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

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:34:05 UTC

Update Date

2024-04-20 06:11:46 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

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: ChEBI                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      16.280  -9.099   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      16.280 -10.639   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.280 -12.179   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.280 -13.719   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.280 -15.259   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      17.614 -16.029   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      17.615  -8.318   0.000  0.00  0.00           O+0
HETATM    8  H   UNK     0      14.740 -10.639   0.000  0.00  0.00           H+0
HETATM    9  H   UNK     0      17.820 -10.639   0.000  0.00  0.00           H+0
HETATM   10  H   UNK     0      14.740 -12.179   0.000  0.00  0.00           H+0
HETATM   11  O   UNK     0      17.820 -12.179   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0      14.740 -13.719   0.000  0.00  0.00           H+0
HETATM   13  O   UNK     0      17.820 -13.719   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3    8    9                                             
CONECT    3    2    4   10   11                                             
CONECT    4    3    5   12   13                                             
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    1                                                            
CONECT    8    2                                                            
CONECT    9    2                                                            
CONECT   10    3                                                            
CONECT   11    3                                                            
CONECT   12    4                                                            
CONECT   13    4                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
2-Deoxy-D-erythro-pentose	ChEBI
Aldehydo-2-deoxy-D-ribose	ChEBI
D-DRib	ChEBI
Deoxyribose	ChEBI
Thyminose	ChEBI
2-Deoxyribose	MeSH
2 Deoxyribose	MeSH

Molecular Formula

C₅H₁₀O₄

Average Mass

134.1305

Monoisotopic Mass

134.057908808

IUPAC Name

(3S,4R)-3,4,5-trihydroxypentanal

Traditional Name

deoxyribose

CAS Registry Number

533-67-5

SMILES

[H]C([H])(C=O)[C@]([H])(O)[C@]([H])(O)CO

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

Description

Belongs to the class of organic compounds known as beta-hydroxy aldehydes. These are organic compounds containing an aldehyde substituted with a hydroxy group on the second carbon atom.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Beta-hydroxy aldehydes

Alternative Parents

Substituents

Beta-hydroxy aldehyde
Alpha-hydrogen aldehyde
Secondary alcohol
Polyol
Organic oxide
Hydrocarbon derivative
Short-chain aldehyde
Primary alcohol
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

deoxypentose (CHEBI:28816 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	709 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-2.2	ChemAxon
logS	0.72	ALOGPS
pKa (Strongest Acidic)	11.6	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	30.04 m³·mol⁻¹	ChemAxon
Polarizability	12.71 Å³	ChemAxon
Number of Rings	0	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
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 3 TMS)	splash10-0q29-1930000000-3b3b7534518a42b65f6c	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 3 TMS)	splash10-0l6u-0920000000-e79f5da8378c43b427b1	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 4 TMS)	splash10-014i-0759000000-9b44bab9c4e1abec9d88	2014-06-16	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0229-9100000000-713dd41c8dce5aaa858b	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kr-3900000000-6f94399f0f1d9b862e3e	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0005-9200000000-ccb4dd4b156851d1ad09	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052g-9000000000-a9eae6d5f2c8ca4f88ad	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-4900000000-5221aaf74ab7d833a28f	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9200000000-d5db3a53add7b4afc509	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-0fc8a929da1442a26b40	2016-09-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

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

Metabolic Reactions

Not Available

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

Source Type	Source Sub-type	Species	Data Source	Reference

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

C00001115

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

2-DEOXYRIBOSE

BiGG ID

Not Available

Wikipedia Link

Deoxyribose

METLIN ID

Not Available

PubChem Compound

5460005

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 2-deoxy-D-ribose (MMDBc0033084)

MOL for #<Metabolite:0x00007fecec00dcb0>

3D MOL for #<Metabolite:0x00007fecec00dcb0>

3D SDF for #<Metabolite:0x00007fecec00dcb0>

3D-SDF for #<Metabolite:0x00007fecec00dcb0>

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3D PDB for #<Metabolite:0x00007fecec00dcb0>

SMILES for #<Metabolite:0x00007fecec00dcb0>

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Structure for #<Metabolite:0x00007fecec00dcb0>

3D Structure for #<Metabolite:0x00007fecec00dcb0>