Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-05-22 15:12:42 UTC
Update Date2023-02-21 17:16:34 UTC
HMDB IDHMDB0003224
Secondary Accession Numbers
  • HMDB03224
Metabolite Identification
Common NameDeoxyribose
DescriptionDeoxyribose is an aldopentose, a monosaccharide containing five carbon atoms, and including an aldehyde functional group. It is derived from the pentose sugar ribose by the replacement of the hydroxyl group at the 2 position with hydrogen, leading to the net loss of an oxygen atom, and has chemical formula C5H10O4. In deoxyribose, the carbon furthest from the attached carbon is stripped of the oxygen atom in what would be a hydroxyl group in ribose. The common base adenine (a purine derivative) coupled to deoxyribose is called deoxyadenosine. The 5-triphosphate derivative of adenosine, commonly called adenosine triphosphate (ATP) is an important energy transport molecule in cells. -- Wikipedia .
Structure
Data?1676999794
Synonyms
ValueSource
2'-Deoxy-D-riboseHMDB
Chemical FormulaC5H10O4
Average Molecular Weight134.1305
Monoisotopic Molecular Weight134.057908808
IUPAC Name(2S,4R,5S)-5-(hydroxymethyl)oxolane-2,4-diol
Traditional Name2-deoxyribose
CAS Registry Number533-67-5
SMILES
OC[C@@H]1O[C@H](O)C[C@H]1O
InChI Identifier
InChI=1S/C5H10O4/c6-2-4-3(7)1-5(8)9-4/h3-8H,1-2H2/t3-,4+,5+/m1/s1
InChI KeyPDWIQYODPROSQH-WISUUJSJSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point91 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1050 g/LALOGPS
logP-2.1ALOGPS
logP-1.4ChemAxon
logS0.89ALOGPS
pKa (Strongest Acidic)12.36ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.92 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity28.45 m³·mol⁻¹ChemAxon
Polarizability12.67 ųChemAxon
Number of Rings1ChemAxon
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]+128.30531661259
DarkChem[M-H]-126.89831661259
DeepCCS[M+H]+131.79130932474
DeepCCS[M-H]-129.50130932474
DeepCCS[M-2H]-164.66830932474
DeepCCS[M+Na]+139.03130932474
AllCCS[M+H]+130.432859911
AllCCS[M+H-H2O]+125.732859911
AllCCS[M+NH4]+134.732859911
AllCCS[M+Na]+135.932859911
AllCCS[M-H]-123.432859911
AllCCS[M+Na-2H]-125.532859911
AllCCS[M+HCOO]-127.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
DeoxyriboseOC[C@@H]1O[C@H](O)C[C@H]1O2534.0Standard polar33892256
DeoxyriboseOC[C@@H]1O[C@H](O)C[C@H]1O1314.1Standard non polar33892256
DeoxyriboseOC[C@@H]1O[C@H](O)C[C@H]1O1272.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Deoxyribose,1TMS,isomer #1C[Si](C)(C)OC[C@@H]1O[C@H](O)C[C@H]1O1353.5Semi standard non polar33892256
Deoxyribose,1TMS,isomer #2C[Si](C)(C)O[C@@H]1C[C@@H](O)[C@H](CO)O11386.0Semi standard non polar33892256
Deoxyribose,1TMS,isomer #3C[Si](C)(C)O[C@@H]1C[C@@H](O)O[C@H]1CO1366.4Semi standard non polar33892256
Deoxyribose,2TMS,isomer #1C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)C[C@H]1O1465.4Semi standard non polar33892256
Deoxyribose,2TMS,isomer #2C[Si](C)(C)OC[C@@H]1O[C@H](O)C[C@H]1O[Si](C)(C)C1446.2Semi standard non polar33892256
Deoxyribose,2TMS,isomer #3C[Si](C)(C)O[C@@H]1C[C@@H](O[Si](C)(C)C)[C@H](CO)O11443.9Semi standard non polar33892256
Deoxyribose,3TMS,isomer #1C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)C[C@H]1O[Si](C)(C)C1513.0Semi standard non polar33892256
Deoxyribose,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](O)C[C@H]1O1580.0Semi standard non polar33892256
Deoxyribose,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@@H]1C[C@@H](O)[C@H](CO)O11588.2Semi standard non polar33892256
Deoxyribose,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@@H]1C[C@@H](O)O[C@H]1CO1590.6Semi standard non polar33892256
Deoxyribose,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C(C)(C)C)C[C@H]1O1885.0Semi standard non polar33892256
Deoxyribose,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](O)C[C@H]1O[Si](C)(C)C(C)(C)C1883.2Semi standard non polar33892256
Deoxyribose,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@@H]1C[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO)O11879.9Semi standard non polar33892256
