4,5-Dihydroxy-2,3-pentanedione (ECMDB20550) (M2MDB001356)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)XML
Proteins (1)
Record Information
Version2.0
Creation Date2012-05-31 14:50:12 -0600
Update Date2015-06-03 17:20:12 -0600
Secondary Accession Numbers
  • ECMDB20550
Identification
Name:4,5-Dihydroxy-2,3-pentanedione
Description4,5-dihydroxy-2,3-pentanedione is a member of the chemical class known as Beta Ketoaldehydes. These are organic compounds containing an aldehyde substituted with a keto group on the second carbon atom. Dihydropyrimidine dehydrogenase (DPD) is the initial and rate-limiting enzyme in the catabolism of 5-FU. (PMID 9865912) E. coli expression system is a valuable tool for examining DPD enzymatic variants. (PMID 9439663)
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms:
  • (S)-4,5-dihydroxypentan-2,3-dione
  • (S)-4,5-dihydroxypentan-2,3-dione
  • DHPD
  • Dihydroxypentanedione
  • DPD
Chemical Formula:C5H8O4
Weight:Average: 132.1146
Monoisotopic: 132.042258744
InChI Key:UYTRITJAZOPLCZ-SCSAIBSYSA-N
InChI:InChI=1S/C5H8O4/c1-3(7)5(9)4(8)2-6/h4,6,8H,2H2,1H3/t4-/m1/s1
CAS number:Not Available
IUPAC Name:(4R)-4,5-dihydroxypentane-2,3-dione
Traditional IUPAC Name:(4R)-4,5-dihydroxypentane-2,3-dione
SMILES:[H][C@@](O)(CO)C(=O)C(C)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentMonosaccharides
Alternative Parents
Substituents
  • Monosaccharide
  • Beta-hydroxy ketone
  • Alpha-diketone
  • Acyloin
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Ketone
  • 1,2-diol
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility272 g/LALOGPS
logP-0.95ALOGPS
logP-0.9ChemAxon
logS0.31ALOGPS
pKa (Strongest Acidic)11.69ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity29.28 m³·mol⁻¹ChemAxon
Polarizability11.94 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
S-Ribosyl-L-homocysteine > 4,5-Dihydroxy-2,3-pentanedione + L-Homocysteine
4,5-Dihydroxy-2,3-pentanedione > (2R,4S)-2-Methyl-2,4-dihydroxydihydrofuran-3-one
4,5-Dihydroxy-2,3-pentanedione > (2R,4S)-2-methyl-2,4-dihydroxydihydrofuran-3-one
4,5-Dihydroxy-2,3-pentanedione > (2S,4S)-2-methyl-2,4-dihydroxydihydrofuran-3-one
4,5-Dihydroxy-2,3-pentanedione + Adenosine triphosphate > Hydrogen ion + P-DPD + ADP
S-ribosyl-L-homocysteine > 4,5-Dihydroxy-2,3-pentanedione + Homocysteine
SMPDB Pathways:
Quorum SensingPW000836 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:Not Available
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00lr-3900000000-6d2a245dcbab05272fc6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03xr-9300000000-3bb219976347e8bbd517View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0btc-9000000000-5a2f0227afbabb99311fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0089-9700000000-87c806aa0eef96279ffaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-05g0-9200000000-2d86733dc438d3ffd1e1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9000000000-c0f0a293355274672fabView in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • 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
  • Kouwaki, M., Hamajima, N., Sumi, S., Nonaka, M., Sasaki, M., Dobashi, K., Kidouchi, K., Togari, H., Wada, Y. (1998). "Identification of novel mutations in the dihydropyrimidine dehydrogenase gene in a Japanese patient with 5-fluorouracil toxicity." Clin Cancer Res 4:2999-3004. Pubmed: 9865912
  • Vreken, P., Van Kuilenburg, A. B., Meinsma, R., van Gennip, A. H. (1997). "Dihydropyrimidine dehydrogenase (DPD) deficiency: identification and expression of missense mutations C29R, R886H and R235W." Hum Genet 101:333-338. Pubmed: 9439663
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID25200942
Kegg IDNot Available
ChemSpider ID23260085
Wikipedia ID4,5-Dihydroxy-2,3-pentanedione
BioCyc IDDIHYDROXYPENTANEDIONE
EcoCyc IDDIHYDROXYPENTANEDIONE

Enzymes

Protein Details
1. S-ribosylhomocysteine lyase
General function:
Involved in catalytic activity
Specific function:
Involved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. The regulation of gene expression in response to changes in cell density is called quorum sensing. Catalyzes the transformation of S-ribosylhomocysteine (RHC) to homocysteine (HC) and 4,5- dihydroxy-2,3-pentadione (DPD)
Gene Name:
luxS
Uniprot ID:
P45578
Molecular weight:
19416
Reactions
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione.