Showing metabocard for Deoxyribose 5-phosphate (BMDB0001031)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:40:07 UTC
Update Date2020-05-21 16:29:00 UTC
BMDB IDBMDB0001031
Secondary Accession Numbers
  • BMDB01031
Metabolite Identification
Common NameDeoxyribose 5-phosphate
DescriptionDeoxyribose 5-phosphate, also known as 2-deoxyribose-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. Deoxyribose 5-phosphate is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Deoxyribose 5-phosphate exists in all eukaryotes, ranging from yeast to humans. Deoxyribose 5-phosphate participates in a number of enzymatic reactions, within cattle. In particular, Deoxyribose 5-phosphate can be biosynthesized from D-glyceraldehyde 3-phosphate and acetaldehyde through its interaction with the enzyme putative deoxyribose-phosphate aldolase. In addition, Deoxyribose 5-phosphate and adenosine diphosphate can be biosynthesized from deoxyribose 1-phosphate and adenosine triphosphate; which is mediated by the enzyme ribokinase. In cattle, deoxyribose 5-phosphate is involved in the metabolic pathway called the pentose phosphate pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
Deoxyribose 5-phosphoric acidGenerator
2-Deoxy-alpha-D-ribose 5-phosphateHMDB
2-Deoxy-alpha-delta-ribose 5-phosphateHMDB
2-Deoxy-D-ribose 5-phosphateHMDB
2-Deoxy-D-ribose-5-phosphateHMDB
2-Deoxyribose 5-phosphateHMDB
2-Deoxyribose-5-pHMDB
2-Deoxyribose-5-phosphateHMDB
Deoxy-ribose-5PHMDB
Deoxyribose-5-pHMDB
Deoxyribose-5-phosphateHMDB
Chemical FormulaC5H11O7P
Average Molecular Weight214.1104
Monoisotopic Molecular Weight214.024239218
IUPAC Name{[(2R,3S,5R)-3,5-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional Namedeoxyribose-5-phosphate
CAS Registry Number102916-66-5
SMILES
O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1
InChI Identifier
InChI=1S/C5H11O7P/c6-3-1-5(7)12-4(3)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1
InChI KeyKKZFLSZAWCYPOC-VPENINKCSA-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
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxide
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
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-1.5ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area116.45 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity39.32 m³·mol⁻¹ChemAxon
Polarizability17.46 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9600000000-bdc9f54852e365293f11View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-006x-9185000000-bfea5991ff0a9475e0b9View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-3970000000-30d79004fa4e6fa5906dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00kb-7910000000-3de23781c803b806a189View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052b-9100000000-25bca847c2e30ed7e327View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03fr-8490000000-6979c10cf3fafe02069dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-43a8b73209f01319d3c2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-16fc473b541d2a247dafView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014j-8910000000-7c465e8be120df2e083aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00r2-9200000000-4f0c0c2bf45b1986dd6aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9100000000-a91ae5a4e7423371ee52View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01r2-9030000000-5eb77e97817ae8e3e50fView 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 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
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001031
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022380
KNApSAcK IDNot Available
Chemspider ID25057464
KEGG Compound IDC00673
BioCyc IDNot Available
BiGG ID35666
Wikipedia LinkNot Available
METLIN ID5956
PubChem Compound45934311
PDB IDAAB
ChEBI ID16132
References
Synthesis ReferenceMethod of preparing 2-deoxyribose 5-phosphate US Patent #7270992
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Deoxyribose-phosphate aldolase
General function:
Nucleotide transport and metabolism
Specific function:
Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. Participates in stress granule (SG) assembly. May allow ATP production from extracellular deoxyinosine in conditions of energy deprivation.
Gene Name:
DERA
Uniprot ID:
Q3T0V9
Molecular weight:
35246.0
Reactions
D-Glyceraldehyde 3-phosphate + Acetaldehyde → Deoxyribose 5-phosphatedetails
Enzyme Details
2. 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
Deoxyribose 1-phosphate + Adenosine triphosphate → Deoxyribose 5-phosphate + ADPdetails