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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-01-30 15:50:18 UTC
Update Date2021-09-14 15:44:40 UTC
HMDB IDHMDB0011640
Secondary Accession Numbers
  • HMDB11640
Metabolite Identification
Common NameUridine 2',3'-cyclic phosphate
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
Data?1582752932
Synonyms
ValueSource
CUMPChEBI
Uridine 2',3'-cyclophosphateChEBI
Uridine, cyclic 2',3'-(hydrogen phosphate)ChEBI
Uridine 2',3'-cyclophosphoric acidGenerator
Uridine, cyclic 2',3'-(hydrogen phosphoric acid)Generator
Uridine 2',3'-cyclic phosphoric acidGenerator
1-(2,3-O-Phosphinico-a-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2,3-O-Phosphinico-alpha-delta-ribofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
2',3'-CUMPHMDB
Uridine 2',3'-cyclic monophosphateHMDB
Uridine 2',3'-cyclophosphate, monosodium saltMeSH
Chemical FormulaC9H11N2O8P
Average Molecular Weight306.166
Monoisotopic Molecular Weight306.02530185
IUPAC Name1-[(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 Name2',3'-cyclic ump
CAS Registry Number40632-52-8
SMILES
OC[C@H]1O[C@H]([C@@H]2OP(O)(=O)O[C@H]12)N1C=CC(=O)NC1=O
InChI Identifier
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
InChI KeyHWDMHJDYMFRXOX-XVFCMESISA-N
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
Ontology
Disposition

