ECMDB: 5'-Deoxyribose (ECMDB21175) (M2MDB001584)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (1)Transporters (1)XML

Proteins (2)

Record Information

Version

2.0

Creation Date

2012-07-30 14:54:46 -0600

Update Date

2015-06-03 17:20:48 -0600

Secondary Accession Numbers

ECMDB21175

Identification

Name:

5'-Deoxyribose

Description

5'-deoxyribose is a deoxy pentose meaning that it is derived from the sugar ribose by loss of an oxygen atom in the 5' position. The more common form of deoxyribose used in DNA is 2'deoxyribose. 5'-deoxyribose can be formed by the breakdown of 5'deoxyadenosine as catalyzed by 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

(2R,3R,4R)-2,3,4-trihydroxypentanal
(2R,3R,4R)-2,3,4-trihydroxyvaleraldehyde
5'-Deoxyribose
5-Deoxy-aldehydo-D-ribose
5-Deoxy-D-ribose
5-Desoxy-D-ribose
D-Ribo-2,3,4-trihydroxyvaleraldehyde

Chemical Formula:

C₅H₁₀O₄

Weight:

Average: 134.1305
Monoisotopic: 134.057908808

InChI Key:

WDRISBUVHBMJEF-MROZADKFSA-N

InChI:

InChI=1S/C5H10O4/c1-3(7)5(9)4(8)2-6/h2-5,7-9H,1H3/t3-,4+,5-/m1/s1

CAS number:

Not Available

IUPAC Name:

(2R,3R,4R)-2,3,4-trihydroxypentanal

Traditional IUPAC Name:

5'-deoxyribose

SMILES:

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

Chemical Taxonomy

Description

belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharides

Alternative Parents

Substituents

Monosaccharide
Beta-hydroxy aldehyde
Alpha-hydroxyaldehyde
Secondary alcohol
Polyol
Organic oxide
Hydrocarbon derivative
Short-chain aldehyde
Carbonyl group
Aldehyde
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

deoxypentose (CHEBI:62012 )

Physical Properties

State:

Not Available

Charge:

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	475 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-1.9	ChemAxon
logS	0.55	ALOGPS
pKa (Strongest Acidic)	12.1	ChemAxon
pKa (Strongest Basic)	-3.1	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	3	ChemAxon
Refractivity	29.84 m³·mol⁻¹	ChemAxon
Polarizability	12.53 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

5'-Deoxyadenosine + Water > 5'-Deoxyribose + Adenine

SMPDB Pathways:

Not Available

KEGG Pathways:

Not Available

EcoCyc Pathways:

Not Available

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kr-3900000000-30d57ef46048d7192e52	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4i-9200000000-ee1514b94bdabf4acfde	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-34bd0cb544ba73cb9e42	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-05ir-9400000000-41ed7612a81abf536ca6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-9200000000-ac0ef23d944837fa803a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-c450c0fcde2dbd7e339e	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Not Available

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	62012
HMDB ID	Not Available
Pubchem Compound ID	45489773
Kegg ID	Not Available
ChemSpider ID	23346160
Wikipedia ID	Not Available
BioCyc ID	CPD0-2167
EcoCyc ID	CPD0-2167

Enzymes

Protein Details

1. 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase

General function:: Involved in adenosylhomocysteine nucleosidase activity
Specific function:: Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively. Can also use 5'-isobutylthioadenosine, 5'-n- butylthioadenosine, S-adenosyl-D-homocysteine, decarboxylated adenosylhomocysteine, deaminated adenosylhomocysteine and S-2-aza- adenosylhomocysteine as substrates
Gene Name:: mtnN
Uniprot ID:: P0AF12
Molecular weight:: 24354

Reactions

S-adenosyl-L-homocysteine + H(2)O = S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine.
S-methyl-5'-thioadenosine + H(2)O = S-methyl-5-thio-D-ribose + adenine.

Transporters

Protein Details

1. Sugar efflux transporter C

General function:: Involved in transmembrane transport
Specific function:: Involved in the efflux of sugars. The physiological role may be the detoxification of non-metabolizable sugar analogs
Gene Name:: setC
Uniprot ID:: P31436
Molecular weight:: 43493

5'-Deoxyribose (ECMDB21175) (M2MDB001584)

Structure for #<Compound:0xa2aa5c10>

Enzymes

Reactions

Transporters