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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:33:47 UTC
Update Date2021-09-14 15:44:29 UTC
HMDB IDHMDB0029956
Secondary Accession Numbers
  • HMDB29956
Metabolite Identification
Common NameNebularine
DescriptionNebularine, also known as N-D-ribosylpurine or 1FKW, belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety. Based on a literature review very few articles have been published on Nebularine.
Structure
Data?1563861915
Synonyms
ValueSource
1FKWHMDB
3-DeazaadenosineHMDB
9-(beta -D-Ribofuranosyl)purineHMDB
9-(beta-D-Ribofuranosyl)-9H-purineHMDB
9-(beta-D-Ribofuranosyl)purineHMDB
9-b-D-Ribofuranosyl-9H-purine, 9ci, 8ciHMDB
9-beta -RibofuranosylpurineHMDB
9-beta-D-Ribofuranosyl-9H-purineHMDB
9-beta-RibofuranosylpurineHMDB
9-Purine ribonucleosideHMDB
9beta-D-Ribofuranosyl-9H-purineHMDB
N-D-RibosylpurineHMDB
Nebularin (e)HMDB
Nebularin e)HMDB
Nebularin(e)HMDB
PURHMDB
Purine nucleosideHMDB
Purine ribonucleosideHMDB
Purine ribosideHMDB
Purine-1-D-ribofuranosideHMDB
Purine-9-beta-D-ribofuranosideHMDB
PurinosineHMDB
Ribosyl-isopurineHMDB
Ribosyl-purineHMDB
RibosylpurineHMDB
NebularineMeSH
Chemical FormulaC10H12N4O4
Average Molecular Weight252.2267
Monoisotopic Molecular Weight252.085854892
IUPAC Name2-(hydroxymethyl)-5-(9H-purin-9-yl)oxolane-3,4-diol
Traditional Namenebularine
CAS Registry Number550-33-4
SMILES
OCC1OC(C(O)C1O)N1C=NC2=C1N=CN=C2
InChI Identifier
InChI=1S/C10H12N4O4/c15-2-6-7(16)8(17)10(18-6)14-4-13-5-1-11-3-12-9(5)14/h1,3-4,6-8,10,15-17H,2H2
InChI KeyMRWXACSTFXYYMV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleosides
Sub ClassNot Available
Direct ParentPurine nucleosides
Alternative Parents
Substituents
  • Purine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Imidazopyrimidine
  • Purine
  • Monosaccharide
  • N-substituted imidazole
  • Pyrimidine
  • Heteroaromatic compound
  • Azole
  • Imidazole
  • Tetrahydrofuran
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Primary alcohol
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point182 - 183 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility100 mg/mLNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility16.8 g/LALOGPS
logP10(-0.99) g/LALOGPS
logP10(-1.9) g/LChemAxon
logS10(-1.2) g/LALOGPS
pKa (Strongest Acidic)12.45ChemAxon
pKa (Strongest Basic)2.05ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.52 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity58.18 m³·mol⁻¹ChemAxon
Polarizability23.46 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]+156.27931661259
DarkChem[M-H]-155.45831661259

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
NebularineOCC1OC(C(O)C1O)N1C=NC2=C1N=CN=C23259.7Standard polar33892256
NebularineOCC1OC(C(O)C1O)N1C=NC2=C1N=CN=C21944.0Standard non polar33892256
NebularineOCC1OC(C(O)C1O)N1C=NC2=C1N=CN=C22454.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Nebularine,1TMS,isomer #1C[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O)C1O2438.1Semi standard non polar33892256
Nebularine,1TMS,isomer #2C[Si](C)(C)OC1C(O)C(CO)OC1N1C=NC2=CN=CN=C212449.4Semi standard non polar33892256
Nebularine,1TMS,isomer #3C[Si](C)(C)OC1C(CO)OC(N2C=NC3=CN=CN=C32)C1O2461.3Semi standard non polar33892256
Nebularine,2TMS,isomer #1C[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O[Si](C)(C)C)C1O2394.3Semi standard non polar33892256
Nebularine,2TMS,isomer #2C[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O)C1O[Si](C)(C)C2413.3Semi standard non polar33892256
Nebularine,2TMS,isomer #3C[Si](C)(C)OC1C(CO)OC(N2C=NC3=CN=CN=C32)C1O[Si](C)(C)C2396.6Semi standard non polar33892256
Nebularine,3TMS,isomer #1C[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O[Si](C)(C)C)C1O[Si](C)(C)C2387.9Semi standard non polar33892256
Nebularine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O)C1O2663.7Semi standard non polar33892256
