You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2018-05-20 18:59:56 UTC
HMDB IDHMDB0001548
Secondary Accession Numbers
  • HMDB01548
Metabolite Identification
Common NameD-Ribose 5-phosphate
DescriptionD-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
Thumb
Synonyms
ValueSource
D-Ribose 5'-phosphateChEBI
D-Ribose-5-PChEBI
Ribose 5-phosphateChEBI
D-Ribose 5'-phosphoric acidGenerator
D-Ribose 5-phosphoric acidGenerator
Ribose 5-phosphoric acidGenerator
D-Ribose-5-phosphateHMDB
D-Ribose-5-phosphorateHMDB
D-Ribose-5-phosphoric acidHMDB
Ribose-5-PHMDB
Ribose-5-phosphateHMDB
Ribose-5-phosphorateHMDB
Ribose-5-phosphoric acidHMDB
Ribose-5PHMDB
Chemical FormulaC5H11O8P
Average Molecular Weight230.1098
Monoisotopic Molecular Weight230.01915384
IUPAC Name{[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional NameD-ribofuranose 5-phosphate
CAS Registry Number3615-55-2
SMILES
OC1O[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-SOOFDHNKSA-N
Chemical Taxonomy
DescriptionThis compound 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
Polarizability18.35 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-014j-1942000000-8c3468eabd202324a3aeView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-0fr2-1943000000-b5d1468f33c224a23bd3View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)splash10-00di-9532000000-693524b08b2ccd6179c5View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)splash10-00di-9421000000-dbcd94d0a73f35716059View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-014j-1942000000-8c3468eabd202324a3aeView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0fr2-1943000000-b5d1468f33c224a23bd3View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9532000000-693524b08b2ccd6179c5View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9421000000-dbcd94d0a73f35716059View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9320000000-9b5fdcbd0e9ea3ece549View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-06vi-9164100000-2305f99f73e0c553d514View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0002-9320000000-7f3d980d223a6b9f5f3fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0002-9000000000-a5df0614f5cbd8b55405View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-056r-0090700000-ea86961dacc666b5fc7dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0002-9100000000-6cbb3e84820a37a47fbbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-004i-0090000000-10949588537786dbae1eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0a4i-0000900000-10d8b4fd09ed514cc12eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-002b-9000000000-49264a7584727750bd70View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0002-9100000000-6cbb3e84820a37a47fbbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-004i-0090000000-10949588537786dbae1eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0a4i-0000900000-10d8b4fd09ed514cc12eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-002b-9000000000-340deaecb0169ce2acd3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-1790000000-a3ced14cd6c2537c6d8fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-5940000000-8bcb763477232ce1dd2cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00y1-9300000000-ff5bd2489969fca00eb7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-7190000000-184075252146923d2684View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-917b1eb059131caa49acView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-579393c266ea056c9e74View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
Biospecimen Locations
  • Blood
  • Cellular Cytoplasm
  • Feces
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
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 Quantified Children (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
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Children (6 - 18 years old)BothUlcerative colitis details
FecesDetected but not Quantified Children (6 - 18 years old)Not SpecifiedCrohns disease details
FecesDetected but not Quantified Children (6 - 18 years old)Not SpecifiedUlcerative colitis details
FecesDetected but not Quantified Children (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
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 ]
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 ]
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 ]
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 ]
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 IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB001615
KNApSAcK IDC00007473
Chemspider ID388313
KEGG Compound IDC00117
BioCyc IDCPD-15317
BiGG ID42420
Wikipedia LinkD-ribose-5-P
METLIN ID6315
PubChem Compound439167
PDB ID1JCY
ChEBI ID52742
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 + D-Glyceraldehyde 3-phosphate → D-Ribose 5-phosphate + Xylulose 5-phosphatedetails
D-Sedoheptulose 7-phosphate + D-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 + D-Glyceraldehyde 3-phosphate → D-Ribose 5-phosphate + Xylulose 5-phosphatedetails
D-Sedoheptulose 7-phosphate + D-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.