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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2023-02-21 17:15:35 UTC

HMDB ID

HMDB0001292

Secondary Accession Numbers

HMDB01292

Metabolite Identification

Common Name

1-Deoxy-D-xylulose

Description

1-Deoxy-D-xylulose belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 1-Deoxy-D-xylulose exists in all living organisms, ranging from bacteria to humans. 1-Deoxy-D-xylulose has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 1-deoxy-D-xylulose a potential biomarker for the consumption of these foods. 1-Deoxy-D-xylulose 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.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1-Deoxy-xylulose	HMDB

Chemical Formula

C₅H₁₀O₄

Average Molecular Weight

134.1305

Monoisotopic Molecular Weight

134.057908808

IUPAC Name

(2S,3S,4R)-2-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

1-deoxy-xylulose

CAS Registry Number

Not Available

SMILES

OC[C@@H]1OC[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2/t3-,4+,5+/m1/s1

InChI Key

KZVAAIRBJJYZOW-WISUUJSJSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Ether
Dialkyl ether
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Cytoplasm (HMDB: HMDB0001292)

Source

Endogenous

Endogenous (HMDB: HMDB0001292)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1050 g/L	ALOGPS
logP	-2	ALOGPS
logP	-1.9	ChemAxon
logS	0.89	ALOGPS
pKa (Strongest Acidic)	12.88	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.92 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	28.93 m³·mol⁻¹	ChemAxon
Polarizability	12.64 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	129.044	31661259
DarkChem	[M-H]-	127.179	31661259
AllCCS	[M+H]+	130.748	32859911
AllCCS	[M-H]-	123.641	32859911
DeepCCS	[M+H]+	130.074	30932474
DeepCCS	[M-H]-	127.94	30932474
DeepCCS	[M-2H]-	162.873	30932474
DeepCCS	[M+Na]+	137.155	30932474
AllCCS	[M+H]+	130.7	32859911
AllCCS	[M+H-H2O]+	126.1	32859911
AllCCS	[M+NH4]+	135.1	32859911
AllCCS	[M+Na]+	136.3	32859911
AllCCS	[M-H]-	123.6	32859911
AllCCS	[M+Na-2H]-	125.7	32859911
AllCCS	[M+HCOO]-	128.1	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter)). Predicted by Afia on May 17, 2022.	0.94 minutes	32390414
Predicted by Siyang on May 30, 2022	9.1233 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.01 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	226.5 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	723.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	311.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	48.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	187.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	60.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	269.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	235.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	608.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	576.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	43.6 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	802.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	190.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	208.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	576.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	303.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	292.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1-Deoxy-D-xylulose	OC[C@@H]1OC[C@@H](O)[C@@H]1O	2636.2	Standard polar	33892256
1-Deoxy-D-xylulose	OC[C@@H]1OC[C@@H](O)[C@@H]1O	1316.4	Standard non polar	33892256
1-Deoxy-D-xylulose	OC[C@@H]1OC[C@@H](O)[C@@H]1O	1288.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1-Deoxy-D-xylulose,1TMS,isomer #1	C[Si](C)(C)OC[C@@H]1OC[C@@H](O)[C@@H]1O	1349.4	Semi standard non polar	33892256
1-Deoxy-D-xylulose,1TMS,isomer #2	C[Si](C)(C)O[C@@H]1CO[C@@H](CO)[C@H]1O	1381.9	Semi standard non polar	33892256
1-Deoxy-D-xylulose,1TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@H](CO)OC[C@H]1O	1374.0	Semi standard non polar	33892256
1-Deoxy-D-xylulose,2TMS,isomer #1	C[Si](C)(C)OC[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H]1O	1458.8	Semi standard non polar	33892256
