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Record Information |
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Version | 4.0 |
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Status | Detected and Quantified |
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Creation Date | 2005-11-16 15:48:42 UTC |
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Update Date | 2020-10-09 21:00:38 UTC |
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HMDB ID | HMDB0000767 |
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Secondary Accession Numbers | - HMDB0006075
- HMDB00767
- HMDB06075
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Metabolite Identification |
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Common Name | Pseudouridine |
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Description | Pseudouridine, also known as psi-uridine or 5-ribosyluracil, belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides such as phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides. Pseudouridine is an extremely weak basic (essentially neutral) compound (based on its pKa). Pseudouridine exists in all living species, ranging from bacteria to humans. It has been detected but not quantified in several different foods, such as cereal products, red bell peppers, sweet rowanberries, bayberries, and cinnamons. This could make pseudouridine a potential biomarker for the consumption of these foods. 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 ). |
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Structure | |
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Synonyms | Value | Source |
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(1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol | ChEBI | 5-(beta-D-Ribofuranosyl)uracil | ChEBI | beta-Pseudouridine | ChEBI | p | ChEBI | Psi-uridine | ChEBI | 5-(b-D-Ribofuranosyl)uracil | Generator | 5-(Β-D-ribofuranosyl)uracil | Generator | b-Pseudouridine | Generator | Β-pseudouridine | Generator | 5-(b-delta-Ribofuranosyl)uracil | HMDB | 5-b-D-Ribofuranosyl-uracil | HMDB | 5-beta-delta-Ribofuranosyl-uracil | HMDB | 5-Ribosyluracil | HMDB | b-D-Pseudouridine | HMDB | beta-delta-Pseudouridine | HMDB | Pseudouridine C | HMDB | Y-uridine | HMDB | 5-beta-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione | HMDB | 5-β-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione | HMDB | Pseudouridine | HMDB | beta-D-Pseudouridine | HMDB | β-D-Pseudouridine | HMDB | ψ-Uridine | HMDB |
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Chemical Formula | C9H12N2O6 |
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Average Molecular Weight | 244.2014 |
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Monoisotopic Molecular Weight | 244.069536126 |
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IUPAC Name | 5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione |
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Traditional Name | β-pseudouridine |
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CAS Registry Number | 1445-07-4 |
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SMILES | OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O |
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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 |
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InChI Key | PTJWIQPHWPFNBW-GBNDHIKLSA-N |
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Chemical Taxonomy |
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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. |
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Kingdom | Organic compounds |
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Super Class | Nucleosides, nucleotides, and analogues |
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Class | Nucleoside and nucleotide analogues |
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Sub Class | Not Available |
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Direct Parent | Nucleoside and nucleotide analogues |
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Alternative Parents | |
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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
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Molecular Framework | Aromatic heteromonocyclic compounds |
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External Descriptors | |
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Ontology |
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Physiological effect | Health effect: |
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Disposition | Route of exposure: Source: Biological location: |
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Physical Properties |
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State | Solid |
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Experimental Properties | Property | Value | Reference |
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Melting Point | Not Available | Not Available | Boiling Point | Not Available | Not Available | Water Solubility | Not Available | Not Available | LogP | Not Available | Not Available |
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Predicted Properties | |
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Spectra |
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| Spectrum Type | Description | Splash Key | View |
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Predicted GC-MS | Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive | splash10-0unc-7930000000-a1e7f343c88a63ac1976 | Spectrum | Predicted GC-MS | Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive | splash10-0fi0-3494100000-8d726ed412554c1f92f0 | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-IT , negative | splash10-0udi-0900000000-6ade42aaa885371e176c | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QTOF 10V, positive | splash10-0a4i-0190000000-129f123affa0ecbf7a59 | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QTOF 20V, positive | splash10-052f-0910000000-302fbdef606070bd5a67 | Spectrum | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QTOF 40V, positive | splash10-001i-9300000000-11f5761be16d1b061df5 | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 10V, Positive | splash10-0002-0490000000-226d044c24dd80a7c2ca | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 20V, Positive | splash10-0h0s-2980000000-add34ee37b95c102114d | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 40V, Positive | splash10-06rm-5900000000-8d66d80928e84e9c93fd | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 10V, Negative | splash10-0006-9360000000-3bd8fcdd66c5d245778e | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 20V, Negative | splash10-0006-9210000000-f551740a13c90ff1d324 | Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 40V, Negative | splash10-0006-9000000000-bf4e4234a47d8aa03828 | Spectrum | 1D NMR | 1H NMR Spectrum | Not Available | Spectrum |
