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Human Metabolome Database Version 3.5

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Showing metabocard for Deoxyribose 1-phosphate (HMDB01351)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:10:23 -0700
HMDB ID HMDB01351
Secondary Accession Numbers None
Metabolite Identification
Common Name Deoxyribose 1-phosphate
Description Deoxyribose 1-phosphate is an intermediate in the metabolism of Pyrimidine. It is a substrate for Purine nucleoside phosphorylase and Thymidine phosphorylase.
Structure Thumb
Download: MOL | SDF | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. 2-Deoxy-alpha-D-ribose 1-phosphate
  2. 2-Deoxy-alpha-delta-ribose 1-phosphate
  3. 2-Deoxy-D-erythro-pentofuranose 1-phosphate
  4. 2-Deoxy-D-ribose 1-phosphate
  5. 2-Deoxy-D-ribose-1-phosphate
  6. 2-Deoxy-delta-erythro-pentofuranose 1-phosphate
  7. 2-Deoxy-delta-ribose 1-phosphate
  8. 2-Deoxy-delta-ribose-1-phosphate
  9. 2-Deoxyribofuranose 1-phosphate
  10. D-2-Deoxy-ribofuranose 1-phosphate
  11. delta-2-Deoxy-ribofuranose 1-phosphate
  12. Deoxyribose 1-phosphate
  13. Deoxyribose-1-phosphate
Chemical Formula C5H11O7P
Average Molecular Weight 214.1104
Monoisotopic Molecular Weight 214.024239218
IUPAC Name {[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid
Traditional IUPAC Name [(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxyphosphonic acid
CAS Registry Number 17210-42-3
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 Key KBDKAJNTYKVSEK-PYHARJCCSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Carbohydrates and Carbohydrate Conjugates
Class Monosaccharides
Sub Class Pentoses
Other Descriptors
  • 2-deoxyribose 1-phosphate(ChEBI)
  • Aliphatic Heteromonocyclic Compounds
Substituents
  • Organic Hypophosphite
  • Organic Phosphite
  • Oxolane
  • Phosphoric Acid Ester
  • Primary Alcohol
  • Secondary Alcohol
Direct Parent Pentoses
Ontology
Status Expected and Not Quantified
Origin
  • Endogenous
Biofunction
  • Component of Purine metabolism
  • Component of Pyrimidine metabolism
Application Not Available
Cellular locations
  • Cytoplasm (predicted from logP)
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 37.6 g/L ALOGPS
LogP -2.14 ALOGPS
LogP -1.5 ChemAxon
LogS -0.76 ALOGPS
pKa (strongest acidic) 1.37 ChemAxon
pKa (strongest basic) -3 ChemAxon
Hydrogen Acceptor Count 6 ChemAxon
Hydrogen Donor Count 4 ChemAxon
Polar Surface Area 116.45 A2 ChemAxon
Rotatable Bond Count 3 ChemAxon
Refractivity 39.32 ChemAxon
Polarizability 17.21 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -2 ChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations Not Available
Tissue Location Not Available
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Pentose Phosphate Pathway SMP00031 map00030 Link_out
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID FDB022571
KNApSAcK ID Not Available
Chemspider ID 388420 Link_out
KEGG Compound ID C00672 Link_out
BioCyc ID DEOXY-RIBOSE-1P Link_out
BiGG ID 35664 Link_out
Wikipedia Link Not Available
NuGOwiki Link HMDB01351 Link_out
Metagene Link HMDB01351 Link_out
METLIN ID 6182 Link_out
PubChem Compound 439287 Link_out
PDB ID Not Available
ChEBI ID 28542 Link_out
References
Synthesis Reference Not 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 Link_out
Enzymes
Name: Ribokinase
Reactions:
  • ATP + D-ribose = ADP + D-ribose 5-phosphate [RN:R01051]
Gene Name: RBKS
Uniprot ID: Q9H477 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA