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Pyrimidine dimer

PubChem CID
22057568
Structure
Pyrimidine dimer_small.png
Pyrimidine dimer_3D_Structure.png
Pyrimidine dimer__Crystal_Structure.png
Molecular Formula
Synonyms
  • pyrimidine phase III
  • Pyrimidine dimer
  • pyrimidine.pyrimidine
  • SCHEMBL10646
  • DTXSID001015753
Molecular Weight
160.18 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Parent Compound
Dates
  • Create:
    2007-12-05
  • Modify:
    2025-01-11
Description
Pyrimidine Dimer is a pair of pyrimidine bases (thymine or cytosine in DNA or uracil in double-stranded RNA) within a nucleic acid covalently linked by a cyclobutane ring, the formation of which was induced by exposure to ultraviolet radiation. The presence of pyrimidine dimers inhibits DNA replication; improper repair of these lesions promotes DNA mutagenesis.
Dimers found in DNA chains damaged by ULTRAVIOLET RAYS. They consist of two adjacent PYRIMIDINE NUCLEOTIDES, usually THYMINE nucleotides, in which the pyrimidine residues are covalently joined by a cyclobutane ring. These dimers block DNA REPLICATION.
See also: Pyrimidine (annotation moved to).

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Pyrimidine dimer.png

1.2 3D Conformer

3D Conformer of Parent

1.3 Crystal Structures

1 of 2
View All
COD Number
Associated Article
Patyk, Ewa; Podsiadło, Marcin; Katrusiak, Andrzej. CH···N Bonds and Dynamics in Isostructural Pyrimidine Polymorphs. Crystal Growth & Design 2015;15(8):4039-. DOI: 10.1021/acs.cgd.5b00657
Crystal Structure Depiction
Crystal Structure Depiction
Hermann-Mauguin space group symbol
P 1 1 21/a
Hall space group symbol
-P 2ac
Space group number
14
a
22.096 Å
b
9.507 Å
c
3.6415 Å
α
90.00 °
β
90.00 °
γ
95.05 °
Z
8
Z'
2
Residual factor
0.0517
Component
2 x c1ccncn1 (Pyrimidine)

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

pyrimidine
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

2.1.2 InChI

InChI=1S/2C4H4N2/c2*1-2-5-4-6-3-1/h2*1-4H
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.3 InChIKey

YMXFJTUQQVLJEN-UHFFFAOYSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.4 SMILES

C1=CN=CN=C1.C1=CN=CN=C1
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

2.2 Molecular Formula

C8H8N4
Computed by PubChem 2.2 (PubChem release 2021.10.14)

2.3 Other Identifiers

2.3.1 CAS

25247-63-6

2.3.2 DSSTox Substance ID

2.3.3 NCI Thesaurus Code

2.4 Synonyms

2.4.1 MeSH Entry Terms

  • Cyclobutane Dimer, Thymine-Thymine
  • Cyclobutane Dimers, Thymine-Thymine
  • Cyclobutane Pyrimidine Dimer
  • Cyclobutane Pyrimidine Dimers
  • Cyclobutane-Pyrimidine Dimer
  • Cyclobutane-Pyrimidine Dimers
  • Cytosine Thymine Dimer
  • Cytosine Thymine Dimers
  • Cytosine-Thymine Dimer
  • Cytosine-Thymine Dimers
  • Pyrimidine Dimer
  • Pyrimidine Dimer, Cyclobutane
  • Pyrimidine Dimers
  • Pyrimidine Dimers, Cyclobutane
  • Thymine Cyclobutane Dimer
  • Thymine Dimer
  • Thymine Dimers
  • Thymine Thymine Cyclobutane Dimer
  • Thymine-Cyclobutane Dimer
  • Thymine-Cyclobutane Dimers
  • Thymine-Thymine Cyclobutane Dimer
  • Thymine-Thymine Cyclobutane Dimers

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
160.18 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
0
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
4
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
0
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
160.074896272 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
160.074896272 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
51.6 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
12
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
32.5
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
0
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
2
Reference
Computed by PubChem
Property Name
Compound Is Canonicalized
Property Value
Yes
Reference
Computed by PubChem (release 2021.10.14)

5 Literature

5.1 Consolidated References

5.2 NLM Curated PubMed Citations

5.3 Springer Nature References

5.4 Chemical Co-Occurrences in Literature

5.5 Chemical-Gene Co-Occurrences in Literature

5.6 Chemical-Disease Co-Occurrences in Literature

6 Patents

6.1 Depositor-Supplied Patent Identifiers

6.2 WIPO PATENTSCOPE

6.3 Chemical Co-Occurrences in Patents

6.4 Chemical-Disease Co-Occurrences in Patents

6.5 Chemical-Gene Co-Occurrences in Patents

7 Classification

7.1 MeSH Tree

8 Information Sources

  1. Crystallography Open Database (COD)
    LICENSE
    All data in the COD and the database itself are dedicated to the public domain and licensed under the CC0 License. Users of the data should acknowledge the original authors of the structural data.
    https://creativecommons.org/publicdomain/zero/1.0/
  2. EPA DSSTox
  3. NCI Thesaurus (NCIt)
    LICENSE
    Unless otherwise indicated, all text within NCI products is free of copyright and may be reused without our permission. Credit the National Cancer Institute as the source.
    https://www.cancer.gov/policies/copyright-reuse
  4. Springer Nature
  5. 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
  6. PubChem
  7. PATENTSCOPE (WIPO)
CONTENTS