P. aeruginosa Metabolome Database: Deoxyribose 5-phosphate (PAMDB000230)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB000230

Identification

Name:

Deoxyribose 5-phosphate

Description:

Deoxyribose 5-phosphate is a a metabolite in the pentose phosphate pathway. It can be generated from D-glyceraldehdye-3 phosphate via the enzyme 2-Deoxyribose 5-phosphate aldolase (DERA). Alternately Deoxyribose 5-phosphate can be converted to D-glyceraldehyde-3 phosphate that can then feed into the pentose phosphate pathway. Deoxyribose 5-phosphate can also be generated from 2-Deoxy-D-ribose via the enzyme Ribokinase (EC 2.7.1.15). It has been shown in a number of organisms that deoxynucleosides or deoxyriboses cause the induction of aldolases (such as DERA) involved in their catabolism, leading to the utilisation of the pentose moiety as carbon and energy source.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

2-Deoxy-a-D-ribose 5-phosphate
2-Deoxy-a-D-ribose 5-phosphoric acid
2-Deoxy-a-delta-ribose 5-phosphate
2-Deoxy-a-delta-ribose 5-phosphoric acid
2-Deoxy-a-δ-ribose 5-phosphate
2-Deoxy-a-δ-ribose 5-phosphoric acid
2-Deoxy-alpha-D-ribose 5-phosphate
2-Deoxy-alpha-D-ribose 5-phosphoric acid
2-Deoxy-alpha-delta-ribose 5-phosphate
2-Deoxy-alpha-delta-ribose 5-phosphoric acid
2-Deoxy-D-ribose 5-phosphate
2-Deoxy-D-ribose 5-phosphoric acid
2-Deoxy-D-ribose-5-phosphate
2-Deoxy-D-ribose-5-phosphoric acid
2-Deoxy-α-D-ribose 5-phosphate
2-Deoxy-α-D-ribose 5-phosphoric acid
2-Deoxy-α-δ-ribose 5-phosphate
2-Deoxy-α-δ-ribose 5-phosphoric acid
2-Deoxyribose 5-phosphate
2-Deoxyribose 5-phosphoric acid
2-Deoxyribose-5-p
2-Deoxyribose-5-phosphate
2-Deoxyribose-5-phosphoric acid
Deoxy-ribose-5p
Deoxyribose 5-phosphate
Deoxyribose 5-phosphoric acid
Deoxyribose-5-p
Deoxyribose-5-phosphate
Deoxyribose-5-phosphoric acid
DR5P

Chemical Formula:

C₅H₁₁O₇P

Average Molecular Weight:

214.1104

Monoisotopic Molecular Weight:

214.024239218

InChI Key:

KKZFLSZAWCYPOC-VPENINKCSA-N

InChI:

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

CAS number:

102916-66-5

IUPAC Name:

{[(2R,3S)-3,5-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional IUPAC Name:

[(2R,3S)-3,5-dihydroxyoxolan-2-yl]methoxyphosphonic acid

SMILES:

O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organooxygen compounds

Class

Carbohydrates and carbohydrate conjugates

Sub Class

Monosaccharides

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Monosaccharide phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic phosphate
Oxolane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

2-deoxy-D-ribose 5-phosphate (CHEBI:55513 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	37.5 mg/mL	ALOGPS
logP	-2.1	ALOGPS
logP	-1.5	ChemAxon
logS	-0.76	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	39.32 m³·mol^-1	ChemAxon
Polarizability	17.2 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

Deoxyribose 1-phosphate <> Deoxyribose 5-phosphate
Deoxyribose 5-phosphate + ADP <> Deoxyribose + Adenosine triphosphate
Deoxyribose 5-phosphate <> Acetaldehyde + D-Glyceraldehyde 3-phosphate

Pathways:

Pentose phosphate pathway pae00030

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-3970000000-cea24354ca1ecb0c0a48	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00kb-7910000000-15b8562df923ebe3a60d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9100000000-b43c0287c08e6bc1db46	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03fr-7490000000-7a526ffdff192213b787	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-07ad0e8899ae08668c78	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-2a1b5224e4fe99513e45	View in MoNA

References

References:

Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064

Synthesis Reference:

Method of preparing 2-deoxyribose 5-phosphate US Patent

Material Safety Data Sheet (MSDS)

Download (PDF)

Links

External Links:

Resource	Link
CHEBI ID	16132
HMDB ID	HMDB01031
Pubchem Compound ID	635
Kegg ID	C00673
ChemSpider ID	25057464
Wikipedia ID	Not Available
BioCyc ID	DEOXY-RIBOSE-5P
EcoCyc ID	DEOXY-RIBOSE-5P

Deoxyribose 5-phosphate (PAMDB000230)

Structure for Deoxyribose 5-phosphate (PAMDB000230)