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Identification
YMDB IDYMDB00650
Namealpha-D-ribose 5-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Descriptionalpha-D-ribose 5-phosphate, also known as 5-O-phosphono-a-D-ribofuranose or a-D-ribose 5-phosphoric acid, belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. alpha-D-ribose 5-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). alpha-D-ribose 5-phosphate may be a unique S. cerevisiae (yeast) metabolite.
Structure
Thumb
Synonyms
  • 5-O-phosphono-alpha-D-ribofuranose
  • alpha-D-ribose 5-phosphate
  • arabinose-5-P
  • arabinose-5P
  • D-Arabinose 5-phosphate
  • d-ribose 5-phosphate
  • d-ribose-5-phosphate
  • ribose 5-phosphate
  • 5-O-Phosphono-a-D-ribofuranose
  • 5-O-Phosphono-α-D-ribofuranose
  • a-D-Ribose 5-phosphate
  • a-D-Ribose 5-phosphoric acid
  • alpha-D-Ribose 5-phosphoric acid
  • Α-D-ribose 5-phosphate
  • Α-D-ribose 5-phosphoric acid
CAS number4300-28-1
WeightAverage: 230.1098
Monoisotopic: 230.01915384
InChI KeyKTVPXOYAKDPRHY-AIHAYLRMSA-N
InChIInChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5+/m1/s1
IUPAC Name{[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Nameα-D-ribose 5-phosphate
Chemical FormulaC5H11O8P
SMILESO[C@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O
Chemical Taxonomy
Description belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentose phosphates
Alternative Parents
Substituents
  • Pentose phosphate
  • Pentose-5-phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • 1,2-diol
  • Secondary alcohol
  • Hemiacetal
  • Polyol
  • Oxacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility33.6 g/LALOGPS
logP-2.1ALOGPS
logP-2.4ChemAxon
logS-0.84ALOGPS
pKa (Strongest Acidic)1.22ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area136.68 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity40.83 m³·mol⁻¹ChemAxon
Polarizability18.25 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Histidine BiosynthesisPW002418 ThumbThumb?image type=greyscaleThumb?image type=simple
RiboneogenesisPW002511 ThumbThumb?image type=greyscaleThumb?image type=simple
xylitol degradationPW002433 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pentose phosphate pathwayec00030 Map00030
Purine metabolismec00230 Map00230
SMPDB ReactionsNot Available
KEGG Reactions
Cytidine monophosphate + waterCytosine + alpha-D-ribose 5-phosphate
Ribose 1-phosphatealpha-D-ribose 5-phosphate
Adenosine triphosphate + alpha-D-ribose 5-phosphateAdenosine monophosphate + hydron + Phosphoribosyl pyrophosphate
Adenosine triphosphate + D-Ribosealpha-D-ribose 5-phosphate + hydron + ADP
alpha-D-ribose 5-phosphateD-ribulose 5-phosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
References
References:
  • 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
  • Reuter, R., Naumann, M., Bar, J., Miosga, T., Kopperschlager, G. (1998). "Ribose-5-phosphate isomerase from Saccharomyces cerevisiae: purification and molecular analysis of the enzyme." Bioseparation 7:107-115.9763699
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID18189
HMDB IDHMDB11734
Pubchem Compound ID230
Kegg IDC00117
ChemSpider ID25946122
FOODB IDNot Available
WikipediaRibose_5-phosphate
BioCyc IDARABINOSE-5P

Enzymes

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.
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.
General function:
Involved in catalytic activity
Specific function:
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
Gene Name:
TKL2
Uniprot ID:
P33315
Molecular weight:
75028.79688
Reactions
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate → D-ribose 5-phosphate + D-xylulose 5-phosphate.
General function:
Involved in catalytic activity
Specific function:
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
Gene Name:
TKL1
Uniprot ID:
P23254
Molecular weight:
73805.0
Reactions
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate → D-ribose 5-phosphate + D-xylulose 5-phosphate.
General function:
Involved in magnesium ion binding
Specific function:
5-phosphoribose 1-diphosphate synthase involved in nucleotide, histidine, and tryptophan biosynthesis. Active in heteromultimeric complexes with other 5-phosphoribose 1- diphosphate synthases (PRS2, PRS3, PRS4 and PRS5)
Gene Name:
PRS5
Uniprot ID:
Q12265
Molecular weight:
53504.19922
Reactions
ATP + D-ribose 5-phosphate → AMP + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in magnesium ion binding
Specific function:
5-phosphoribose 1-diphosphate synthase involved in nucleotide, histidine, and tryptophan biosynthesis. Active in heteromultimeric complexes with other 5-phosphoribose 1- diphosphate synthases (PRS2, PRS3, PRS4 and PRS5)
Gene Name:
PRS2
Uniprot ID:
P38620
Molecular weight:
34764.60156
Reactions
ATP + D-ribose 5-phosphate → AMP + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in magnesium ion binding
Specific function:
5-phosphoribose 1-diphosphate synthase involved in nucleotide, histidine, and tryptophan biosynthesis. Active in heteromultimeric complexes with other 5-phosphoribose 1- diphosphate synthases (PRS2, PRS3, PRS4 and PRS5)
Gene Name:
PRS1
Uniprot ID:
P32895
Molecular weight:
47047.0
Reactions
ATP + D-ribose 5-phosphate → AMP + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in magnesium ion binding
Specific function:
5-phosphoribose 1-diphosphate synthase involved in nucleotide, histidine, and tryptophan biosynthesis. Active in heteromultimeric complexes with other 5-phosphoribose 1- diphosphate synthases (PRS2, PRS3, PRS4 and PRS5)
Gene Name:
PRS3
Uniprot ID:
P38689
Molecular weight:
35123.30078
Reactions
ATP + D-ribose 5-phosphate → AMP + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine at positions 27 and 28 in the anticodon stem and loop of transfer RNAs; at positions 34 and 36 of intron-containing precursor tRNA(Ile) and at position 35 in the intron-containing tRNA(Tyr)
Gene Name:
PUS1
Uniprot ID:
Q12211
Molecular weight:
62142.0
Reactions
tRNA uridine → tRNA pseudouridine.
General function:
Involved in RNA processing
Specific function:
Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
Gene Name:
PUS4
Uniprot ID:
P48567
Molecular weight:
45273.10156
Reactions
tRNA uridine → tRNA pseudouridine.
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS2
Uniprot ID:
P53167
Molecular weight:
41874.80078
Reactions
tRNA uridine → tRNA pseudouridine.
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridines at positions 38 and 39 in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS3
Uniprot ID:
P31115
Molecular weight:
50888.30078
Reactions
tRNA uridine → tRNA pseudouridine.
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.
General function:
Involved in ribose-5-phosphate isomerase activity
Specific function:
D-ribose 5-phosphate = D-ribulose 5-phosphate
Gene Name:
RKI1
Uniprot ID:
Q12189
Molecular weight:
28257.80078
Reactions
D-ribose 5-phosphate → D-ribulose 5-phosphate.
General function:
Involved in magnesium ion binding
Specific function:
5-phosphoribose 1-diphosphate synthase involved in nucleotide, histidine, and tryptophan biosynthesis. Active in heteromultimeric complexes with other 5-phosphoribose 1- diphosphate synthases (PRS2, PRS3, PRS4 and PRS5)
Gene Name:
PRS4
Uniprot ID:
P38063
Molecular weight:
35845.69922
Reactions
ATP + D-ribose 5-phosphate → AMP + 5-phospho-alpha-D-ribose 1-diphosphate.