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Biological Properties |
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Cellular Locations | - Cytoplasm (predicted from logP)
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Biospecimen Locations | - Amniotic Fluid
- Blood
- Feces
- Urine
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Tissue Locations | |
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Pathways | |
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Normal Concentrations |
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Amniotic Fluid | Detected and Quantified | 1.29 +/- 1.07 uM | Adult (>18 years old) | Female | Normal | | details | Blood | Detected and Quantified | 2.0492 +/- 23.770 uM | Children (3 months - 6 years old) | Not Specified | Normal | | details | Blood | Detected and Quantified | 3.18 +/- 0.99 uM | Adult (>18 years old) | Both | Normal | | details | Feces | Detected but not Quantified | Not Quantified | Adult (>18 years old) | Both | Normal | | details | Feces | Detected but not Quantified | Not Quantified | Adult (>18 years old) | Both | Normal | | details | Feces | Detected but not Quantified | Not Quantified | Adult (>18 years old) | Both | Normal | | details | Urine | Detected and Quantified | 63.47 +/- 32.76 umol/mmol creatinine | Infant (0-1 year old) | Both | Normal | | details | Urine | Detected and Quantified | 29.8 (21.8-47.3) umol/mmol creatinine | Adult (>18 years old) | Both | Normal | | details | Urine | Detected and Quantified | 12.5 (6.5-20.4) umol/mmol creatinine | Adult (>18 years old) | Both | Normal | | details | Urine | Detected and Quantified | 26.02 +/- 4.62 umol/mmol creatinine | Adult (>18 years old) | Female | Normal | | details | Urine | Detected and Quantified | 25.0 +/- 5.0 umol/mmol creatinine | Adult (>18 years old) | Male | Normal | | details | Urine | Detected and Quantified | 25.5 +/- 4.8 umol/mmol creatinine | Adult (>18 years old) | Both | Normal | | details | Urine | Detected but not Quantified | Not Quantified | Adult (>18 years old) | Both | Normal | | details | Urine | Detected but not Quantified | Not Quantified | Adult (>18 years old) | Both | Normal | | details | Urine | Detected and Quantified | 13.467 (8.307-18.627) umol/mmol creatinine | Adult (>18 years old) | Both | Normal | | details | Urine | Detected and Quantified | 28.9 (13.3-41.3) umol/mmol creatinine | Adult (>18 years old) | Both | Normal | | details |
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Abnormal Concentrations |
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Blood | Detected and Quantified | 53.689 +/- 87.705 uM | Children (3 months - 6 years old) | Not Specified | Uremia | | details | Blood | Detected and Quantified | 16.70 +/- 3.72 uM | Adult (>18 years old) | Both | Canavan disease | | details | Feces | Detected but not Quantified | Not Quantified | Adult (>18 years old) | Both | Colorectal cancer | | details | Feces | Detected but not Quantified | Not Quantified | Adult (>18 years old) | Both | Colorectal Cancer | | details | Feces | Detected but not Quantified | Not Quantified | Adult (>18 years old) | Both | Colorectal Cancer | | details | Urine | Detected but not Quantified | Not Quantified | Adult (>18 years old) | Female | Epithelial ovarian cancer | | details |
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Associated Disorders and Diseases |
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Disease References | Canavan disease |
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- 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 ]
| Uremia |
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- Vanholder R, De Smet R, Glorieux G, Argiles A, Baurmeister U, Brunet P, Clark W, Cohen G, De Deyn PP, Deppisch R, Descamps-Latscha B, Henle T, Jorres A, Lemke HD, Massy ZA, Passlick-Deetjen J, Rodriguez M, Stegmayr B, Stenvinkel P, Tetta C, Wanner C, Zidek W: Review on uremic toxins: classification, concentration, and interindividual variability. Kidney Int. 2003 May;63(5):1934-43. doi: 10.1046/j.1523-1755.2003.00924.x. [PubMed:12675874 ]
| Colorectal cancer |
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- Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
- Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
- Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
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Associated OMIM IDs | |
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External Links |
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DrugBank ID | Not Available |
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Phenol Explorer Compound ID | Not Available |
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FooDB ID | FDB031139 |
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KNApSAcK ID | C00001508 |
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Chemspider ID | 14319 |
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KEGG Compound ID | C02067 |
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BioCyc ID | CPD-497 |
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BiGG ID | Not Available |
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Wikipedia Link | Pseudouridine |
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METLIN ID | 5734 |
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PubChem Compound | 15047 |
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PDB ID | Not Available |
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ChEBI ID | 17802 |
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Food Biomarker Ontology | Not Available |
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VMH ID | Not Available |
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MarkerDB ID | MDB00000249 |
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References |
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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. |
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Material Safety Data Sheet (MSDS) | Not Available |
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General References | - 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 ]
- Uziel M, Smith LH, Taylor SA: Modified nucleosides in urine: selective removal and analysis. Clin Chem. 1976 Sep;22(9):1451-5. [PubMed:954194 ]
- 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 ]
- 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 ]
- 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 ]
- 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 ]
- 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 ]
- Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
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