Nebularine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC1C(O)C(CO)OC1N1C=NC2=CN=CN=C212664.9Semi standard non polar33892256
Nebularine,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC1C(CO)OC(N2C=NC3=CN=CN=C32)C1O2674.2Semi standard non polar33892256
Nebularine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O[Si](C)(C)C(C)(C)C)C1O2831.8Semi standard non polar33892256
Nebularine,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O)C1O[Si](C)(C)C(C)(C)C2846.7Semi standard non polar33892256
Nebularine,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC1C(CO)OC(N2C=NC3=CN=CN=C32)C1O[Si](C)(C)C(C)(C)C2848.7Semi standard non polar33892256
Nebularine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C3006.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Nebularine GC-MS (Non-derivatized) - 70eV, Positivesplash10-05c6-9320000000-8568cb65887589a7c24c2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nebularine GC-MS (3 TMS) - 70eV, Positivesplash10-0umr-6549300000-2f2e367dec1b5b795a902017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nebularine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Nebularine LC-ESI-QTOF , positive-QTOFsplash10-0079-0900000000-56dbcaa78636ebb05d352017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nebularine LC-ESI-QTOF , positive-QTOFsplash10-0079-0900000000-88d4f77072df7340a9242017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nebularine LC-ESI-QTOF , positive-QTOFsplash10-00y0-0900000000-e3a077bcd64184c0deba2017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 10V, Positive-QTOFsplash10-00di-0940000000-558c13580fe37e7be7cc2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 20V, Positive-QTOFsplash10-00di-2900000000-15f6248a2b75854f25d72015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 40V, Positive-QTOFsplash10-00dl-9800000000-6bd857bf607d73c94c212015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 10V, Negative-QTOFsplash10-0uxr-0790000000-52cdec17cf806f6a8d602015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 20V, Negative-QTOFsplash10-014i-1900000000-28abc2355f386333f1142015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 40V, Negative-QTOFsplash10-00kf-9600000000-fb33005da35ddacd66d12015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 10V, Negative-QTOFsplash10-0ue9-1490000000-6dc9f80c37f021faecb52021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 20V, Negative-QTOFsplash10-014i-3900000000-b5dcc04009267c01b3432021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 40V, Negative-QTOFsplash10-014i-3900000000-f19c5dbdfad54ebaea772021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 10V, Positive-QTOFsplash10-00di-1920000000-fa2d03f63315e32001232021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 20V, Positive-QTOFsplash10-00di-1910000000-7e964acf962463d5cccc2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nebularine 40V, Positive-QTOFsplash10-00dl-4900000000-23f6f050c47dd1bef6732021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB001236
KNApSAcK IDC00018685
Chemspider ID217498
KEGG Compound IDC01736
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound248425
PDB IDNot Available
ChEBI ID139743
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1812481
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

General function:
Involved in deaminase activity
Specific function:
Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. Plays an important role in purine metabolism and in adenosine homeostasis. Modulates signaling by extracellular adenosine, and so contributes indirectly to cellular signaling events. Acts as a positive regulator of T-cell coactivation, by binding DPP4. Its interaction with DPP4 regulates lymphocyte-epithelial cell adhesion.
Gene Name:
ADA
Uniprot ID:
P00813
Molecular weight:
40764.13
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.
Gene Name:
PNP
Uniprot ID:
P00491
Molecular weight:
32117.69
Reactions
Nebularine + Phosphate → Purine + Ribose 1-phosphatedetails