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Identification
YMDB IDYMDB00119
NameD-Ribose 5-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionD-Ribose 5-phosphate, also known as D-ribose-5-p, 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. D-Ribose 5-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). D-Ribose 5-phosphate exists in all living species, ranging from bacteria to humans.
Structure
Thumb
Synonyms
  • D-Ribose 5-phosphate
  • D-Ribose 5-phosphic acid
  • D-ribose-5-P
  • D-ribose-5-phosphate
  • D-ribose-5-phosphorate
  • D-ribose-5-phosphoric acid
  • ribose-5-P
  • Ribose-5-phosphate
  • ribose-5-phosphorate
  • ribose-5-phosphoric acid
  • ribose-5P
  • D-Ribose 5'-phosphate
  • Ribose 5-phosphate
  • D-Ribose 5'-phosphoric acid
  • Ribose 5-phosphoric acid
  • D-Ribose 5-phosphoric acid
CAS number3615-55-2
WeightAverage: 230.1098
Monoisotopic: 230.01915384
InChI KeyKTVPXOYAKDPRHY-SOOFDHNKSA-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)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC NameD-ribofuranose 5-phosphate
Chemical FormulaC5H11O8P
SMILES[H]OC1([H])O[C@]([H])(C([H])([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 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
Polarizability18.35 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 Reactions
D-Ribose 5-phosphate + Adenosine triphosphateAdenosine monophosphate + hydron + Phosphoribosyl pyrophosphate
D-ribulose 5-phosphateD-Ribose 5-phosphate
D-Ribose 5-phosphateD-ribulose 5-phosphate
Xylulose 5-phosphate + D-Ribose 5-phosphate → L-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
Xylulose 5-phosphate + D-Ribose 5-phosphateD-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
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
  • Graille, M., Meyer, P., Leulliot, N., Sorel, I., Janin, J., Van Tilbeurgh, H., Quevillon-Cheruel, S. (2005). "Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archaeal and bacterial enzymes." Biochimie 87:763-769.16054529
  • Vaseghi, S., Baumeister, A., Rizzi, M., Reuss, M. (1999). "In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae." Metab Eng 1:128-140.10935926
  • Senac, T., Hahn-Hagerdal, B. (1990). "Intermediary Metabolite Concentrations in Xylulose- and Glucose-Fermenting Saccharomyces cerevisiae Cells." Appl Environ Microbiol 56:120-126.16348083
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID52742
HMDB IDHMDB01548
Pubchem Compound ID77982
Kegg IDC00117
ChemSpider ID388313
FOODB IDFDB001615
WikipediaRibose_5-phosphate
BioCyc IDRIBOSE-5P

Enzymes

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 hydrolase activity
Specific function:
ADP-ribose + H(2)O = AMP + D-ribose 5- phosphate
Gene Name:
YSA1
Uniprot ID:
Q01976
Molecular weight:
26086.80078
Reactions
ADP-ribose + H(2)O → AMP + D-ribose 5-phosphate.
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.