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
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:04:55 UTC
HMDB IDHMDB01548
Secondary Accession NumbersNone
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-phosphateChEBI
D-Ribose-5-PChEBI
Ribose 5-phosphateChEBI
D-Ribose 5'-phosphoric acidGenerator
D-Ribofuranose 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 KeyInChIKey=KTVPXOYAKDPRHY-SOOFDHNKSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.
KingdomOrganic compounds
Super ClassOrganooxygen compounds
ClassCarbohydrates and carbohydrate conjugates
Sub ClassMonosaccharides
Direct ParentMonosaccharide phosphates
Alternative Parents
Substituents
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Oxolane
  • Secondary alcohol
  • Polyol
  • Hemiacetal
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Purine metabolism
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Mitochondria
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 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count3ChemAxon
Refractivity40.83 m3·mol-1ChemAxon
Polarizability18.35 Å3ChemAxon
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
Predicted GC-MSPredicted GC-MS Spectrum - GC-MSNot Available
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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
Biofluid Locations
  • Blood
  • Cellular Cytoplasm
  • Saliva
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Adenine phosphoribosyltransferase deficiency (APRT)SMP00535Not Available
Adenosine Deaminase DeficiencySMP00144Not Available
Adenylosuccinate Lyase DeficiencySMP00167Not Available
AICA-RibosiduriaSMP00168Not Available
Azathioprine PathwaySMP00427Not Available
Glucose-6-phosphate dehydrogenase deficiencySMP00518Not Available
Gout or Kelley-Seegmiller SyndromeSMP00365Not Available
Lesch-Nyhan Syndrome (LNS)SMP00364Not Available
Mercaptopurine PathwaySMP00428Not Available
Mitochondrial DNA depletion syndromeSMP00536Not Available
Molybdenum Cofactor DeficiencySMP00203Not Available
Myoadenylate deaminase deficiencySMP00537Not Available
Pentose Phosphate PathwaySMP00031map00030
Purine MetabolismSMP00050map00230
Purine Nucleoside Phosphorylase DeficiencySMP00210Not Available
Ribose-5-phosphate isomerase deficiencySMP00519Not Available
Thioguanine PathwaySMP00430Not Available
Transaldolase deficiencySMP00520Not Available
Warburg EffectSMP00654Not Available
Xanthine Dehydrogenase Deficiency (Xanthinuria)SMP00220Not Available
Xanthinuria type ISMP00512Not Available
Xanthinuria type IISMP00513Not Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
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
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
BiofluidStatusValueAgeSexConditionReferenceDetails
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 ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB001615
KNApSAcK IDC00007473
Chemspider ID388313
KEGG Compound IDC00117
BioCyc IDRIBOSE-5P
BiGG ID42420
Wikipedia LinkD-ribose-5-P
NuGOwiki LinkHMDB01548
Metagene LinkHMDB01548
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(1):18. [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. [6699001 ]

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
General function:
Involved in ribose-5-phosphate isomerase activity
Specific function:
Not Available
Gene Name:
RPIA
Uniprot ID:
P49247
Molecular weight:
33268.72
Reactions
D-Ribose 5-phosphate → D-Ribulose 5-phosphatedetails
General function:
Involved in ion channel activity
Specific function:
Nonselective, voltage-independent cation channel mediating sodium and calcium ion influx in response to oxidative stress. Extracellular calcium passes through the channel and acts from the intracellular side as a positive regulator in channel activation. Activated by ADP-ribose, nicotinamide adenine dinucleotide (NAD(+)), reactive nitrogen species and arachidonic acid. Inactivated by intracellular ATP. Confers susceptibility to cell death following oxidative stress. Isoform 2 does not seem to be regulated by ADPR. Has ADP-ribose pyrophosphatase activity.
Gene Name:
TRPM2
Uniprot ID:
O94759
Molecular weight:
171224.9
Reactions
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
Catalyzes the conversion of the nucleoside breakdown products ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. May also catalyze the interconversion of glucose-1-phosphate and glucose-6-phosphate. Has low glucose 1,6-bisphosphate synthase activity.
Gene Name:
PGM2
Uniprot ID:
Q96G03
Molecular weight:
68282.765
Reactions
Ribose 1-phosphate → D-Ribose 5-phosphatedetails
General function:
Involved in catalytic activity
Specific function:
Plays an essential role in total transketolase activity and cell proliferation in cancer cells; after transfection with anti-TKTL1 siRNA, total transketolase activity dramatically decreases and proliferation was significantly inhibited in cancer cells. Plays a pivotal role in carcinogenesis.
Gene Name:
TKTL2
Uniprot ID:
Q9H0I9
Molecular weight:
67876.625
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:
Nucleotide transport and metabolism
Specific function:
Not Available
Gene Name:
PRPS2
Uniprot ID:
A6NMS2
Molecular weight:
16130.4
General function:
Involved in magnesium ion binding
Specific function:
ATP + D-ribose 5-phosphate = AMP + 5-phospho- alpha-D-ribose 1-diphosphate
Gene Name:
Not Available
Uniprot ID:
Q53FW2
Molecular weight:
34863.8
General function:
Not Available
Specific function:
Hydrolyzes ADP-ribose, IDP-ribose, CDP-glycerol, CDP-choline and CDP-ethanolamine, but not other non-reducing ADP-sugars or CDP-glucose. May be involved in immune cell signaling as suggested by the second-messenger role of ADP-ribose, which activates TRPM2 as a mediator of oxidative/nitrosative stress (By similarity).
Gene Name:
ADPRM
Uniprot ID:
Q3LIE5
Molecular weight:
39529.105
Reactions
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails