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1-Methylpseudouridine

PubChem CID
99543
Structure
1-Methylpseudouridine_small.png
1-Methylpseudouridine_3D_Structure.png
Molecular Formula
Synonyms
  • 1-Methylpseudouridine
  • 13860-38-3
  • N1-Methylpseudouridine
  • N1-methyl-pseudouridine
  • 2,4(1H,3H)-Pyrimidinedione, 1-methyl-5-beta-D-ribofuranosyl-
Molecular Weight
258.23 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2005-08-08
  • Modify:
    2024-12-28
Description
1-methylpseudouridine is a methylpseudouridine in which the methyl group is located at position N-1 on the uracil ring.
1-Methylpseudouridine has been reported in Streptomyces platensis and Streptomyces lincolnensis with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
1-Methylpseudouridine.png

1.2 3D Conformer

2 Biologic Description

IUPAC Condensed
m1Yra-Ribf
Sequence
N
HELM
RNA1{R([*c1cn(c(=O)[nH]c1=O)C |$_R1;;;;;;;;;$|])}$$$$
IUPAC
1-methyl-pseudouridine

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1-methylpyrimidine-2,4-dione
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

3.1.2 InChI

InChI=1S/C10H14N2O6/c1-12-2-4(9(16)11-10(12)17)8-7(15)6(14)5(3-13)18-8/h2,5-8,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,8+/m1/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.3 InChIKey

UVBYMVOUBXYSFV-XUTVFYLZSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.4 SMILES

CN1C=C(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
Computed by OEChem 2.3.0 (PubChem release 2021.10.14)

3.2 Molecular Formula

C10H14N2O6
Computed by PubChem 2.2 (PubChem release 2021.10.14)

3.3 Other Identifiers

3.3.1 CAS

3.3.2 European Community (EC) Number

3.3.3 UNII

3.3.4 ChEBI ID

3.3.5 DSSTox Substance ID

3.3.6 Metabolomics Workbench ID

3.3.7 Nikkaji Number

3.3.8 Wikidata

3.3.9 Wikipedia

3.4 Synonyms

3.4.1 MeSH Entry Terms

  • 1-methylpseudouridine
  • N1-methyl-pseudouridine

3.4.2 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
258.23 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
-2.6
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
4
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
2
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
258.08518617 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
258.08518617 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
119Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
18
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
409
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
4
Reference
Computed by PubChem
Property Name
Undefined Atom Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Covalently-Bonded Unit Count
Property Value
1
Reference
Computed by PubChem
Property Name
Compound Is Canonicalized
Property Value
Yes
Reference
Computed by PubChem (release 2021.10.14)

5 Spectral Information

5.1 1D NMR Spectra

5.1.1 13C NMR Spectra

Copyright
Copyright © 2016-2024 W. Robien, Inst. of Org. Chem., Univ. of Vienna. All Rights Reserved.
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5.2 Mass Spectrometry

5.2.1 GC-MS

Copyright
Copyright © 2020-2024 John Wiley & Sons, Inc. All Rights Reserved.
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5.2.2 LC-MS

1 of 3
View All
MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M-H]-
Precursor m/z
257.0776
Instrument
Thermo Q Exactive HF
Instrument Type
LC-ESI-QFT
Ionization Mode
negative
Collision Energy
HCD (NCE 20-30-40%)
Retention Time
4.949333
Top 5 Peaks

124.03921 100

257.07785 60.68

154.04996 12.78

98.05983 8.30

166.05016 6.90

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2 of 3
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MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
259.0919
Instrument
SCIEX TripleTOF 6600
Instrument Type
LC-ESI-QTOF
Ionization Mode
positive
Collision Energy
35 eV
Retention Time
4.866467
Top 5 Peaks

139.05139 100

96.0434 24.85

205.05646 18.64

177.06039 12.43

193.0609 12.43

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7 Chemical Vendors

8 Safety and Hazards

8.1 Hazards Identification

8.1.1 GHS Classification

GHS Hazard Statements

Not Classified

Reported as not meeting GHS hazard criteria by 1 of 1 companies. For more detailed information, please visit ECHA C&L website.

