Livestock Metabolome Database: Showing metabocard for D-Ribose 5-phosphate (LMDB00792)

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

Record Information

Version

1.0

Creation Date

2016-07-30 18:19:47 UTC

Update Date

2016-08-02 20:15:38 UTC

Lmdb

LMDB00792

Secondary Accession Numbers

None

Metabolite Identification

Common Name

D-Ribose 5-phosphate

Description

D-Ribose 5-phosphate, also known as D-ribose-5-p, 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-Ribose 5-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). D-Ribose 5-phosphate exists in all living species, ranging from bacteria to humans. Within humans, D-ribose 5-phosphate participates in a number of enzymatic reactions. In particular, D-ribose 5-phosphate can be biosynthesized from D-ribulose 5-phosphate; which is mediated by the enzyme ribose-5-phosphate isomerase. In addition, D-ribose 5-phosphate can be biosynthesized from D-ribose; which is catalyzed by the enzyme ribokinase. In humans, D-ribose 5-phosphate is involved in pentose phosphate pathway. Outside of the human body, D-Ribose 5-phosphate has been detected, but not quantified in, milk (cow) and rices. This could make D-ribose 5-phosphate a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
D-Ribose 5'-phosphate	ChEBI
D-Ribose-5-p	ChEBI
Ribose 5-phosphate	ChEBI
D-Ribose 5'-phosphoric acid	Generator
Ribose 5-phosphoric acid	Generator
D-Ribose 5-phosphoric acid	Generator
D-Ribose-5-phosphate	HMDB
D-Ribose-5-phosphorate	HMDB
D-Ribose-5-phosphoric acid	HMDB
Ribose-5-p	HMDB
Ribose-5-phosphate	HMDB
Ribose-5-phosphorate	HMDB
Ribose-5-phosphoric acid	HMDB
Ribose-5P	HMDB
Ribose-5-phosphoric acid, (D-ribose)-isomer	HMDB
Ribose phosphate	HMDB
Ribose-5-phosphoric acid, (D-ribofuranose)-isomer	HMDB
Ribose 5-monophosphate	HMDB

Chemical Formula

C₅H₁₁O₈P

Average Molecular Weight

230.1098

Monoisotopic Molecular Weight

230.01915384

IUPAC Name

{[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

D-ribofuranose 5-phosphate

CAS Registry Number

Not Available

SMILES

OC1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5?/m1/s1

InChI Key

KTVPXOYAKDPRHY-SOOFDHNKSA-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
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Tetrahydrofuran
1,2-diol
Secondary alcohol
Hemiacetal
Polyol
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-ribose 5-phosphate (CHEBI:52742 )

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	-2.1	ALOGPS
logP	-2.4	ChemAxon
logS	-0.84	ALOGPS
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	136.68 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	40.83 m³·mol⁻¹	ChemAxon
Polarizability	18.21 Å³	ChemAxon
Number of Rings	1	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-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)	splash10-014j-1942000000-8c3468eabd202324a3ae	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)	splash10-0fr2-1943000000-b5d1468f33c224a23bd3	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)	splash10-00di-9532000000-693524b08b2ccd6179c5	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)	splash10-00di-9421000000-dbcd94d0a73f35716059	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014j-1942000000-8c3468eabd202324a3ae	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0fr2-1943000000-b5d1468f33c224a23bd3	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-9532000000-693524b08b2ccd6179c5	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-9421000000-dbcd94d0a73f35716059	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9320000000-9b5fdcbd0e9ea3ece549	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-06vi-9164100000-2305f99f73e0c553d514	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0002-9320000000-7f3d980d223a6b9f5f3f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0002-9000000000-a5df0614f5cbd8b55405	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-056r-0090700000-ea86961dacc666b5fc7d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0002-9100000000-6cbb3e84820a37a47fbb	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-004i-0090000000-10949588537786dbae1e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0a4i-0000900000-10d8b4fd09ed514cc12e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-002b-9000000000-49264a7584727750bd70	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0002-9100000000-6cbb3e84820a37a47fbb	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-004i-0090000000-10949588537786dbae1e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0a4i-0000900000-10d8b4fd09ed514cc12e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-002b-9000000000-340deaecb0169ce2acd3	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-1790000000-a3ced14cd6c2537c6d8f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-5940000000-8bcb763477232ce1dd2c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00y1-9300000000-ff5bd2489969fca00eb7	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-7190000000-184075252146923d2684	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-917b1eb059131caa49ac	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-579393c266ea056c9e74	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
1D NMR	1H NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D 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	Kurt J. Boudonck,...	details
Milk	Detected but not Quantified	Not Applicable	Not Available	Bovine	Kurt J. Boudonck,...	details