MiMeDB: Showing metabocard for 2-deoxy-D-ribose (MMDBc0033084)

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:34:05 UTC

Update Date

2024-10-17 18:13:57 UTC

Metabolite ID

MMDBc0033084

Metabolite Identification

Common Name

2-deoxy-D-ribose

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 SDF PDB SMILES InChI

Synonyms

Not Available

Molecular Formula

C₅H₁₀O₄

Average Mass

134.1305

Monoisotopic Mass

134.057908808

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

533-67-5

SMILES

Not Available

InChI Identifier

InChI=1S/C5H10O4/c6-2-1-4(8)5(9)3-7/h2,4-5,7-9H,1,3H2/t4-,5+/m0/s1

InChI Key

ASJSAQIRZKANQN-CRCLSJGQSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Not Available

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	327.9
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	264.5
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	39.9
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	244.0
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	272.3
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	305.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	601.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	496.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	689.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	168.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	306.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	184.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	50.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	301.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	601.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	53.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	225.0
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	775.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	568.9

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	2-deoxy-D-ribose_TMS_1	C[Si](C)(C)O[C@@H](CC=O)[C@H](O)CO	standard non polar	2025-10-24	2107.15
Gas Chromatography	2-deoxy-D-ribose_TMS_2	C[Si](C)(C)O[C@H](CO)[C@@H](O)CC=O	standard non polar	2025-10-24	1936.63
Gas Chromatography	2-deoxy-D-ribose_TMS_3	C[Si](C)(C)OC[C@@H](O)[C@@H](O)CC=O	standard non polar	2025-10-24	1966.05
Gas Chromatography	2-deoxy-D-ribose_TMS_4	C[Si](C)(C)OC=C[C@H](O)[C@H](O)CO	standard non polar	2025-10-24	1772.7
Gas Chromatography	2-deoxy-D-ribose_TMS_5	C[Si](C)(C)O[C@@H](CC=O)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	2039.66
Gas Chromatography	2-deoxy-D-ribose_TMS_6	C[Si](C)(C)OC[C@@H](O)[C@H](CC=O)O[Si](C)(C)C	standard non polar	2025-10-24	1969.16
Gas Chromatography	2-deoxy-D-ribose_TMS_7	C[Si](C)(C)OC=C[C@H](O[Si](C)(C)C)[C@H](O)CO	standard non polar	2025-10-24	1622.81
Gas Chromatography	2-deoxy-D-ribose_TMS_8	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)CC=O	standard non polar	2025-10-24	2371.69
Gas Chromatography	2-deoxy-D-ribose_TMS_9	C[Si](C)(C)OC=C[C@H](O)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	2013.47
Gas Chromatography	2-deoxy-D-ribose_TMS_10	C[Si](C)(C)OC=C[C@H](O)[C@H](O)CO[Si](C)(C)C	standard non polar	2025-10-24	2109.25
Gas Chromatography	2-deoxy-D-ribose_TMS_11	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](CC=O)O[Si](C)(C)C	standard non polar	2025-10-24	2432.66
Gas Chromatography	2-deoxy-D-ribose_TMS_12	C[Si](C)(C)OC=C[C@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	1983.06
Gas Chromatography	2-deoxy-D-ribose_TMS_13	C[Si](C)(C)OC=C[C@H](O[Si](C)(C)C)[C@H](O)CO[Si](C)(C)C	standard non polar	2025-10-24	2465.2
Gas Chromatography	2-deoxy-D-ribose_TMS_14	C[Si](C)(C)OC=C[C@H](O)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1544.76
Gas Chromatography	2-deoxy-D-ribose_TMS_15	C[Si](C)(C)OC=C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2030.45
Gas Chromatography	2-deoxy-D-ribose_TMS_1	C[Si](C)(C)O[C@@H](CC=O)[C@H](O)CO	standard polar	2025-10-24	2232.74
Gas Chromatography	2-deoxy-D-ribose_TMS_2	C[Si](C)(C)O[C@H](CO)[C@@H](O)CC=O	standard polar	2025-10-24	2061.7
Gas Chromatography	2-deoxy-D-ribose_TMS_3	C[Si](C)(C)OC[C@@H](O)[C@@H](O)CC=O	standard polar	2025-10-24	2406.21
Gas Chromatography	2-deoxy-D-ribose_TMS_4	C[Si](C)(C)OC=C[C@H](O)[C@H](O)CO	standard polar	2025-10-24	1919.19
Gas Chromatography	2-deoxy-D-ribose_TMS_5	C[Si](C)(C)O[C@@H](CC=O)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	2312.95
Gas Chromatography	2-deoxy-D-ribose_TMS_6	C[Si](C)(C)OC[C@@H](O)[C@H](CC=O)O[Si](C)(C)C	standard polar	2025-10-24	2376.59
Gas Chromatography	2-deoxy-D-ribose_TMS_7	C[Si](C)(C)OC=C[C@H](O[Si](C)(C)C)[C@H](O)CO	standard polar	2025-10-24	1722.42
Gas Chromatography	2-deoxy-D-ribose_TMS_8	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)CC=O	standard polar	2025-10-24	1646.69
Gas Chromatography	2-deoxy-D-ribose_TMS_9	C[Si](C)(C)OC=C[C@H](O)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	2030.35
Gas Chromatography	2-deoxy-D-ribose_TMS_10	C[Si](C)(C)OC=C[C@H](O)[C@H](O)CO[Si](C)(C)C	standard polar	2025-10-24	2315.02
Gas Chromatography	2-deoxy-D-ribose_TMS_11	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](CC=O)O[Si](C)(C)C	standard polar	2025-10-24	2294.71
Gas Chromatography	2-deoxy-D-ribose_TMS_12	C[Si](C)(C)OC=C[C@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	1443.48
Gas Chromatography	2-deoxy-D-ribose_TMS_13	C[Si](C)(C)OC=C[C@H](O[Si](C)(C)C)[C@H](O)CO[Si](C)(C)C	standard polar	2025-10-24	1896.16
Gas Chromatography	2-deoxy-D-ribose_TMS_14	C[Si](C)(C)OC=C[C@H](O)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1828.54
Gas Chromatography	2-deoxy-D-ribose_TMS_15	C[Si](C)(C)OC=C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2209.02

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Fibroblasts

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Fibroblasts	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

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. doi: 10.1002/bms.1200061010. [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. doi: 10.1016/0167-4838(92)90052-f. [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. doi: 10.1007/BF01800736. [PubMed:6422138 ]
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. doi: 10.1016/0304-4165(93)90129-v. [PubMed:8427873 ]
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. doi: 10.1016/s0006-2952(02)01391-6. [PubMed:12429355 ]
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. doi: 10.1002/jcp.20662. [PubMed:16646085 ]

Showing metabocard for 2-deoxy-D-ribose (MMDBc0033084)

MOL for #<Metabolite:0x00007f9ab53af550>

3D MOL for #<Metabolite:0x00007f9ab53af550>

3D SDF for #<Metabolite:0x00007f9ab53af550>

3D-SDF for #<Metabolite:0x00007f9ab53af550>

PDB for #<Metabolite:0x00007f9ab53af550>

3D PDB for #<Metabolite:0x00007f9ab53af550>

SMILES for #<Metabolite:0x00007f9ab53af550>

INCHI for #<Metabolite:0x00007f9ab53af550>

Structure for #<Metabolite:0x00007f9ab53af550>

3D Structure for #<Metabolite:0x00007f9ab53af550>