Biological location

Source

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular 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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+170.6331661259
DarkChem[M-H]-160.15231661259
DeepCCS[M-2H]-198.38730932474
DeepCCS[M+Na]+173.61630932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Uridine 2',3'-cyclic phosphateOC[C@H]1O[C@H]([C@@H]2OP(O)(=O)O[C@H]12)N1C=CC(=O)NC1=O3414.1Standard polar33892256
Uridine 2',3'-cyclic phosphateOC[C@H]1O[C@H]([C@@H]2OP(O)(=O)O[C@H]12)N1C=CC(=O)NC1=O2432.9Standard non polar33892256
Uridine 2',3'-cyclic phosphateOC[C@H]1O[C@H]([C@@H]2OP(O)(=O)O[C@H]12)N1C=CC(=O)NC1=O3015.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Uridine 2',3'-cyclic phosphate,1TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)[C@@H]2OP(=O)(O)O[C@H]122708.6Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,1TMS,isomer #2C[Si](C)(C)OP1(=O)O[C@@H]2[C@@H](CO)O[C@@H](N3C=CC(=O)[NH]C3=O)[C@@H]2O12713.9Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,1TMS,isomer #3C[Si](C)(C)N1C(=O)C=CN([C@@H]2O[C@H](CO)[C@H]3OP(=O)(O)O[C@H]32)C1=O2779.4Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@H]122727.0Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@H]122710.8Standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@H]123428.7Standard polar33892256
Uridine 2',3'-cyclic phosphate,2TMS,isomer #2C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)[C@@H]2OP(=O)(O)O[C@H]122780.0Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TMS,isomer #2C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)[C@@H]2OP(=O)(O)O[C@H]122727.4Standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TMS,isomer #2C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)[C@@H]2OP(=O)(O)O[C@H]123705.9Standard polar33892256
Uridine 2',3'-cyclic phosphate,2TMS,isomer #3C[Si](C)(C)OP1(=O)O[C@@H]2[C@@H](CO)O[C@@H](N3C=CC(=O)N([Si](C)(C)C)C3=O)[C@@H]2O12785.3Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TMS,isomer #3C[Si](C)(C)OP1(=O)O[C@@H]2[C@@H](CO)O[C@@H](N3C=CC(=O)N([Si](C)(C)C)C3=O)[C@@H]2O12735.4Standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TMS,isomer #3C[Si](C)(C)OP1(=O)O[C@@H]2[C@@H](CO)O[C@@H](N3C=CC(=O)N([Si](C)(C)C)C3=O)[C@@H]2O13436.9Standard polar33892256
Uridine 2',3'-cyclic phosphate,3TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@H]122798.0Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,3TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@H]122788.3Standard non polar33892256
Uridine 2',3'-cyclic phosphate,3TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@H]123162.1Standard polar33892256
Uridine 2',3'-cyclic phosphate,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)[C@@H]2OP(=O)(O)O[C@H]122928.0Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OP1(=O)O[C@@H]2[C@@H](CO)O[C@@H](N3C=CC(=O)[NH]C3=O)[C@@H]2O12939.9Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)N1C(=O)C=CN([C@@H]2O[C@H](CO)[C@H]3OP(=O)(O)O[C@H]32)C1=O2985.0Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C(C)(C)C)O[C@H]123134.8Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C(C)(C)C)O[C@H]123139.1Standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C(C)(C)C)O[C@H]123622.4Standard polar33892256
Uridine 2',3'-cyclic phosphate,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@@H]2OP(=O)(O)O[C@H]123199.7Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@@H]2OP(=O)(O)O[C@H]123169.6Standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@@H]2OP(=O)(O)O[C@H]123730.5Standard polar33892256
Uridine 2',3'-cyclic phosphate,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OP1(=O)O[C@@H]2[C@@H](CO)O[C@@H](N3C=CC(=O)N([Si](C)(C)C(C)(C)C)C3=O)[C@@H]2O13214.1Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OP1(=O)O[C@@H]2[C@@H](CO)O[C@@H](N3C=CC(=O)N([Si](C)(C)C(C)(C)C)C3=O)[C@@H]2O13144.8Standard non polar33892256
Uridine 2',3'-cyclic phosphate,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OP1(=O)O[C@@H]2[C@@H](CO)O[C@@H](N3C=CC(=O)N([Si](C)(C)C(C)(C)C)C3=O)[C@@H]2O13544.1Standard polar33892256
Uridine 2',3'-cyclic phosphate,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C(C)(C)C)O[C@H]123410.9Semi standard non polar33892256
Uridine 2',3'-cyclic phosphate,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C(C)(C)C)O[C@H]123378.5Standard non polar33892256
Uridine 2',3'-cyclic phosphate,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@@H]2OP(=O)(O[Si](C)(C)C(C)(C)C)O[C@H]123402.7Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Uridine 2',3'-cyclic phosphate GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-3930000000-eeef1c59101eac3457402017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Uridine 2',3'-cyclic phosphate GC-MS (1 TMS) - 70eV, Positivesplash10-00di-4970000000-ba43e7e87e9b1da0ce7c2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Uridine 2',3'-cyclic phosphate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 10V, Positive-QTOFsplash10-03di-1901000000-0d360d67bf767c95b2c92015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 20V, Positive-QTOFsplash10-03di-5900000000-a9897f40443893ba53422015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 40V, Positive-QTOFsplash10-08fu-9400000000-239eade290faab347bc02015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 10V, Negative-QTOFsplash10-0bt9-5497000000-784d39c6cdcea534b6262015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 20V, Negative-QTOFsplash10-01ox-9440000000-c6d0dde6755d0f4cdb282015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 40V, Negative-QTOFsplash10-0006-9100000000-0c839a884da572f801c32015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 10V, Negative-QTOFsplash10-0a4i-0009000000-296e5af1cfc5c172dc292021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 20V, Negative-QTOFsplash10-0a4i-3389000000-ed033e9972509ec4ffa02021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 40V, Negative-QTOFsplash10-002f-7390000000-0be4168504ae9e2d56912021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 10V, Positive-QTOFsplash10-002b-0901000000-13423eb865c91fd69b032021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 20V, Positive-QTOFsplash10-0bta-1905000000-eac4b0d63e2e24bf36d42021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Uridine 2',3'-cyclic phosphate 40V, Positive-QTOFsplash10-03di-3950000000-bfe76f46f1ed6470e0812021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028337
KNApSAcK IDNot Available
Chemspider ID388781
KEGG Compound IDC02355
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439715
PDB IDNot Available
ChEBI ID28637
Food Biomarker OntologyNot Available
VMH ID23CUMP
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]

Enzymes

General function:
Involved in 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
Specific function:
May participate in RNA metabolism in the myelinating cell, CNP is the third most abundant protein in central nervous system myelin (By similarity).
Gene Name:
CNP
Uniprot ID:
P09543
Molecular weight:
47578.22