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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-11-09 23:15:49 UTC
HMDB IDHMDB0001548
Secondary Accession Numbers
  • HMDB01548
Metabolite Identification
Common NameD-Ribose 5-phosphate
DescriptionD-Ribose 5-phosphate (CAS: 4300-28-1), also known as R-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. Within humans, D-ribose 5-phosphate participates in a number of enzymatic reactions. In particular, D-ribose 5-phosphate can be biosynthesized from D-ribulose 5-phosphate; which is mediated by the enzyme ribose-5-phosphate isomerase. In addition, D-ribose 5-phosphate can be biosynthesized from D-ribose; which is catalyzed by the enzyme ribokinase. Outside of the human body, D-ribose 5-phosphate has been detected, but not quantified in, milk (cow) and rices. This could make D-ribose 5-phosphate a potential biomarker for the consumption of these foods. D-Ribose 5-phosphate is an important intermediate metabolite in the pentose phosphate pathway (KEGG, map00030) and in the Purine metabolism pathway (KEGG, map00230). The intracellular ribose 5-phosphate concentration is an important determinant of the rate of de novo purine synthesis (PMID: 6699001 ).
Structure
Data?1583514458
Synonyms
ValueSource
5-O-Phosphono-alpha-D-ribofuranoseChEBI
5-O-Phosphono-a-D-ribofuranoseGenerator
5-O-Phosphono-α-D-ribofuranoseGenerator
a-D-Ribose 5-phosphateGenerator
a-D-Ribose 5-phosphoric acidGenerator
alpha-D-Ribose 5-phosphoric acidGenerator
Α-D-ribose 5-phosphateGenerator
Α-D-ribose 5-phosphoric acidGenerator
D-Ribofuranose 5-phosphateHMDB
D-Ribose 5-phosphateHMDB
R-5-PHMDB
Ribose 5-(dihydrogen phosphate)HMDB
Ribose 5-monophosphateHMDB
Ribose 5-phosphateHMDB
alpha-D-Ribose-5-phosphateHMDB
α-D-Ribose-5-phosphateHMDB
Chemical FormulaC5H11O8P
Average Molecular Weight230.1098
Monoisotopic Molecular Weight230.01915384
IUPAC Name{[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional Nameα-D-ribose 5-phosphate
CAS Registry Number34980-65-9
SMILES
O[C@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O
InChI Identifier
InChI=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
InChI KeyKTVPXOYAKDPRHY-AIHAYLRMSA-N
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
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-014j-1942000000-8c3468eabd202324a3aeSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-0fr2-1943000000-b5d1468f33c224a23bd3Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)splash10-00di-9532000000-693524b08b2ccd6179c5Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)splash10-00di-9421000000-dbcd94d0a73f35716059Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-014j-1942000000-8c3468eabd202324a3aeSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0fr2-1943000000-b5d1468f33c224a23bd3Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9532000000-693524b08b2ccd6179c5Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9421000000-dbcd94d0a73f35716059Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9320000000-9b5fdcbd0e9ea3ece549Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0002-9320000000-7f3d980d223a6b9f5f3fSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0002-9000000000-a5df0614f5cbd8b55405Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-056r-0090700000-ea86961dacc666b5fc7dSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0002-9100000000-6cbb3e84820a37a47fbbSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-004i-0090000000-10949588537786dbae1eSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0a4i-0000900000-10d8b4fd09ed514cc12eSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-002b-9000000000-49264a7584727750bd70Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0002-9100000000-6cbb3e84820a37a47fbbSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-004i-0090000000-10949588537786dbae1eSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0a4i-0000900000-10d8b4fd09ed514cc12eSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-002b-9000000000-340deaecb0169ce2acd3Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-1790000000-a3ced14cd6c2537c6d8fSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-5940000000-8bcb763477232ce1dd2cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00y1-9300000000-ff5bd2489969fca00eb7Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-7190000000-184075252146923d2684Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-917b1eb059131caa49acSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-579393c266ea056c9e74Spectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableSpectrum
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableSpectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
Biospecimen Locations
  • Blood
  • Cellular Cytoplasm
  • Feces
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
BloodDetected and Quantified13.2 +/- 4.8 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
Cellular CytoplasmDetected and Quantified0.281 uMAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedNormal details
SalivaDetected and Quantified0.720 +/- 0.402 uMAdult (>18 years old)Not Specified
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified1.31 +/- 0.77 uMAdult (>18 years old)FemaleNormal details
SalivaDetected and Quantified0.264 +/- 0.406 uMAdult (>18 years old)Not Specified
Normal
    • Sugimoto et al. (...
details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)BothUlcerative colitis details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedCrohns disease details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedUlcerative colitis details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedUnclassified IBD details
SalivaDetected and Quantified1.00 +/- 0.44 uMAdult (>18 years old)MaleAlzheimer's disease details
SalivaDetected and Quantified1.32 +/- 0.68 uMAdult (>18 years old)MaleFrontotemporal lobe dementia details
SalivaDetected and Quantified1.79 +/- 1.79 uMAdult (>18 years old)BothLewy body disease details
Associated Disorders and Diseases
Disease References
Ulcerative colitis
  1. Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Crohn's disease
  1. Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Alzheimer's disease
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Frontotemporal dementia
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Lewy body disease
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Associated OMIM IDs
DrugBank IDDB02053
Phenol Explorer Compound IDNot Available
FooDB IDFDB001615
KNApSAcK IDNot Available
Chemspider ID389102
KEGG Compound IDC03736
BioCyc IDRIBOSE-5P
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440101
PDB IDNot Available
ChEBI ID18189
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000336
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Nakayama Y, Kinoshita A, Tomita M: Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor Biol Med Model. 2005 May 9;2:18. [PubMed:15882454 ]
  2. Pilz RB, Willis RC, Boss GR: The influence of ribose 5-phosphate availability on purine synthesis of cultured human lymphoblasts and mitogen-stimulated lymphocytes. J Biol Chem. 1984 Mar 10;259(5):2927-35. [PubMed:6699001 ]

