MiMeDB: Showing metabocard for Deoxyribose (MMDBc0000422)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:37:24 UTC

Update Date

2022-08-31 06:06:51 UTC

Metabolite ID

MMDBc0000422

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

Synonyms

Value	Source
2'-Deoxy-D-ribose	HMDB

Molecular Formula

C₅H₁₀O₄

Average Mass

134.1305

Monoisotopic Mass

134.057908808

IUPAC Name

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

Traditional Name

2-deoxyribose

CAS Registry Number

Not Available

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

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-052f-9100000000-8265d06b93bc980794aa	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0f79-7492000000-9d5168c6f14abe682d00	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kr-1900000000-90110d36692d2fa02034	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014r-5900000000-a2fc5c56decd9a9dd270	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-059b-9000000000-af78f6c0618e210b1719	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-2900000000-3fa7ba0b3105a4089704	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-067r-9500000000-3672c628038bf5b3bdc5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9000000000-a63ae9417695ec37c8ac	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00ks-9600000000-a7f9409171edeff8fcf4	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0005-9000000000-9bb8c9028eb625126525	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0005-9000000000-2e5c391ffb81e872ef7b	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-4900000000-ff4899ff4892b60c2b7c	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0k9l-9400000000-7af33b132f52656b3dd3	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9000000000-85ba102746204240f82f	2021-09-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Feces
Fibroblasts

Tissue Locations

Fibroblasts

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192694	Ribokinase	Enzyme	Q9H477	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0000040	Deoxyribose 1-phosphate	Deoxyribose	Not Available	2-Deoxy-D-Ribose 1-Phosphate Phosphorylase	VMH	9693094
MMDBr0000827	Deoxyribose	Deoxyribose	Not Available	Transport of Deoxyribose via Diffusion	VMH	9693094
MMDBr0007754	Adenosine triphosphate	Deoxyribose 5-phosphate	Not Available	Deoxyribokinase	VMH	30371894
MMDBr0007755	Adenosine triphosphate	ADP	Not Available	Deoxyribose transport via ABC system	VMH	30371894

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
Bacteria	Firmicutes	562	Human feces; Human stool; Human pleural fluid plaque; Human ; Human urine; Human mucosa; Human sputum; Human saliva; Human supragingival plaque; Pig ; Cattle ; Human subgingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	238	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Metabolic reconstruction
Bacteria	Actinobacteria	162	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	106	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human supragingival plaque; Human subgingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	7	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	2	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	38	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	2		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Fibroblasts	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0003224

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

References

Synthesis Reference

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 Deoxyribose (MMDBc0000422)

MOL for #<Metabolite:0x00007f5abdf6af30>

3D MOL for #<Metabolite:0x00007f5abdf6af30>

3D SDF for #<Metabolite:0x00007f5abdf6af30>

3D-SDF for #<Metabolite:0x00007f5abdf6af30>

PDB for #<Metabolite:0x00007f5abdf6af30>

3D PDB for #<Metabolite:0x00007f5abdf6af30>

SMILES for #<Metabolite:0x00007f5abdf6af30>

INCHI for #<Metabolite:0x00007f5abdf6af30>

Structure for #<Metabolite:0x00007f5abdf6af30>

3D Structure for #<Metabolite:0x00007f5abdf6af30>