8.1.2 Hazard Classes and Categories

Not Classified

9 Literature

9.1 Consolidated References

9.2 NLM Curated PubMed Citations

9.3 Springer Nature References

9.4 Chemical Co-Occurrences in Literature

9.5 Chemical-Gene Co-Occurrences in Literature

9.6 Chemical-Disease Co-Occurrences in Literature

10 Patents

10.1 Depositor-Supplied Patent Identifiers

10.2 WIPO PATENTSCOPE

10.3 Chemical Co-Occurrences in Patents

10.4 Chemical-Disease Co-Occurrences in Patents

10.5 Chemical-Gene Co-Occurrences in Patents

11 Interactions and Pathways

11.1 Protein Bound 3D Structures

11.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

12 Taxonomy

The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata) | DOI:10.5281/zenodo.5794106

13 Classification

13.1 MeSH Tree

13.2 ChEBI Ontology

13.3 ChemIDplus

13.4 UN GHS Classification

13.5 EPA DSSTox Classification

13.6 The Natural Products Atlas Classification

13.7 LOTUS Tree

13.8 MolGenie Organic Chemistry Ontology

14 Information Sources

  1. CAS Common Chemistry
    LICENSE
    The data from CAS Common Chemistry is provided under a CC-BY-NC 4.0 license, unless otherwise stated.
    https://creativecommons.org/licenses/by-nc/4.0/
  2. ChemIDplus
    ChemIDplus Chemical Information Classification
    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  3. EPA DSSTox
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  4. European Chemicals Agency (ECHA)
    LICENSE
    Use of the information, documents and data from the ECHA website is subject to the terms and conditions of this Legal Notice, and subject to other binding limitations provided for under applicable law, the information, documents and data made available on the ECHA website may be reproduced, distributed and/or used, totally or in part, for non-commercial purposes provided that ECHA is acknowledged as the source: "Source: European Chemicals Agency, http://echa.europa.eu/". Such acknowledgement must be included in each copy of the material. ECHA permits and encourages organisations and individuals to create links to the ECHA website under the following cumulative conditions: Links can only be made to webpages that provide a link to the Legal Notice page.
    https://echa.europa.eu/web/guest/legal-notice
  5. FDA Global Substance Registration System (GSRS)
    LICENSE
    Unless otherwise noted, the contents of the FDA website (www.fda.gov), both text and graphics, are not copyrighted. They are in the public domain and may be republished, reprinted and otherwise used freely by anyone without the need to obtain permission from FDA. Credit to the U.S. Food and Drug Administration as the source is appreciated but not required.
    https://www.fda.gov/about-fda/about-website/website-policies#linking
  6. ChEBI
  7. LOTUS - the natural products occurrence database
    LICENSE
    The code for LOTUS is released under the GNU General Public License v3.0.
    https://lotus.nprod.net/
  8. Japan Chemical Substance Dictionary (Nikkaji)
  9. The Natural Products Atlas
    LICENSE
    The Natural Products Atlas is licensed under a Creative Commons Attribution 4.0 International License.
    https://www.npatlas.org/terms
    The Natural Products Atlas Classification
    https://www.npatlas.org/
  10. MassBank of North America (MoNA)
    LICENSE
    The content of the MoNA database is licensed under CC BY 4.0.
    https://mona.fiehnlab.ucdavis.edu/documentation/license
  11. Metabolomics Workbench
  12. Protein Data Bank in Europe (PDBe)
  13. RCSB Protein Data Bank (RCSB PDB)
    LICENSE
    Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data.
    https://www.rcsb.org/pages/policies
  14. SpectraBase
    Uracil, 1-methyl-5-.beta.-D-ribofuranosyl-
    https://spectrabase.com/spectrum/NiEjiX51Ed
  15. Springer Nature
  16. Wikidata
  17. Wikipedia
  18. PubChem
  19. Medical Subject Headings (MeSH)
    LICENSE
    Works produced by the U.S. government are not subject to copyright protection in the United States. Any such works found on National Library of Medicine (NLM) Web sites may be freely used or reproduced without permission in the U.S.
    https://www.nlm.nih.gov/copyright.html
  20. GHS Classification (UNECE)
  21. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  22. PATENTSCOPE (WIPO)
CONTENTS