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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-12-20 20:29:41 UTC
HMDB IDHMDB0001351
Secondary Accession Numbers
  • HMDB01351
Metabolite Identification
Common NameDeoxyribose 1-phosphate
Description2-deoxy-d-ribofuranose 1-phosphate, also known as 2-deoxy-1-O-phosphono-D-erythro-pentofuranose, is a member of the class of compounds known as pentoses. Pentoses are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 2-deoxy-d-ribofuranose 1-phosphate is soluble (in water) and a moderately acidic compound (based on its pKa). Within the cell, 2-deoxy-d-ribofuranose 1-phosphate is primarily located in the cytoplasm (predicted from logP). 2-deoxy-d-ribofuranose 1-phosphate exists in all living species, ranging from bacteria to humans. In humans, 2-deoxy-d-ribofuranose 1-phosphate is involved in several metabolic pathways, some of which include mercaptopurine pathway, pyrimidine metabolism, thioguanine pathway, and pentose phosphate pathway. 2-deoxy-d-ribofuranose 1-phosphate is also involved in several metabolic disorders, some of which include gout or kelley-seegmiller syndrome, ribose-5-phosphate isomerase deficiency, adenine phosphoribosyltransferase deficiency (APRT), and xanthinuria type I. Deoxyribose 1-phosphate is an intermediate in the metabolism of Pyrimidine. It is a substrate for Purine nucleoside phosphorylase and Thymidine phosphorylase..
Structure
Thumb
Synonyms
ValueSource
2-Deoxy-1-O-phosphono-D-erythro-pentofuranoseChEBI
2-Deoxy-1-O-phosphono-D-ribofuranoseChEBI
2-Deoxy-D-ribose 1-phosphateChEBI
Deoxyribose 1-phosphoric acidGenerator
2-Deoxy-D-ribose 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-phosphateMeSH
2-Deoxyribose 1-phosphate, (alpha-D-erythro)-isomerMeSH
2-Deoxyribose 1-phosphate, (beta-D-erythro)-isomerMeSH
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
DescriptionThis compound 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
Disposition

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 Solubility37.6 g/LALOGPS
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
Bioavailability1ChemAxon
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 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
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022571
KNApSAcK IDNot Available
Chemspider ID388420
KEGG Compound IDC00672
BioCyc IDDEOXY-RIBOSE-1P
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 References
  1. Holmberg I, Stal P, Hamberg M: Quantitative determination of 8-hydroxy-2'-deoxyguanosine in human urine by isotope dilution mass spectrometry: normal levels in hemochromatosis. Free Radic Biol Med. 1999 Jan;26(1-2):129-35. [PubMed:9890648 ]

Enzymes

General function:
Involved in ribokinase activity
Specific function:
Not Available
Gene Name:
RBKS
Uniprot ID:
Q9H477
Molecular weight:
34142.685
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
Deoxyribose 1-phosphate → Deoxyribose 5-phosphatedetails
Deoxyribose 1-phosphate → Deoxyribose 5-monophosphatedetails
General function:
Involved in purine-nucleoside phosphorylase activity
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:
P00491
Molecular weight:
32117.69
Reactions
Deoxyguanosine + Phosphoric acid → Guanine + Deoxyribose 1-phosphatedetails
Deoxyuridine + Phosphoric acid → Uracil + Deoxyribose 1-phosphatedetails
Deoxyadenosine + Phosphoric acid → Adenine + Deoxyribose 1-phosphatedetails
Deoxyinosine + Phosphoric acid → Hypoxanthine + Deoxyribose 1-phosphatedetails
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
TYMP
Uniprot ID:
P19971
Molecular weight:
49954.965
Reactions
Thymidine + Phosphoric acid → Thymine + Deoxyribose 1-phosphatedetails
Deoxyuridine + Phosphoric acid → Uracil + Deoxyribose 1-phosphatedetails
Fluorouracil + Deoxyribose 1-phosphate → Floxuridine + Phosphoric aciddetails