Ribose 1-phosphate (YMDB00061)

You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Identification

YMDB ID

YMDB00061

Name

Ribose 1-phosphate

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Ribose 1-phosphate, also known as D-ribose-1P, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Ribose 1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Ribose 1-phosphate exists in all living species, ranging from bacteria to humans.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

1-o-phosphono-D-ribofuranose
a-D-ribofuranose 1-(dihydrogen phosphate)
a-D-ribose 1-phosphate
alpha-D-ribofuranose 1-(dihydrogen phosphate)
alpha-D-ribofuranose 1-phosphate
alpha-D-ribose 1-phosphate
D-ribofuranose 1-(dihydrogen phosphate)
D-ribofuranose 1-phosphate
D-ribose-1-phosphate
D-ribose-1P
ribofuranose 1-phosphate
Ribose 1-phosphate
Ribose 1-phosphic acid
1-O-Phosphono-alpha-D-ribofuranose
1-Phospho-alpha-D-ribofuranose
D-Ribose 1-phosphate
1-O-Phosphono-a-D-ribofuranose
1-O-Phosphono-α-D-ribofuranose
1-Phospho-a-D-ribofuranose
1-Phospho-α-D-ribofuranose
D-Ribose 1-phosphoric acid
Ribose 1-phosphoric acid
Ribose 1-phosphate, (beta-D)-isomer
Ribose 1-phosphate, (alpha-D)-isomer

CAS number

14075-00-4

Weight

Average: 230.1098
Monoisotopic: 230.01915384

InChI Key

YXJDFQJKERBOBM-TXICZTDVSA-N

InChI

InChI=1S/C5H11O8P/c6-1-2-3(7)4(8)5(12-2)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1

IUPAC Name

{[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid

Traditional IUPAC Name

ribose 1-phosphate

Chemical Formula

C₅H₁₁O₈P

SMILES

[H]OC([H])([H])[C@@]1([H])O[C@]([H])(OP(=O)(O[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
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-ribose 1-phosphate (CHEBI:16300 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	35.2 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.4	ChemAxon
logS	-0.82	ALOGPS
pKa (Strongest Acidic)	1.16	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	136.68 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	40.83 m³·mol⁻¹	ChemAxon
Polarizability	18.17 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

mitochondrion
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Not Available

KEGG Pathways

Pentose phosphate pathway	ec00030
Purine metabolism	ec00230

SMPDB Reactions

Not Available

KEGG Reactions

Ribose 1-phosphate ↔ alpha-D-ribose 5-phosphate

phosphate + Nicotinamide riboside ↔ hydron + Niacinamide + Ribose 1-phosphate

Adenosine + phosphate ↔ Ribose 1-phosphate + Adenine

phosphate + Guanosine ↔ Ribose 1-phosphate + Guanine

phosphate + Inosine ↔ Hypoxanthine + Ribose 1-phosphate

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9110000000-add01bb15cc1fd9e2e29	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-014i-2931000000-fe633c386d1b3ab9db9a	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 (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-0090000000-e2c9f6f60320b17dd479	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-01t9-9250000000-029c27941ed85100b53c	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9000000000-311ca08c80d0a6c765da	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9000000000-36d97c26c72c69ab56c6	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9000000000-08796c6cb24ecefd9abf	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-9230000000-bf825c0a48e8f3fb1db5	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9330000000-af34500034734754adda	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9000000000-ea509fab4675ba638745	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-9180000000-4449ca89ca00716d8cef	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9110000000-c74e6f3e6a87ec4b57fb	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-81a191a3e73e8031cb23	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0159-0900000000-6d6c0c7544f77dfb0c41	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00lr-7910000000-9441b177b385255d831b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4m-9000000000-a9998928687caae44190	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-3090000000-4bb2aedb7cfc3f4c2255	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-e5ae44d04fcc61ba1d70	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-00ffef4ac2a980d6a310	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
1D NMR	1H 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
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
Belenky, P., Racette, F. G., Bogan, K. L., McClure, J. M., Smith, J. S., Brenner, C. (2007). "Nicotinamide riboside promotes Sir2 silencing and extends lifespan via Nrk and Urh1/Pnp1/Meu1 pathways to NAD+." Cell 129:473-484.17482543

Synthesis Reference:

Tochikura, Tatsurokuro; Sakai, Takuo; Ogata, Koichi. Ribose 1-phosphate production by fermentation. Jpn. Tokkyo Koho (1969), 3 pp.

External Links:

Resource	Link
CHEBI ID	16300
HMDB ID	HMDB01489
Pubchem Compound ID	123732
Kegg ID	C00620
ChemSpider ID	388373
FOODB ID	FDB031271
Wikipedia ID	Not Available
BioCyc ID	RIBOSE-1P

Enzymes

Protein Details

1. Purine nucleoside phosphorylase

General function:: Involved in purine-nucleoside phosphorylase activity
Specific function:: Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules
Gene Name:: PNP1
Uniprot ID:: Q05788
Molecular weight:: 33754.60156

Reactions

Purine nucleoside + phosphate → purine + alpha-D-ribose 1-phosphate.

Protein Details

2. Phosphoglucomutase-2

General function:: Involved in intramolecular transferase activity, phosphotransferases
Specific function:: This enzyme participates in both the breakdown and synthesis of glucose. Can also act on mannose
Gene Name:: PGM2
Uniprot ID:: P37012
Molecular weight:: 63088.0

Reactions

Alpha-D-glucose 1-phosphate → alpha-D-glucose 6-phosphate.

Protein Details

3. Phosphoglucomutase-1

General function:: Involved in intramolecular transferase activity, phosphotransferases
Specific function:: This enzyme participates in both the breakdown and synthesis of glucose. Can also act on mannose
Gene Name:: PGM1
Uniprot ID:: P33401
Molecular weight:: 63111.30078

Reactions

Alpha-D-glucose 1-phosphate → alpha-D-glucose 6-phosphate.

Protein Details

4. 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:0xaf1e3318>

Enzymes

Reactions

Reactions

Reactions

Reactions