1-Deoxy-D-xylulose,2TMS,isomer #2	C[Si](C)(C)OC[C@@H]1OC[C@@H](O)[C@@H]1O[Si](C)(C)C	1458.2	Semi standard non polar	33892256
1-Deoxy-D-xylulose,2TMS,isomer #3	C[Si](C)(C)O[C@@H]1CO[C@@H](CO)[C@H]1O[Si](C)(C)C	1445.7	Semi standard non polar	33892256
1-Deoxy-D-xylulose,3TMS,isomer #1	C[Si](C)(C)OC[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	1539.1	Semi standard non polar	33892256
1-Deoxy-D-xylulose,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1OC[C@@H](O)[C@@H]1O	1575.5	Semi standard non polar	33892256
1-Deoxy-D-xylulose,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1CO[C@@H](CO)[C@H]1O	1586.0	Semi standard non polar	33892256
1-Deoxy-D-xylulose,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](CO)OC[C@H]1O	1595.0	Semi standard non polar	33892256
1-Deoxy-D-xylulose,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	1884.0	Semi standard non polar	33892256
1-Deoxy-D-xylulose,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@@H]1OC[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	1890.4	Semi standard non polar	33892256
1-Deoxy-D-xylulose,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1CO[C@@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C	1889.7	Semi standard non polar	33892256
1-Deoxy-D-xylulose,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2182.0	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Deoxy-D-xylulose GC-MS (Non-derivatized) - 70eV, Positive	splash10-00di-9200000000-bc8cd8af91e7c9a197a1	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Deoxy-D-xylulose GC-MS (3 TMS) - 70eV, Positive	splash10-0uds-4291000000-59ca220656793d44d9b7	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Deoxy-D-xylulose GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 10V, Positive-QTOF	splash10-000i-1900000000-7090a6712cf92fc92b47	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 20V, Positive-QTOF	splash10-014r-3900000000-1e02762bd5d3754a4e36	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 40V, Positive-QTOF	splash10-052b-9000000000-88975f87661b595c76bd	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 10V, Negative-QTOF	splash10-001i-0900000000-e0e5e2d68edb8bbc84f0	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 20V, Negative-QTOF	splash10-00lr-2900000000-ff5858ced75ca8f420e2	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 40V, Negative-QTOF	splash10-0006-9200000000-f94dc6ccbc9cbdbfeed6	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 10V, Negative-QTOF	splash10-0f89-4900000000-8a6afa76074a3daf9196	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 20V, Negative-QTOF	splash10-0a4l-9200000000-149f3dceb4c97219beb6	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 40V, Negative-QTOF	splash10-052f-9000000000-3ec198bd54c97fa0e89c	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 10V, Positive-QTOF	splash10-0ap1-9400000000-9a51cae153c12e261a4d	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 20V, Positive-QTOF	splash10-0a4j-9000000000-1ce0654ed02bead3e749	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 40V, Positive-QTOF	splash10-0005-9000000000-78c20bbe447917d1f4b6	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6138

PubChem Compound

12444984

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Backstrom, Allyson D.; Austin, R.; McMordie Austin S.; Begley, Tadhg P. A new synthesis of 1-deoxy-D-threo-2-pentulose, a biosynthetic precursor to the thiazole moiety of thiamin. Journal of Carbohydrate Chemistry (1995), 14(1), 171-5.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 1-Deoxy-D-xylulose (HMDB0001292)

MOL for HMDB0001292 (1-Deoxy-D-xylulose)

3D MOL for HMDB0001292 (1-Deoxy-D-xylulose)

3D SDF for HMDB0001292 (1-Deoxy-D-xylulose)

3D-SDF for HMDB0001292 (1-Deoxy-D-xylulose)

PDB for HMDB0001292 (1-Deoxy-D-xylulose)

3D PDB for HMDB0001292 (1-Deoxy-D-xylulose)

SMILES for HMDB0001292 (1-Deoxy-D-xylulose)

INCHI for HMDB0001292 (1-Deoxy-D-xylulose)

Structure for HMDB0001292 (1-Deoxy-D-xylulose)

3D Structure for HMDB0001292 (1-Deoxy-D-xylulose)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra