D-Ribose (YMDB00253)

Identification

YMDB ID

YMDB00253

Name

D-Ribose

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

D-Ribose, also known as D-ribofuranoside or ribose, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Ribose is an extremely weak basic (essentially neutral) compound (based on its pKa). D-Ribose exists in all living species, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Alpha-d-ribose
alpha-D-ribose-5
Alpha-delta-ribose
alpha-delta-ribose-5
D-(-)-ribose
D-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
d-Ribose
delta-(-)-ribose
delta-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
delta-Ribose
Ribose
(3R,4S,5R)-5-(Hydroxymethyl)tetrahydrofuran-2,3,4-triol
D-Ribofuranoside
D-Ribofuranose
Ribofuranoside
Ribofuranose

CAS number

50-69-1

Weight

Average: 150.1299
Monoisotopic: 150.05282343

InChI Key

HMFHBZSHGGEWLO-SOOFDHNKSA-N

InChI

InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1

IUPAC Name

(3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol

Traditional IUPAC Name

D-ribofuranoside

Chemical Formula

C₅H₁₀O₅

SMILES

[H]OC([H])([H])[C@@]1([H])OC([H])(O[H])[C@]([H])(O[H])[C@]1([H])O[H]

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
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-ribose (CHEBI:47013 )
ribofuranose (CHEBI:47013 )
Aldoses (C00121 )

Physical Properties

State

Solid

Charge

Melting point

95 °C

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	-2.32 [HANSCH,C ET AL. (1995)]	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	1070 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-2.3	ChemAxon
logS	0.85	ALOGPS
pKa (Strongest Acidic)	11.31	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	29.96 m³·mol⁻¹	ChemAxon
Polarizability	13.68 Å³	ChemAxon
Number of Rings	1	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

Not Available

Organoleptic Properties

Not Available

SMPDB Pathways

NAD metabolism

PW002421

KEGG Pathways

Pentose phosphate pathway

ec00030

SMPDB Reactions

Nicotinamide riboside + water → hydron + D-Ribose + Niacinamide

KEGG Reactions

Adenosine + water → D-Ribose + Adenine

water + Guanosine → D-Ribose + Guanine

Adenosine triphosphate + D-Ribose → alpha-D-ribose 5-phosphate + hydron + ADP

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0udi-0920000000-c414574c94624914be8c	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0fk9-9831000000-d0b33cef6c46219ea9a8	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0udi-0920000000-e3647dbf79b8733c3bfd	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0udi-0921000000-e8a202c64cf867b21cef	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0udi-0920000000-272c588a02a550b79c74	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0ldi-0941000000-999cd264e51df6d784b4	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0udi-0910000000-54f42f17ff952d787b86	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0uxr-0920000000-d29b5079ba0fde220b0d	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS; 1 MEOX)	splash10-0fk9-8920000000-71080ebc024c820bf8fd	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0920000000-c414574c94624914be8c	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0fk9-9831000000-d0b33cef6c46219ea9a8	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0920000000-e3647dbf79b8733c3bfd	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0921000000-e8a202c64cf867b21cef	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0920000000-272c588a02a550b79c74	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0ldi-0941000000-999cd264e51df6d784b4	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0910000000-54f42f17ff952d787b86	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uxr-0920000000-d29b5079ba0fde220b0d	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0fk9-8920000000-71080ebc024c820bf8fd	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-05cu-9300000000-e24e80da64b2475ddfd8	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-00g0-7349300000-49b1e72358e4fd020b5d	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-014r-4900000000-76daa3235c9f82ef4f5a	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-000i-9100000000-b44f013dcb4efe64039d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0a4i-9000000000-64a1b88f0cb22f5b729a	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0a4i-9000000000-a05552744534bc6dc8c5	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-9000000000-23b475cbcd2c9fafde18	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-9000000000-88ff2c607ed1b08ed6b9	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0a4i-9000000000-7c7662a3e6e7923d84cb	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0a4i-9000000000-ce0d2af497d6da39f1f1	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0a4i-9000000000-f0409fb19110a197badc	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0udi-8900000000-41d386e0f57f435290c8	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9300000000-2ea2e21fb5412f962d7f	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ue9-2900000000-6c1199d377747f0e5b49	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0f89-2900000000-8a9f89ac0a25c323249e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052p-9100000000-eaebbbf2fa629ce04160	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1900000000-6c48df798a58fc7029d9	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001j-2900000000-816419eb5dad5bd99819	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9200000000-91d11d896b253dfd9693	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0gc0-1900000000-346af5e1437ac746833b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0nc4-9400000000-74fd6af917cb088bef2b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-55c82f4fa793a5fd288b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0pc1-5900000000-6953077be254812d8b25	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-9100000000-fcc3022a655e16f83b2c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-750ecddfae4eefc71996	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089

Synthesis Reference:

Park, Yong-Cheol; Choi, Jin-Ho; Bennett, George N.; Seo, Jin-Ho. Characterization of D-ribose biosynthesis in Bacillus subtilis JY200 deficient in transketolase gene. Journal of Biotechnology (2006), 121(4), 508-516.

External Links:

Resource	Link
CHEBI ID	47013
HMDB ID	HMDB00283
Pubchem Compound ID	5779
Kegg ID	C00121
ChemSpider ID	5575
FOODB ID	FDB031292
Wikipedia	Ribose
BioCyc ID	CPD-560

Enzymes

Protein Details

1. Probable ribokinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: ATP + D-ribose = ADP + D-ribose 5-phosphate
Gene Name:: RBK1
Uniprot ID:: P25332
Molecular weight:: 36923.80078

Reactions

ATP + D-ribose → ADP + D-ribose 5-phosphate.

Protein Details

2. Uridine nucleosidase

General function:: Involved in hydrolase activity, hydrolyzing N-glycosyl compounds
Specific function:: Also acts on cytidine
Gene Name:: URH1
Uniprot ID:: Q04179
Molecular weight:: 37960.0

Reactions

Uridine + H(2)O → D-ribose + uracil.

Structure for #<Compound:0x047fa630>

Enzymes

Reactions

Reactions