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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:45:38 UTC
HMDB IDHMDB0001213
Secondary Accession Numbers
  • HMDB01213
Metabolite Identification
Common Name1-Deoxy-D-xylulose 5-phosphate
Description1-Deoxy-D-xylulose 5-phosphate 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. 1-Deoxy-D-xylulose 5-phosphate exists in all living species, ranging from bacteria to plants to humans. 1-Deoxy-D-xylulose 5-phosphate has been detected, but not quantified in, several different foods, such as limes (Citrus aurantiifolia), anises (Pimpinella anisum), european chestnuts (Castanea sativa), yellow bell peppers (Capsicum annuum), and silver lindens (Tilia argentea). This could make 1-deoxy-D-xylulose 5-phosphate a potential biomarker for the consumption of these foods. 1-Deoxy-D-xylulose 5-phosphate is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on 1-Deoxy-D-xylulose 5-phosphate.
Structure
Data?1589494052
Synonyms
ValueSource
1-Deoxy-D-xylulose 5-phosphoric acidGenerator
1-Deoxy-D-threo-pentulose 5-phosphateHMDB
D-1-Deoxyxylulose-5-PHMDB
Deoxyxylulose-5-phosphateHMDB
DOXPHMDB
DXPHMDB
1-Deoxylulose 5-phosphateMeSH, HMDB
Chemical FormulaC5H11O7P
Average Molecular Weight214.1104
Monoisotopic Molecular Weight214.024239218
IUPAC Name{[(2R,3S)-2,3-dihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional Name1-deoxy-D-xylulose-5-phosphate
CAS Registry Number190079-18-6
SMILES
CC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O
InChI Identifier
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
InChI KeyAJPADPZSRRUGHI-RFZPGFLSSA-N
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentose phosphates
Alternative Parents
Substituents
  • Pentose-5-phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Acyloin
  • Beta-hydroxy ketone
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Alpha-hydroxy ketone
  • Ketone
  • 1,2-diol
  • Secondary alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Alcohol
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Biological location:

Source:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility27.6 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity40.77 m³·mol⁻¹ChemAxon
Polarizability17.18 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Collision Cross Sections

NameAdductTypeData SourceValueReference
DeepCCS[M-H]-ExperimentalMetCCS_train_neg134.47730932474
AllCCS[M-H]-ExperimentalNot Available134.477http://allccs.zhulab.cn/database/detail?ID=AllCCS00000386
DarkChem[M+H]+PredictedNot Available146.16631661259
DarkChem[M-H]-PredictedNot Available141.12931661259
AllCCS[M+H]+PredictedNot Available146.54132859911
AllCCS[M-H]-PredictedNot Available138.25632859911

Retention Indices

Underivatized

Not Available

Derivatized

DerivativeValueReference
1-Deoxy-D-xylulose 5-phosphate,1TMS,#11739.4989https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,1TMS,#21738.4432https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,1TMS,#31797.8816https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,1TMS,#41908.9613https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,1TMS,#51831.1094https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TMS,#11778.9906https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TMS,#21829.6564https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TMS,#31910.3428https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TMS,#41857.7002https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TMS,#51813.3274https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TMS,#61926.3683https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TMS,#71854.9312https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TMS,#81851.6793https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TMS,#91961.1606https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TMS,#101866.3066https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,1TBDMS,#11987.6294https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,1TBDMS,#21967.4948https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,1TBDMS,#32022.2488https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,1TBDMS,#42124.6985https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,1TBDMS,#52053.7754https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TBDMS,#12216.6978https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TBDMS,#22263.4797https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TBDMS,#32325.1006https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TBDMS,#42294.5166https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TBDMS,#52231.3606https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TBDMS,#62334.8757https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TBDMS,#72272.1392https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TBDMS,#82272.1018https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TBDMS,#92365.9436https://arxiv.org/abs/1905.12712
1-Deoxy-D-xylulose 5-phosphate,2TBDMS,#102293.394https://arxiv.org/abs/1905.12712
Spectra

GC-MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0007-9500000000-8bdb536a3dd0ef5e39ff2016-09-22View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-03dj-7591000000-ee5996fd8cd465a4edc02017-10-06View Spectrum

LC-MS/MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
LC-MS/MSLC-MS/MS Spectrum - QTOF 3V, negativesplash10-01ot-9270000000-b40ebd2ce0f33b3f693e2020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 4V, negativesplash10-01ot-9260000000-313f108a7d35cb99b1622020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 5V, negativesplash10-01ot-9240000000-f72fd1d5f497f6d989ef2020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 7V, negativesplash10-0002-9210000000-d382f418d8862323dc752020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 10V, negativesplash10-0002-9200000000-a6b735cea549110efe422020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 15V, negativesplash10-002b-9100000000-9742f6b19565894a0d8b2020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 17V, negativesplash10-002b-9100000000-bd325d267b7e6b71673e2020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 20V, negativesplash10-004j-9000000000-f1c6ab4253b6848315922020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 23V, negativesplash10-004i-9000000000-a6e482b3b78021124eba2020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 25V, negativesplash10-004i-9000000000-4334bb5f5a870626df312020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 27V, negativesplash10-004i-9000000000-98754795005ce7805b4e2020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 30V, negativesplash10-004i-9000000000-b0d36103ede8b31d79432020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 33V, negativesplash10-004i-9000000000-f0ffb61356bcf5c5199c2020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 35V, negativesplash10-004i-9000000000-ff08b6632b019189148b2020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 40V, negativesplash10-004i-9000000000-be768ed2b60441a509e02020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 45V, negativesplash10-004i-9000000000-7ad3b32caec174e842b12020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 4V, negativesplash10-03fr-1090600000-cf9d96109f22ac8ed3802020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 5V, negativesplash10-03di-1090400000-aaf200bf4025563ede892020-07-21View Spectrum
LC-MS/MSLC-MS/MS Spectrum - QTOF 7V, negativesplash10-03di-1090100000-a3ccf75dc5cacdd462a82020-07-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014j-2940000000-5e70f58c1f6619c745962015-09-14View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0005-7900000000-67299c05b993067eaee52015-09-14View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0005-9200000000-303ff032b1dd45390bac2015-09-14View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-9320000000-41ec442dafa3cc090e2d2015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-5d0fcbc94e864a9d20062015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-2ee0f7b4883b35fcb5522015-09-15View Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02496
Phenol Explorer Compound IDNot Available
FooDB IDFDB022494
KNApSAcK IDC00007292
Chemspider ID391473
KEGG Compound IDC11437
BioCyc IDDEOXYXYLULOSE-5P
BiGG IDNot Available
Wikipedia Link1-Deoxy-D-xylulose 5-phosphate
METLIN ID6085
PubChem Compound443201
PDB IDNot Available
ChEBI ID16493
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
References
Synthesis ReferenceBlagg, 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
General References
  1. Kuzuyama T, Takagi M, Takahashi S, Seto H: Cloning and characterization of 1-deoxy-D-xylulose 5-phosphate synthase from Streptomyces sp. Strain CL190, which uses both the mevalonate and nonmevalonate pathways for isopentenyl diphosphate biosynthesis. J Bacteriol. 2000 Feb;182(4):891-7. [PubMed:10648511 ]