Showing metabocard for Thymidine 3',5'-cyclic monophosphate (BMDB0001570)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 22:47:49 UTC
Update Date2020-04-22 15:08:45 UTC
BMDB IDBMDB0001570
Secondary Accession Numbers
  • BMDB01570
Metabolite Identification
Common NameThymidine 3',5'-cyclic monophosphate
DescriptionThymidine 3',5'-cyclic monophosphate, also known as 3',5'-cyclic TMP or 3',5'-cyclic thymidine monophosphate, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Thymidine 3',5'-cyclic monophosphate is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
Thymidine 3',5'-cyclic monophosphoric acidGenerator
3',5'-Cyclic thymidine monophosphateHMDB
3',5'-Cyclic TMPHMDB
4H-Furo[3,2-D]-1,3,2-dioxaphosphorin thymidine deriv.HMDB
CTMPHMDB
Cyclic 3',5'-dTMPHMDB
Cyclic 3',5'-thymidylateHMDB
Cyclic 3',5'-thymidylic acidHMDB
Cyclic TMPHMDB
Thymidine 3,5-cyclic monophosphate sodium saltHMDB
Thymidine cyclic 3',5'-phosphateHMDB
Thymidine cyclophosphateHMDB
Thymidine phosphate (cyclic)HMDB
3',5'-Cyclic dTMPHMDB
Cyclic 3',5'-thymidine monophosphateHMDB
Chemical FormulaC10H13N2O7P
Average Molecular Weight304.1932
Monoisotopic Molecular Weight304.046037292
IUPAC Name1-[(6R)-2-hydroxy-2-oxo-hexahydro-2lambda5-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name1-[(6R)-2-hydroxy-2-oxo-tetrahydro-4H-2lambda5-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-5-methyl-3H-pyrimidine-2,4-dione
CAS Registry Number6453-60-7
SMILES
CC1=CN([C@H]2CC3OP(O)(=O)OCC3O2)C(=O)NC1=O
InChI Identifier
InChI=1S/C10H13N2O7P/c1-5-3-12(10(14)11-9(5)13)8-2-6-7(18-8)4-17-20(15,16)19-6/h3,6-8H,2,4H2,1H3,(H,15,16)(H,11,13,14)/t6?,7?,8-/m1/s1
InChI KeyQSJFDOVQWZVUQG-KAVNDROISA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Vinylogous amide
  • Lactam
  • Urea
  • Oxacycle
  • Azacycle
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.91ALOGPS
logP-0.35ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-4.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area114.4 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity62.51 m³·mol⁻¹ChemAxon
Polarizability25.51 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004r-3920000000-fa087eafaf28aa10e71dView 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, Positivesplash10-004i-0900000000-f2776d29a1a3861169b0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-5900000000-1fe99e1c7b6b1795e591View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-055b-9500000000-6ffff7f8cd1316dc5fdaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-3259000000-9beab42162941871abf9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9241000000-c19bc3f132001e531528View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-421497715d00a39ac466View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0009000000-3d6273a0f39a6bebcfcdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufr-5279000000-02bec4525b2cfc8dd947View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-002f-9460000000-cb76093e416c58997e8aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0009000000-286c2eb7e88f7c24dde3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-0229000000-a97de09fdefe30a245bbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-4920000000-696c0224910c7b1cfb9cView in MoNA
1D NMR1H NMR Spectrum (1D, 600 MHz, 100%_DMSO, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, 100%_DMSO, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001570
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022695
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC00364
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53477735
PDB IDNot Available
ChEBI ID17013
References
Synthesis ReferenceKhorana, H. G.; Vizsolyi, J. P. Studies on polynucleotides. VIII. Experiments on the polymerization of mononucleotides. Improved preparation and separation of linear thymidine polynucleotides. Synthesis of corresponding members terminated in deoxycytidine residues. Journal of the American Chemical Society (1961), 83 675-85.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available