Livestock Metabolome Database: Showing metabocard for D-Ribulose 5-phosphate (LMDB00192)

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

Record Information

Version

1.0

Creation Date

2016-07-13 19:44:22 UTC

Update Date

2016-07-20 20:57:33 UTC

Lmdb

LMDB00192

Secondary Accession Numbers

None

Metabolite Identification

Common Name

D-Ribulose 5-phosphate

Description

D-Ribulose 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. D-Ribulose 5-phosphate is a metabolite in the following pathways: pentose phosphate pathway, pentose and glucuronate interconversions, and riboflavin metabolism (KEGG). D-Ribulose 5-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Within humans, D-ribulose 5-phosphate participates in a number of enzymatic reactions. In particular, D-ribulose 5-phosphate can be converted into D-ribose 5-phosphate through its interaction with the enzyme ribose-5-phosphate isomerase. In addition, D-ribulose 5-phosphate can be converted into xylulose 5-phosphate; which is mediated by the enzyme ribulose-phosphate 3-epimerase. In humans, D-ribulose 5-phosphate is involved in pentose phosphate pathway. Outside of the human body, D-Ribulose 5-phosphate has been detected, but not quantified in, several different foods, such as winter squash, japanese chestnuts, barley, strawberries, and abiyuchs. This could make D-ribulose 5-phosphate a potential biomarker for the consumption of these foods. D-Ribulose 5-phosphate, with regard to humans, has been found to be associated with several diseases such as lewy body disease, frontotemporal dementia, and alzheimer's disease; D-ribulose 5-phosphate has also been linked to the inborn metabolic disorder transaldolase deficiency.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
D-Erythro-pent-2-ulose 5-(dihydrogen phosphate)	ChEBI
D-Erythro-pent-2-ulose 5-(dihydrogen phosphoric acid)	Generator
D-Ribulose 5-phosphoric acid	Generator
Ribulose 5-phosphate	HMDB
Ribulose 5-phosphate, (D)-isomer	HMDB
Ribulose 5-phosphate, (L)-isomer	HMDB

Chemical Formula

C₅H₁₁O₈P

Average Molecular Weight

230.1098

Monoisotopic Molecular Weight

230.01915384

IUPAC Name

{[(2R,3R)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid

Traditional Name

Ara

CAS Registry Number

4151-19-3

SMILES

OCC(=O)[C@H](O)[C@H](O)COP(O)(O)=O

InChI Identifier

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5+/m1/s1

InChI Key

FNZLKVNUWIIPSJ-UHNVWZDZSA-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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Monosaccharide phosphate
Monoalkyl phosphate
Acyloin
Beta-hydroxy ketone
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Polyol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
Primary alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ribulose 5-phosphate (CHEBI:17363 )

Ontology

Status

Detected but not Quantified

Origin

Not Available

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
logP	-1.8	ALOGPS
logP	-2.8	ChemAxon
logS	-0.95	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	144.52 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	42.47 m³·mol⁻¹	ChemAxon
Polarizability	17.95 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)	splash10-0a4i-2936000000-adde71232cd79c7c92aa	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)	splash10-0a4i-2947000000-ae4da5853e1b24392d1d	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0a4j-1935000000-dfb75754c9a7045f108f	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0a4j-1935000000-31be2cabeeebc480c1b8	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0pba-1924000000-11aca642135096a8e378	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014j-1943000000-34588179b9bd7796e907	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0pbj-2914000000-d91b422c677fd9231297	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0592-9800000000-d336b0e2eff1402939d8	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-029t-9327100000-10a5d90f15e25f16925c	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-004j-9010000000-49c14e85e3a3dee61721	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QTOF 10V, positive	splash10-00ec-0970000000-6e833fd34cda3327e6ae	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QTOF 15V, positive	splash10-007o-0930000000-72bf0b63618d4b200421	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QTOF 17V, positive	splash10-007o-0920000000-fe7037f21876801587ec	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QTOF 20V, positive	splash10-007o-0910000000-5dacb5e16b8a32f079c0	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QTOF 23V, positive	splash10-007o-0900000000-1d35981b82e13d258d9d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QTOF 25V, positive	splash10-00ec-0900000000-23938808d1a77a77203d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QTOF 27V, positive	splash10-00dl-0900000000-abc2b8be05c39eef69e6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, positive	splash10-00di-0190000000-f09b49c51cfa01814ef3	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, positive	splash10-00di-0490000000-acd1f6a33bd147e29ac3	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, positive	splash10-00ec-0980000000-e8070ccdca137f841520	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 7V, positive	splash10-007o-0940000000-0e8aaff469756dafc2ee	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 8V, positive	splash10-000x-0920000000-bef5b5a1a6528a057748	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 9V, positive	splash10-000x-0910000000-7a57ccc066185b618224	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 11V, positive	splash10-007o-0900000000-0412a8fa5b22fb04ec87	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 12V, positive	splash10-007o-0900000000-e655723668ec0397d76e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 14V, positive	splash10-00dl-0900000000-4d7aa68ec0ea7a05fe8b	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 18V, positive	splash10-00di-1900000000-ef58c4a909999b72f8fa	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 22V, positive	splash10-0229-4900000000-6c4c40d2771cf3aec25f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-3790000000-6f5913e9948fa7667e41	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btd-9710000000-3724bb9f611bbdc1fe11	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-8bc9cecb2dddad8ca5e3	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-9520000000-c36fdbcc1d3b19b2fafd	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-b67b8ea484aa4ddb40e3	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-82b17cf4f5a8c927fe64	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Not Available

Biofluid Locations and Tissue Locations

Milk

Concentrations

Biofluid	Status	Value	Condition	Species	Reference	Details
Milk	Detected but not Quantified	Not Applicable	Not Available	Bovine	25599412	details
Milk	Detected but not Quantified	Not Applicable	Not Available	Bovine	23438684	details