Deoxyribose,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C(C)(C)C)C[C@H]1O[Si](C)(C)C(C)(C)C2168.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyribose GC-MS (Non-derivatized) - 70eV, Positivesplash10-052f-9100000000-8265d06b93bc980794aa2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyribose GC-MS (3 TMS) - 70eV, Positivesplash10-0f79-7492000000-9d5168c6f14abe682d002017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyribose GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyribose 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 - Deoxyribose 10V, Positive-QTOFsplash10-00kr-1900000000-90110d36692d2fa020342015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 20V, Positive-QTOFsplash10-014r-5900000000-a2fc5c56decd9a9dd2702015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 40V, Positive-QTOFsplash10-059b-9000000000-af78f6c0618e210b17192015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 10V, Negative-QTOFsplash10-001i-2900000000-3fa7ba0b3105a40897042015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 20V, Negative-QTOFsplash10-067r-9500000000-3672c628038bf5b3bdc52015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 40V, Negative-QTOFsplash10-052f-9000000000-a63ae9417695ec37c8ac2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 10V, Positive-QTOFsplash10-00ks-9600000000-a7f9409171edeff8fcf42021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 20V, Positive-QTOFsplash10-0005-9000000000-9bb8c9028eb6251265252021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 40V, Positive-QTOFsplash10-0005-9000000000-2e5c391ffb81e872ef7b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 10V, Negative-QTOFsplash10-001i-4900000000-ff4899ff4892b60c2b7c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 20V, Negative-QTOFsplash10-0k9l-9400000000-7af33b132f52656b3dd32021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyribose 40V, Negative-QTOFsplash10-052f-9000000000-85ba102746204240f82f2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Feces
Tissue Locations
  • Fibroblasts
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023126
KNApSAcK IDC00001115
Chemspider ID17216222
KEGG Compound IDC01801
BioCyc IDCPD-7298
BiGG ID38440
Wikipedia LinkDeoxyribose
METLIN ID3258
PubChem Compound22833604
PDB IDNot Available
ChEBI ID28816
Food Biomarker OntologyNot Available
VMH IDDRIB
MarkerDB IDNot Available
Good Scents IDrw1175031
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Formichi P, Radi E, Battisti C, Tarquini E, Leonini A, Di Stefano A, Federico A: Human fibroblasts undergo oxidative stress-induced apoptosis without internucleosomal DNA fragmentation. J Cell Physiol. 2006 Aug;208(2):289-97. [PubMed:16646085 ]
  2. Lapenna D, Ciofani G, Festi D, Neri M, Pierdomenico SD, Giamberardino MA, Cuccurullo F: Antioxidant properties of ursodeoxycholic acid. Biochem Pharmacol. 2002 Dec 1;64(11):1661-7. [PubMed:12429355 ]
  3. Gutteridge JM, Quinlan GJ: Antioxidant protection against organic and inorganic oxygen radicals by normal human plasma: the important primary role for iron-binding and iron-oxidising proteins. Biochim Biophys Acta. 1993 Feb 13;1156(2):144-50. [PubMed:8427873 ]
  4. Truscott RJ, Halpern B, Hammond J, Hunt S, Cotton RG, Haan EA, Danks DM: Abnormal deoxyribose metabolites in the urine of a child with a possible new inborn error of metabolism. Biomed Mass Spectrom. 1979 Oct;6(10):453-9. [PubMed:526564 ]
  5. Gutteridge JM, Quinlan GJ: Antioxidant protection against organic and inorganic oxygen radicals by normal human plasma: the important primary role for iron-binding and iron-oxidising proteins. Biochim Biophys Acta. 1992 Oct 20;1159(3):248-54. [PubMed:1327159 ]
  6. Chappel A, Scholem RD, Brown GK, Truscott RM, Cotton RG, Haan EA, Danks DM: Deoxyribose-5-phosphate aldolase deficiency--a harmless inborn error of metabolism. J Inherit Metab Dis. 1983;6(3):105-7. [PubMed:6422138 ]

Enzymes

General function:
Involved in ribokinase activity
Specific function:
Not Available
Gene Name:
RBKS
Uniprot ID:
Q9H477
Molecular weight:
34142.685
Reactions
Deoxyribose 5-monophosphate + ADP → Deoxyribose + Adenosine triphosphatedetails