2',3'-Cyclic UMP (ECMDB20062) (M2MDB000911)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)Transporters (4)XML
Proteins (132)
Record Information
Version2.0
Creation Date2012-05-31 14:25:28 -0600
Update Date2015-06-03 17:19:14 -0600
Secondary Accession Numbers
  • ECMDB20062
Identification
Name:2',3'-Cyclic UMP
DescriptionUridine 2',3'-cyclic phosphate is a cyclic nucleotide. A cyclic nucleotide is any nucleotide in which the phosphate group is bonded to two of the sugar's hydroxyl groups, forming a cyclical or ring structure. Cyclic phosphates are commonly found at the 3' end of mRNAs and other small RNAs. Uridine 2',3'-cyclic phosphate is a substrate for the enzyme 2',3'-cyclic nucleotide-3'-phosphodiesterase (CNPase, EC 3.1.4.37) which hydrolyses it to Uridine 2'-phosphate. CNPase is a unique RNase in that it only cleaves nucleoside 2',3'-cyclic phosphates and not the RNA internucleotide linkage, like other RNases such as RNase A and RNase T1.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 1-(2,3-O-Phosphinico-a-D-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  • 1-(2,3-O-phosphinico-a-delta-Ribofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2,3-O-phosphinico-a-δ-Ribofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2,3-O-Phosphinico-alpha-delta-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  • 1-(2,3-O-phosphinico-α-δ-Ribofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 2',3'-cUMP
  • 2',3'-Cyclic UMP
  • Uridine 2',3'-cyclic monophosphate
  • Uridine 2',3'-cyclic monophosphoric acid
Chemical Formula:C9H11N2O8P
Weight:Average: 306.166
Monoisotopic: 306.02530185
InChI Key:HWDMHJDYMFRXOX-XVFCMESISA-N
InChI:InChI=1S/C9H11N2O8P/c12-3-4-6-7(19-20(15,16)18-6)8(17-4)11-2-1-5(13)10-9(11)14/h1-2,4,6-8,12H,3H2,(H,15,16)(H,10,13,14)/t4-,6-,7-,8-/m1/s1
CAS number:40632-52-8
IUPAC Name:1-[(3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxo-tetrahydro-2H-2λ⁵-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name:2',3'-cyclic ump
SMILES:OC[C@H]1O[C@H]([C@@H]2OP(O)(=O)O[C@H]12)N1C=CC(=O)NC1=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as 2',3'-cyclic pyrimidine nucleotides. These are pyrimidine nucleotides in which the oxygen atoms linked to the C2 and C3 carbon atoms of the ribose moiety are both bonded the same phosphorus atom of the phosphate group.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassCyclic pyrimidine nucleotides
Direct Parent2',3'-cyclic pyrimidine nucleotides
Alternative Parents
Substituents
  • 2',3'-cyclic pyrimidine ribonucleotide
  • Ribonucleoside 3'-phosphate
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Pyrimidine
  • 1,3_dioxaphospholane
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Vinylogous amide
  • Urea
  • Lactam
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Alcohol
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility20.8 g/LALOGPS
logP-1.3ALOGPS
logP-1.6ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)1.76ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area134.63 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity59.66 m³·mol⁻¹ChemAxon
Polarizability24.7 ųChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
2',3'-Cyclic UMP + Water > 3'-UMP + Hydrogen ion
2',3'-Cyclic UMP + Water <> 3'-UMP
SMPDB Pathways:
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine ribonucleosides degradtionPW002024 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-3930000000-eeef1c59101eac345740View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00di-4970000000-ba43e7e87e9b1da0ce7cView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1901000000-0d360d67bf767c95b2c9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-a9897f40443893ba5342View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-08fu-9400000000-239eade290faab347bc0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0bt9-5497000000-784d39c6cdcea534b626View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ox-9440000000-c6d0dde6755d0f4cdb28View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-0c839a884da572f801c3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0009000000-296e5af1cfc5c172dc29View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-3389000000-ed033e9972509ec4ffa0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-002f-7390000000-0be4168504ae9e2d5691View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-002b-0901000000-13423eb865c91fd69b03View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0bta-1905000000-eac4b0d63e2e24bf36d4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3950000000-bfe76f46f1ed6470e081View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID28637
HMDB IDHMDB0011640
Pubchem Compound ID193315
Kegg IDC02355
ChemSpider ID388781
Wikipedia IDNot Available
BioCyc IDCPD-3725
EcoCyc IDCPD-3725

Enzymes

Protein Details
1. 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase
General function:
Involved in hydrolase activity
Specific function:
This bifunctional enzyme catalyzes two consecutive reactions during ribonucleic acid degradation. Converts a 2',3'- cyclic nucleotide to a 3'-nucleotide and then the 3'-nucleotide to the corresponding nucleoside and phosphate
Gene Name:
cpdB
Uniprot ID:
P08331
Molecular weight:
70832
Reactions
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 3'-phosphate.
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.

Transporters

Protein Details
1. Outer membrane protein N
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
Protein Details
2. Outer membrane pore protein E
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
Protein Details
3. Outer membrane protein F
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
Protein Details
4. Outer membrane protein C
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368