Human Metabolome Database Version 3.5

Showing metabocard for Pseudouridine (HMDB00767)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:09:17 -0700
HMDB ID HMDB00767
Secondary Accession Numbers
  • HMDB06075
Metabolite Identification
Common Name Pseudouridine
Description Pseudouridine 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
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
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 Formula C9H12N2O6
Average Molecular Weight 244.2014
Monoisotopic Molecular Weight 244.069536126
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 pseudouridine
CAS Registry Number 1445-07-4
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 Key PTJWIQPHWPFNBW-GBNDHIKLSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Carbohydrates and Carbohydrate Conjugates
Class Glycosyl Compounds
Sub Class C-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 Parent C-glycosyl Compounds
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
Application Not Available
Cellular locations
  • Cytoplasm (predicted from logP)
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 63.8 g/L ALOGPS
LogP -2.01 ALOGPS
LogP -3.1 ChemAxon
LogS -0.58 ALOGPS
pKa (strongest acidic) 9.55 ChemAxon
pKa (strongest basic) -3 ChemAxon
Hydrogen Acceptor Count 6 ChemAxon
Hydrogen Donor Count 5 ChemAxon
Polar Surface Area 128.12 A2 ChemAxon
Rotatable Bond Count 2 ChemAxon
Refractivity 52.44 ChemAxon
Polarizability 21.81 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
Gas-MS Spectrum
1H NMR Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations
  • Amniotic Fluid
  • Blood
  • Urine
Tissue Location Not Available
Pathways Not Available
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Amniotic Fluid Detected and Quantified
1.29 +/- 1.07 uM Adult (>18 years old) Female Normal
Blood Detected and Quantified
3.18 +/- 0.99 uM Adult (>18 years old) Both Normal
Urine Detected and Quantified
63.47 +/- 32.76 umol/mmol creatinine Infant (0-1 year old) Both Normal
Urine Detected and Quantified
29.8 (21.8-47.3) umol/mmol creatinine Adult (>18 years old) Both Comment Normal
Urine Detected and Quantified
12.5 (6.5-20.4) umol/mmol creatinine Adult (>18 years old) Both Normal
  • Geigy Scient...
Urine Detected and Quantified
26.02 +/- 4.62 umol/mmol creatinine Adult (>18 years old) Female Normal
Urine Detected and Quantified
25.0 +/- 5.0 umol/mmol creatinine Adult (>18 years old) Male Normal
Urine Detected and Quantified
25.5 +/- 4.8 umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected but not Quantified
Not Applicable Adult (>18 years old) Both Normal
Urine Detected but not Quantified
Not Applicable Adult (>18 years old) Both Comment Normal
Urine Detected and Quantified
13.467 (8.307-18.627) umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
28.9 (13.3-41.3) umol/mmol creatinine Adult (>18 years old) Both Comment Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 16.70 +/- 3.72 uM Adult (>18 years old) Both Canavan 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 Link_out
      Associated OMIM IDs
      DrugBank ID Not Available
      DrugBank Metabolite ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB014724
      KNApSAcK ID C00001508 Link_out
      Chemspider ID 14319 Link_out
      KEGG Compound ID C02067 Link_out
      BioCyc ID Not Available
      BiGG ID Not Available
      Wikipedia Link Pseudouridine Link_out
      NuGOwiki Link HMDB00767 Link_out
      Metagene Link HMDB00767 Link_out
      METLIN ID 5734 Link_out
      PubChem Compound 15047 Link_out
      PDB ID Not Available
      ChEBI ID 17802 Link_out
      References
      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
      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 Link_out
      2. Uziel M, Smith LH, Taylor SA: Modified nucleosides in urine: selective removal and analysis. Clin Chem. 1976 Sep;22(9):1451-5. Pubmed: 954194 Link_out
      3. 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 Link_out
      4. 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 Link_out
      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 Link_out
      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 Link_out
      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 Link_out

      Enzymes
      Name: tRNA pseudouridine synthase A, mitochondrial
      Reactions: Not Available
      Gene Name: PUS1
      Uniprot ID: Q9Y606 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: H/ACA ribonucleoprotein complex subunit 4
      Reactions: Not Available
      Gene Name: DKC1
      Uniprot ID: O60832 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Putative tRNA pseudouridine synthase Pus10
      Reactions: Not Available
      Gene Name: PUS10
      Uniprot ID: Q3MIT2 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: tRNA pseudouridine synthase 3
      Reactions: Not Available
      Gene Name: PUS3
      Uniprot ID: Q9BZE2 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Pseudouridylate synthase 7 homolog
      Reactions: Not Available
      Gene Name: PUS7
      Uniprot ID: Q96PZ0 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Pseudouridylate synthase 7 homolog-like protein
      Reactions: Not Available
      Gene Name: PUS7L
      Uniprot ID: Q9H0K6 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: RNA pseudouridylate synthase domain-containing protein 1
      Reactions: Not Available
      Gene Name: RPUSD1
      Uniprot ID: Q9UJJ7 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: RNA pseudouridylate synthase domain-containing protein 2
      Reactions: Not Available
      Gene Name: RPUSD2
      Uniprot ID: Q8IZ73 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: RNA pseudouridylate synthase domain-containing protein 3
      Reactions: Not Available
      Gene Name: RPUSD3
      Uniprot ID: Q6P087 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: RNA pseudouridylate synthase domain-containing protein 4
      Reactions: Not Available
      Gene Name: RPUSD4
      Uniprot ID: Q96CM3 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Probable tRNA pseudouridine synthase 1
      Reactions: Not Available
      Gene Name: TRUB1
      Uniprot ID: Q8WWH5 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Probable tRNA pseudouridine synthase 2
      Reactions: Not Available
      Gene Name: TRUB2
      Uniprot ID: O95900 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: tRNA pseudouridine synthase-like 1
      Reactions: Not Available
      Gene Name: PUSL1
      Uniprot ID: Q8N0Z8 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Pseudouridine-5'-monophosphatase
      Reactions:
      pseudouridine 5'-monophosphate + Water unknown Pseudouridine + Phosphoric acid details
      Gene Name: HDHD1
      Uniprot ID: Q08623 Link_out
      Protein Sequence: FASTA