Showing metabocard for Deoxyribose 1-phosphate (BMDB0001351)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:44:34 UTC
Update Date2020-05-21 16:29:00 UTC
BMDB IDBMDB0001351
Secondary Accession Numbers
  • BMDB01351
Metabolite Identification
Common NameDeoxyribose 1-phosphate
DescriptionDeoxyribose 1-phosphate belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Deoxyribose 1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Deoxyribose 1-phosphate exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
2-Deoxy-1-O-phosphono-D-erythro-pentofuranoseChEBI
2-Deoxy-1-O-phosphono-D-ribofuranoseChEBI
2-Deoxy-D-ribose 1-phosphateChEBI
2-Deoxy-D-ribose 1-phosphoric acidGenerator
Deoxyribose 1-phosphoric acidGenerator
2-Deoxy-alpha-D-ribose 1-phosphateHMDB
2-Deoxy-alpha-delta-ribose 1-phosphateHMDB
2-Deoxy-D-erythro-pentofuranose 1-phosphateHMDB
2-Deoxy-D-ribose-1-phosphateHMDB
2-Deoxy-delta-erythro-pentofuranose 1-phosphateHMDB
2-Deoxy-delta-ribose 1-phosphateHMDB
2-Deoxy-delta-ribose-1-phosphateHMDB
2-Deoxyribofuranose 1-phosphateHMDB
D-2-Deoxy-ribofuranose 1-phosphateHMDB
delta-2-Deoxy-ribofuranose 1-phosphateHMDB
Deoxyribose-1-phosphateHMDB
2-Deoxyribose 1-phosphateHMDB
2-Deoxyribose 1-phosphate, (alpha-D-erythro)-isomerHMDB
2-Deoxyribose 1-phosphate, (beta-D-erythro)-isomerHMDB
Chemical FormulaC5H11O7P
Average Molecular Weight214.1104
Monoisotopic Molecular Weight214.024239218
IUPAC Name{[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid
Traditional Namedeoxyribose-1-phosphate
CAS Registry Number17210-42-3
SMILES
OC[C@H]1OC(C[C@@H]1O)OP(O)(O)=O
InChI Identifier
InChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5?/m0/s1
InChI KeyKBDKAJNTYKVSEK-PYHARJCCSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • 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)1.37ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area116.45 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity39.32 m³·mol⁻¹ChemAxon
Polarizability17.21 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, Positivesplash10-0002-9100000000-0b83a26b67c41b7ca8c9View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0002-9120000000-ed5a733798dcf4d7c439View 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, Positivesplash10-00kb-9430000000-ef11f7c98a651dbe59d7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-9400000000-5e3754bb21aff6c3ce06View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9300000000-615ca1fa907e42aa9c9dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03fs-9260000000-5a7b6b1faaba56e1c97dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-5f0b0b093f8d726f7076View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-b1cd1b026728c07d36bbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-3690000000-41b666017994305912b8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-9200000000-99440f284bdeb59e2f04View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052b-9000000000-f613851350f97d5430bcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03fr-9080000000-e66a31856a5562cb0b9dView 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, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001351
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022571
KNApSAcK IDNot Available
Chemspider ID388420
KEGG Compound IDC00672
BioCyc IDNot Available
BiGG ID35664
Wikipedia LinkNot Available
METLIN ID6182
PubChem Compound439287
PDB IDNot Available
ChEBI ID28542
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Purine nucleoside phosphorylase
General function:
Nucleotide transport and metabolism
Specific function:
The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.
Gene Name:
PNP
Uniprot ID:
P55859
Molecular weight:
32037.0
Reactions
Deoxyguanosine + Hydrogen phosphate → Guanine + Deoxyribose 1-phosphatedetails
Deoxyinosine + Hydrogen phosphate → Hypoxanthine + Deoxyribose 1-phosphatedetails
Deoxyadenosine + Hydrogen phosphate → Adenine + Deoxyribose 1-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