Bovine Metabolome Database: Showing metabocard for D-Ribulose (BMDB0000621)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:33:43 UTC

Update Date

2020-05-11 20:37:20 UTC

BMDB ID

BMDB0000621

Secondary Accession Numbers

BMDB00621

Metabolite Identification

Common Name

D-Ribulose

Description

D-Ribulose, also known as D-arabinoketose or D-rul, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Ribulose is an extremely weak basic (essentially neutral) compound (based on its pKa). D-Ribulose exists in all living organisms, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
D-Arabinoketose	ChEBI
D-Arabinulose	ChEBI
D-Erythro-2-pentulose	ChEBI
D-Erythro-pent-2-ulose	ChEBI
D-Riboketose	ChEBI
D-Rul	ChEBI
D(-)-Ribulose	HMDB
D-Adonose	HMDB
D-Araboketose	HMDB
D-erythro-2-Keptopentose	HMDB
D-erythro-Pentulose	HMDB
D-Erythropentulose	HMDB
D-Ribosone	HMDB
Ribulose, (erythro-L)-isomer	MeSH, HMDB
DL-erythro-Pentulose	MeSH, HMDB
Ribulose	MeSH, HMDB
Ribulose, (erythro-D)-isomer	MeSH, HMDB

Chemical Formula

C₅H₁₀O₅

Average Molecular Weight

150.1299

Monoisotopic Molecular Weight

150.05282343

IUPAC Name

(3R,4R)-1,3,4,5-tetrahydroxypentan-2-one

Traditional Name

D-ribulose

CAS Registry Number

488-84-6

SMILES

OC[C@@H](O)[C@@H](O)C(=O)CO

InChI Identifier

InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2/t3-,5-/m1/s1

InChI Key

ZAQJHHRNXZUBTE-NQXXGFSBSA-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
Beta-hydroxy ketone
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Polyol
Organic oxide
Hydrocarbon derivative
Primary alcohol
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ribulose (CHEBI:17173 )

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm

Physical Properties

State

Solid

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	-2.2	ALOGPS
logP	-2.6	ChemAxon
logS	0.65	ALOGPS
pKa (Strongest Acidic)	10.57	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	31.6 m³·mol⁻¹	ChemAxon
Polarizability	13.47 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
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 4 TMS)	splash10-0lk9-2940000000-d972512c3992f5630d13	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0uyi-1920000000-4abe1c31075112542e5a	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0uyi-1920000000-cb182758b043e586b8d1	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0lk9-2940000000-d972512c3992f5630d13	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0uyi-1920000000-4abe1c31075112542e5a	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0uyi-1920000000-cb182758b043e586b8d1	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-9000000000-5e0dfc74544a16cb6a2b	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-00e9-9182200000-14fd007ef0237ffd6a29	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-000i-9200000000-afb0904788db599c35ed	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-02t9-7900000000-10c3cccbf8dbb87ffeeb	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0229-9800000000-a764f771911e773c02ef	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-1900000000-9e2cd6df86b714a2a578	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-9300000000-d2b653e8f893ae77c1e3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dm-9000000000-a0e9bde284b6cf02f608	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000j-9400000000-eff46a0627a1f3901e27	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06ri-9100000000-3ed3e568d42e85a3a856	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-6e049d13c9659949bd3e	View in MoNA

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Fibroblasts
Placenta

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0160638

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00001131

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

D-RIBULOSE

BiGG ID

Not Available

Wikipedia Link

Ribulose

METLIN ID

Not Available

PubChem Compound

151261

PDB ID

Not Available

ChEBI ID

17173

References

Synthesis Reference

Drueckhammer, D.G.; Durrwachter, J.R.; Pederson, R.L.; Crans, D.C.; Wong, C.H. Reversible and in situ formation of organic arsenates and vanadates as organic phosphate mimics in enzymatic-reactions - mechanistic investigation of aldol reactions and synthetic applications. J.Org. Chem. 1989, 54, 70.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for D-Ribulose (BMDB0000621)

Structure for BMDB0000621 (D-Ribulose)