Only showing the first 10 proteins. There are 17 proteins in total.

Enzymes

General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
Gene Name:
PRPS1L1
Uniprot ID:
P21108
Molecular weight:
34838.915
Reactions
Adenosine triphosphate + D-Ribose 5-phosphate → Adenosine monophosphate + Phosphoribosyl pyrophosphatedetails
General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes with similar activities ADP-ribose ADP-mannose, ADP-glucose, 8-oxo-GDP and 8-oxo-dGDP. Can also hydrolyze other nucleotide sugars with low activity.
Gene Name:
NUDT5
Uniprot ID:
Q9UKK9
Molecular weight:
24327.41
Reactions
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
Gene Name:
PRPS1
Uniprot ID:
P60891
Molecular weight:
12324.195
Reactions
Adenosine triphosphate + D-Ribose 5-phosphate → Adenosine monophosphate + Phosphoribosyl pyrophosphatedetails
General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
Gene Name:
PRPS2
Uniprot ID:
P11908
Molecular weight:
35054.06
Reactions
Adenosine triphosphate + D-Ribose 5-phosphate → Adenosine monophosphate + Phosphoribosyl pyrophosphatedetails
General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes ADP-ribose (ADPR) to AMP and ribose 5'-phosphate.
Gene Name:
NUDT9
Uniprot ID:
Q9BW91
Molecular weight:
35448.725
Reactions
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
General function:
Involved in catalytic activity
Specific function:
Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate (By similarity).
Gene Name:
TKTL1
Uniprot ID:
P51854
Molecular weight:
59302.195
Reactions
D-Sedoheptulose 7-phosphate + Glyceraldehyde 3-phosphate → D-Ribose 5-phosphate + Xylulose 5-phosphatedetails
D-Sedoheptulose 7-phosphate + Glyceraldehyde 3-phosphate → D-Ribose 5-phosphate + Xylulose 5-phosphatedetails
Aminofructose 6-phosphate + D-Ribose 5-phosphate → Iminoerythrose 4-phosphate + D-Sedoheptulose 7-phosphatedetails
General function:
Involved in catalytic activity
Specific function:
Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.
Gene Name:
TKT
Uniprot ID:
P29401
Molecular weight:
67876.95
Reactions
D-Sedoheptulose 7-phosphate + Glyceraldehyde 3-phosphate → D-Ribose 5-phosphate + Xylulose 5-phosphatedetails
D-Sedoheptulose 7-phosphate + Glyceraldehyde 3-phosphate → D-Ribose 5-phosphate + Xylulose 5-phosphatedetails
Aminofructose 6-phosphate + D-Ribose 5-phosphate → Iminoerythrose 4-phosphate + D-Sedoheptulose 7-phosphatedetails
General function:
Involved in ribokinase activity
Specific function:
Not Available
Gene Name:
RBKS
Uniprot ID:
Q9H477
Molecular weight:
34142.685
Reactions
Adenosine triphosphate + D-Ribose → ADP + D-Ribose 5-phosphatedetails
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
This enzyme participates in both the breakdown and synthesis of glucose.
Gene Name:
PGM1
Uniprot ID:
P36871
Molecular weight:
63789.985
Reactions
Ribose 1-phosphate → D-Ribose 5-phosphatedetails
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
Interconverts GlcNAc-6-P and GlcNAc-1-P.
Gene Name:
PGM3
Uniprot ID:
O95394
Molecular weight:
62940.905

Only showing the first 10 proteins. There are 17 proteins in total.