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Cytidine 3',5'-diphosphate

PubChem CID
3081380
Structure
Cytidine 3',5'-diphosphate_small.png
Cytidine 3',5'-diphosphate_3D_Structure.png
Molecular Formula
Synonyms
  • Cytidine 3',5'-diphosphate
  • 2922-94-3
  • 3',5'-Cdp
  • 5'-Phosphocytidine 3'-phosphate
  • 3'-Cytidylic acid, 5'-(dihydrogen phosphate)
Molecular Weight
403.18 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2005-08-09
  • Modify:
    2025-01-18

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Cytidine 3',5'-diphosphate.png

1.2 3D Conformer

2 Biologic Description

IUPAC Condensed
P-rCyd-P
Sequence
C
HELM
RNA1{PR(C).P}$$$$
IUPAC
5'-phosphono-3'-cytidylic acid

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-4-hydroxy-2-(phosphonooxymethyl)oxolan-3-yl] dihydrogen phosphate
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

3.1.2 InChI

InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(14)11-5)8-6(13)7(23-25(18,19)20)4(22-8)3-21-24(15,16)17/h1-2,4,6-8,13H,3H2,(H2,10,11,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7-,8-/m1/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.3 InChIKey

MVGIITUCOOTSAP-XVFCMESISA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.4 SMILES

C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)OP(=O)(O)O)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

3.2 Molecular Formula

C9H15N3O11P2
Computed by PubChem 2.2 (PubChem release 2021.10.14)

3.3 Other Identifiers

3.3.1 CAS

2922-94-3

3.3.2 DSSTox Substance ID

3.3.3 Nikkaji Number

3.3.4 Wikidata

3.4 Synonyms

3.4.1 MeSH Entry Terms

  • 3',5'-CDP
  • 5'-phosphocytidine 3'-phosphate
  • cytidine 3',5'-diphosphate

3.4.2 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
403.18 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3
Property Value
-4.5
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
11
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
403.01818230 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
403.01818230 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
222 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
25
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
684
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)

6 Chemical Vendors

7 Literature

7.1 Consolidated References

7.2 NLM Curated PubMed Citations

7.3 Springer Nature References

7.4 Chemical Co-Occurrences in Literature

7.5 Chemical-Gene Co-Occurrences in Literature

7.6 Chemical-Disease Co-Occurrences in Literature

8 Patents

8.1 Depositor-Supplied Patent Identifiers

8.2 WIPO PATENTSCOPE

8.3 Chemical Co-Occurrences in Patents

8.4 Chemical-Disease Co-Occurrences in Patents

8.5 Chemical-Gene Co-Occurrences in Patents

9 Interactions and Pathways

9.1 Protein Bound 3D Structures

9.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

10 Classification

10.1 MeSH Tree

10.2 ChemIDplus

10.3 EPA DSSTox Classification

11 Information Sources

  1. ChemIDplus
    ChemIDplus Chemical Information Classification
    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  2. EPA DSSTox
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  3. Japan Chemical Substance Dictionary (Nikkaji)
  4. Protein Data Bank in Europe (PDBe)
  5. Springer Nature
  6. Wikidata
    cytidine 3',5'-bis(dihydrogen phosphate)
    https://www.wikidata.org/wiki/Q27465101
  7. PubChem
  8. 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
  9. PATENTSCOPE (WIPO)
CONTENTS