18 years old)FemaleNormal
UrineDetected and Quantified25.0 +/- 5.0 umol/mmol creatinineAdult (>18 years old)MaleNormal
UrineDetected and Quantified25.5 +/- 4.8 umol/mmol creatinineAdult (>18 years old)BothNormal
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)BothNormal
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)BothCommentNormal
UrineDetected and Quantified13.467 (8.307-18.627) umol/mmol creatinineAdult (>18 years old)BothNormal
UrineDetected and Quantified28.9 (13.3-41.3) umol/mmol creatinineAdult (>18 years old)BothCommentNormal
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReference
BloodDetected and Quantified16.70 +/- 3.72 uMAdult (>18 years old)BothCanavan disease
Associated Disorders and Diseases
Disease References
Canavan disease
  • Tavazzi B, Lazzarino G, Leone P, Amorini AM, Bellia F, Janson CG, Di Pietro V, Ceccarelli L, Donzelli S, Francis JS, Giardina B: Simultaneous high performance liquid chromatographic separation of purines, pyrimidines, N-acetylated amino acids, and dicarboxylic acids for the chemical diagnosis of inborn errors of metabolism. Clin Biochem. 2005 Nov;38(11):997-1008. Epub 2005 Sep 1. Pubmed: 16139832
Associated OMIM IDs
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB014724
KNApSAcK IDC00001508
Chemspider ID14319
KEGG Compound IDC02067
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPseudouridine
NuGOwiki LinkHMDB00767
Metagene LinkHMDB00767
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. 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
  2. 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
  3. Uziel M, Smith LH, Taylor SA: Modified nucleosides in urine: selective removal and analysis. Clin Chem. 1976 Sep;22(9):1451-5. Pubmed: 954194
  4. 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
  5. 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
  6. 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
  7. 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

Enzymes

Gene Name:
PUS3
Uniprot ID:
Q9BZE2
Gene Name:
PUS7
Uniprot ID:
Q96PZ0
Gene Name:
TRUB1
Uniprot ID:
Q8WWH5
Gene Name:
TRUB2
Uniprot ID:
O95900
Gene Name:
PUSL1
Uniprot ID:
Q8N0Z8
Gene Name:
HDHD1
Uniprot ID:
Q08623
Reactions
pseudouridine 5'-monophosphate + Water unknown Pseudouridine + Phosphoric aciddetails