You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.

Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

enzymes (1) Show 1 protein

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2006-05-22 15:12:42 UTC

Update Date

2023-02-21 17:16:34 UTC

HMDB ID

HMDB0003224

Secondary Accession Numbers

HMDB03224

Metabolite Identification

Common Name

Deoxyribose

Description

Deoxyribose 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2'-Deoxy-D-ribose	HMDB

Chemical Formula

C₅H₁₀O₄

Average Molecular Weight

134.1305

Monoisotopic Molecular Weight

134.057908808

IUPAC Name

(2S,4R,5S)-5-(hydroxymethyl)oxolane-2,4-diol

Traditional Name

2-deoxyribose

CAS Registry Number

533-67-5

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 Key

PDWIQYODPROSQH-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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Tetrahydrofuran
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0003224)

Excreta

Biofluid or Excreta

Feces (HMDB: HMDB0003224)

Cell

Fibroblast

Fibroblast (HMDB: HMDB0003224)

Fibroblasts (HMDB: HMDB0003224)

Source

Endogenous

Endogenous (HMDB: HMDB0003224)

Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)
Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)

Equine

Horse (FooDB: FOOD00378)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	91 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	1000000 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1050 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-1.4	ChemAxon
logS	0.89	ALOGPS
pKa (Strongest Acidic)	12.36	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.92 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	28.45 m³·mol⁻¹	ChemAxon
Polarizability	12.67 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	128.305	31661259
DarkChem	[M-H]-	126.898	31661259
DeepCCS	[M+H]+	131.791	30932474
DeepCCS	[M-H]-	129.501	30932474
DeepCCS	[M-2H]-	164.668	30932474
DeepCCS	[M+Na]+	139.031	30932474
AllCCS	[M+H]+	130.4	32859911
AllCCS	[M+H-H2O]+	125.7	32859911
AllCCS	[M+NH4]+	134.7	32859911
AllCCS	[M+Na]+	135.9	32859911
AllCCS	[M-H]-	123.4	32859911
AllCCS	[M+Na-2H]-	125.5	32859911
AllCCS	[M+HCOO]-	127.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Deoxyribose	OC[C@@H]1O[C@H](O)C[C@H]1O	2534.0	Standard polar	33892256
Deoxyribose	OC[C@@H]1O[C@H](O)C[C@H]1O	1314.1	Standard non polar	33892256
Deoxyribose	OC[C@@H]1O[C@H](O)C[C@H]1O	1272.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Deoxyribose,1TMS,isomer #1	C[Si](C)(C)OC[C@@H]1O[C@H](O)C[C@H]1O	1353.5	Semi standard non polar	33892256
Deoxyribose,1TMS,isomer #2	C[Si](C)(C)O[C@@H]1C[C@@H](O)[C@H](CO)O1	1386.0	Semi standard non polar	33892256
Deoxyribose,1TMS,isomer #3	C[Si](C)(C)O[C@@H]1C[C@@H](O)O[C@H]1CO	1366.4	Semi standard non polar	33892256
Deoxyribose,2TMS,isomer #1	C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)C[C@H]1O	1465.4	Semi standard non polar	33892256
Deoxyribose,2TMS,isomer #2	C[Si](C)(C)OC[C@@H]1O[C@H](O)C[C@H]1O[Si](C)(C)C	1446.2	Semi standard non polar	33892256
Deoxyribose,2TMS,isomer #3	C[Si](C)(C)O[C@@H]1C[C@@H](O[Si](C)(C)C)[C@H](CO)O1	1443.9	Semi standard non polar	33892256
Deoxyribose,3TMS,isomer #1	C[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C)C[C@H]1O[Si](C)(C)C	1513.0	Semi standard non polar	33892256
Deoxyribose,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](O)C[C@H]1O	1580.0	Semi standard non polar	33892256
Deoxyribose,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1C[C@@H](O)[C@H](CO)O1	1588.2	Semi standard non polar	33892256
Deoxyribose,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1C[C@@H](O)O[C@H]1CO	1590.6	Semi standard non polar	33892256
Deoxyribose,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](O[Si](C)(C)C(C)(C)C)C[C@H]1O	1885.0	Semi standard non polar	33892256
Deoxyribose,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](O)C[C@H]1O[Si](C)(C)C(C)(C)C	1883.2	Semi standard non polar	33892256
Deoxyribose,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1C[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO)O1	1879.9	Semi standard non polar	33892256
Deoxyribose,3TBDMS,isomer #1	CC(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)C	2168.9	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Deoxyribose GC-MS (Non-derivatized) - 70eV, Positive	splash10-052f-9100000000-8265d06b93bc980794aa	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Deoxyribose GC-MS (3 TMS) - 70eV, Positive	splash10-0f79-7492000000-9d5168c6f14abe682d00	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Deoxyribose GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Deoxyribose GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 10V, Positive-QTOF	splash10-00kr-1900000000-90110d36692d2fa02034	2015-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 20V, Positive-QTOF	splash10-014r-5900000000-a2fc5c56decd9a9dd270	2015-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 40V, Positive-QTOF	splash10-059b-9000000000-af78f6c0618e210b1719	2015-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 10V, Negative-QTOF	splash10-001i-2900000000-3fa7ba0b3105a4089704	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 20V, Negative-QTOF	splash10-067r-9500000000-3672c628038bf5b3bdc5	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 40V, Negative-QTOF	splash10-052f-9000000000-a63ae9417695ec37c8ac	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 10V, Positive-QTOF	splash10-00ks-9600000000-a7f9409171edeff8fcf4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 20V, Positive-QTOF	splash10-0005-9000000000-9bb8c9028eb625126525	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 40V, Positive-QTOF	splash10-0005-9000000000-2e5c391ffb81e872ef7b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 10V, Negative-QTOF	splash10-001i-4900000000-ff4899ff4892b60c2b7c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 20V, Negative-QTOF	splash10-0k9l-9400000000-7af33b132f52656b3dd3	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 40V, Negative-QTOF	splash10-052f-9000000000-85ba102746204240f82f	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Feces

Tissue Locations

Fibroblasts

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	details

Associated Disorders and Diseases

Disease References

Colorectal cancer
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

114500 (Colorectal cancer)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

28816

Food Biomarker Ontology

Not Available

VMH ID

DRIB

MarkerDB ID

Not Available

Good Scents ID

rw1175031

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

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 ]
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 ]
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 ]
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 ]
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 ]
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

Enzyme Details

1. Ribokinase

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 triphosphate	details

Showing metabocard for Deoxyribose (HMDB0003224)

MOL for HMDB0003224 (Deoxyribose)

3D MOL for HMDB0003224 (Deoxyribose)

3D SDF for HMDB0003224 (Deoxyribose)

3D-SDF for HMDB0003224 (Deoxyribose)

PDB for HMDB0003224 (Deoxyribose)

3D PDB for HMDB0003224 (Deoxyribose)

SMILES for HMDB0003224 (Deoxyribose)

INCHI for HMDB0003224 (Deoxyribose)

Structure for HMDB0003224 (Deoxyribose)

3D Structure for HMDB0003224 (Deoxyribose)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

Reactions