Showing metabocard for D-Ribose 5-phosphate (BMDB0001548)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (9) Show 9 proteinsXML
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Record Information
Version1.0
Creation Date2016-09-30 22:47:32 UTC
Update Date2020-05-21 16:29:00 UTC
BMDB IDBMDB0001548
Secondary Accession Numbers
  • BMDB01548
Metabolite Identification
Common NameD-Ribose 5-phosphate
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 possibly soluble (in water) and 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
MOLSDFPDBSMILESInChI
Synonyms
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 Number3615-55-2
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
StatusDetected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
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
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 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 (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0159-1900000000-c7b876b70c54c880bdf3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01c1-9600000000-649e860a529bc7f5b4f8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-053s-9000000000-f9d938955d2446665511View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004j-9040000000-9ee7ba6767ffa3f356dbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fView in MoNA
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
2D NMR[1H, 1H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
Biospecimen Locations
  • Mammary Gland
  • Milk
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Mammary GlandDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Mammary GlandDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
    • Characterization ...
 details
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
    • Kurt J. Boudonck,...
 details
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
    • Kurt J. Boudonck,...
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0001548
DrugBank IDNot Available
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
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff and John A. Ryals (2009). Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff, John A. Ryals. Characterization of the biochemical variability of bovine milk using metabolomics. Metabolomics (2009) 5:375-386 doi: 10.1007/s11306-009-0160-8. Metabolomics.
  2. Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff, John A. Ryals (2009). Characterization of the biochemical variability of bovine milk using metabolomics. Metabolomics.

Enzymes

Enzyme Details
1. Ribose-5-phosphate isomerase
General function:
Carbohydrate transport and metabolism
Specific function:
Not Available
Gene Name:
RPIA
Uniprot ID:
Q3T186
Molecular weight:
28753.0
Enzyme Details
2. Phosphoglucomutase-1
General function:
Carbohydrate transport and metabolism
Specific function:
This enzyme participates in both the breakdown and synthesis of glucose.
Gene Name:
PGM1
Uniprot ID:
Q08DP0
Molecular weight:
61589.0
Reactions
Ribose 1-phosphate → D-Ribose 5-phosphatedetails
Enzyme Details
3. LOC504248 protein
General function:
Nucleotide transport and metabolism
Specific function:
Not Available
Gene Name:
LOC504248
Uniprot ID:
A6QQ58
Molecular weight:
35727.0
Enzyme Details
4. Ribose-phosphate pyrophosphokinase 1
General function:
Nucleotide transport and metabolism
Specific function:
Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
Gene Name:
PRPS1
Uniprot ID:
Q2HJ58
Molecular weight:
34834.0
Reactions
D-Ribose 5-phosphate + Adenosine triphosphate → Phosphoribosyl pyrophosphate + Adenosine monophosphatedetails
Enzyme Details
5. Transketolase-like protein 1
General function:
Energy production and conversion
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:
TKTL1
Uniprot ID:
Q2NL26
Molecular weight:
64966.0
Enzyme Details
6. Transketolase-like protein 2
General function:
Energy production and conversion
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 (By similarity).
Gene Name:
TKTL2
Uniprot ID:
Q2NKZ4
Molecular weight:
67501.0
Enzyme Details
7. Transketolase
General function:
Energy production and conversion
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:
Q6B855
Molecular weight:
67906.0
Enzyme Details
8. Nudix hydrolase 5
General function:
Not Available
Specific function:
Not Available
Gene Name:
NUDT5
Uniprot ID:
F1MMR8
Molecular weight:
18648.0
Reactions
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
Enzyme Details
9. Ribokinase
General function:
Not Available
Specific function:
Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.
Gene Name:
RBKS
Uniprot ID:
E1BJH7
Molecular weight:
40192.0
Reactions
D-Ribose + Adenosine triphosphate → D-Ribose 5-phosphate + ADPdetails