1-Deoxy-D-xylulose 5-phosphate (PAMDB000301)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000301
Identification
Name: 1-Deoxy-D-xylulose 5-phosphate
Description:1-Deoxy-D-xylulose 5-phosphate is an intermediate in the non-mevalonate pathway. This is an alternative metabolic pathway leading to the formation of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The key enzyme in the non-mevalonate pathway of isoprenoid biosynthesis is 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR).
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 1-Deoxy-D-threo-pentulose 5-phosphate
  • 1-Deoxy-D-threo-pentulose 5-phosphoric acid
  • 1-Deoxy-D-xylulose 5-phosphate
  • 1-Deoxy-D-xylulose 5-phosphoric acid
  • 1DX5P
  • D-1-Deoxyxylulose-5-P
  • Deoxyxylulose-5-phosphate
  • Deoxyxylulose-5-phosphoric acid
  • DOXP
  • DXP
Chemical Formula: C5H11O7P
Average Molecular Weight: 214.1104
Monoisotopic Molecular Weight: 214.024239218
InChI Key: AJPADPZSRRUGHI-RFZPGFLSSA-N
InChI:InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h4-5,7-8H,2H2,1H3,(H2,9,10,11)/t4-,5-/m1/s1
CAS number: 190079-18-6
IUPAC Name:{[(2R,3S)-2,3-dihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional IUPAC Name: 1-deoxy-D-xylulose-5-phosphate
SMILES:CC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Carbohydrates and carbohydrate conjugates
Sub ClassMonosaccharides
Direct Parent Pentose phosphates
Alternative Parents
Substituents
  • Pentose-5-phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Beta-hydroxy ketone
  • Beta-ketoaldehyde
  • Acyloin
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Ketone
  • 1,2-diol
  • Hydrocarbon derivative
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility27.6 mg/mLALOGPS
logP-1.9ALOGPS
logP-1.9ChemAxon
logS-0.89ALOGPS
pKa (Strongest Acidic)1.48ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area124.29 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity40.77 m3·mol-1ChemAxon
Polarizability17.18 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
1-Deoxy-D-xylulose 5-phosphate + NAD + O-Phospho-4-hydroxy-L-threonine > Carbon dioxide + Hydrogen ion +2 Water + NADH + Pyridoxine 5'-phosphate + Phosphate
Adenosine triphosphate + Dehydroglycine + 1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion + IscS with bound sulfur + NADPH > 4-Methyl-5-(2-phosphoethyl)-thiazole + Adenosine monophosphate + Carbon dioxide +2 Water + IscS sulfur acceptor protein + NADP + Pyrophosphate
1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion + NADPH <> 2-C-Methyl-D-erythritol-4-phosphate + NADP
D-Glyceraldehyde 3-phosphate + Hydrogen ion + Pyruvic acid <> Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate
Pyruvic acid + D-Glyceraldehyde 3-phosphate <> 1-Deoxy-D-xylulose 5-phosphate + Carbon dioxide
3-Amino-2-oxopropyl phosphate + 1-Deoxy-D-xylulose 5-phosphate + 3-Amino-2-oxopropyl phosphate <> Pyridoxine 5'-phosphate + Phosphate +2 Water
1-Amino-propan-2-one-3-phosphate + 1-Deoxy-D-xylulose 5-phosphate > Hydrogen ion + Pyridoxine 5'-phosphate + Phosphate + Water
Adenosine triphosphate + 1-Deoxy-D-xylulose > Hydrogen ion + 1-Deoxy-D-xylulose 5-phosphate + ADP
1-Deoxy-D-xylulose 5-phosphate + 2-iminoacetate + thiocarboxy-adenylate-[sulfur-carrier protein ThiS] > 2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + [sulfur-carrier protein ThiS] +2 Water
1-Deoxy-D-xylulose 5-phosphate + 2-iminoacetate <> 2-[(2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate +2 Water
1-Deoxy-D-xylulose 5-phosphate + 2-Amino-3-phosphonopropionic acid + 1-Deoxy-D-xylulose 5-phosphate + 2-Amino-3-phosphonopropionic acid > Pyridoxine 5'-phosphate + Phosphate + Hydrogen ion +2 Water
D-Glyceraldehyde 3-phosphate + Pyruvic acid + Hydrogen ion + D-Glyceraldehyde 3-phosphate > 1-Deoxy-D-xylulose 5-phosphate + Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate
D-Glyceraldehyde 3-phosphate + Hydrogen ion + D-Glyceraldehyde 3-phosphate > Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate + 1-Deoxy-D-xylulose 5-phosphate
NADPH + Hydrogen ion + 1-Deoxy-D-xylulose 5-phosphate + NADPH + 1-Deoxy-D-xylulose 5-phosphate > NADP + 2-C-methyl-D-erythritol 4-phosphate
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MSNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014j-2940000000-5e70f58c1f6619c74596View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0005-7900000000-67299c05b993067eaee5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0005-9200000000-303ff032b1dd45390bacView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-9320000000-41ec442dafa3cc090e2dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-5d0fcbc94e864a9d2006View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-2ee0f7b4883b35fcb552View in MoNA
References
References:
  • 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
Synthesis Reference: Blagg, Brian S. J.; Poulter, C. Dale. Synthesis of 1-Deoxy-D-xylulose and 1-Deoxy-D-xylulose-5-phosphate. Journal of Organic Chemistry (1999), 64(5), 1508-1511.
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID16493
HMDB IDHMDB01213
Pubchem Compound ID443201
Kegg IDC11437
ChemSpider ID391473
Wikipedia1-Deoxy-D-xylulose 5-phosphate
BioCyc IDDEOXYXYLULOSE-5P
EcoCyc IDDEOXYXYLULOSE-5P
Ligand ExpoDXP