Cannabis Compound Database: Showing Compound Card for D-Ribulose 5-phosphate (CDB004850)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (15) Show 23 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 18:43:14 UTC

Updated at

2020-11-18 16:38:51 UTC

CannabisDB ID

CDB004850

Secondary Accession Numbers

Not Available

Cannabis Compound 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. D-Ribulose 5-phosphate is expected to be in Cannabis as all living plants are known to produce and metabolize it.

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

230.11

Monoisotopic Molecular Weight

230.0192

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

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Animal

Biological location:

Organ and components:

Prostate

Biofluid and excreta:

Subcellular:

Endoplasmic reticulum

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	-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	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
GC-MS	D-Ribulose 5-phosphate, 1 MEOX; 5 TMS, GC-MS Spectrum	splash10-0a4i-2936000000-adde71232cd79c7c92aa	Spectrum
GC-MS	D-Ribulose 5-phosphate, 1 MEOX; 5 TMS, GC-MS Spectrum	splash10-0a4i-2947000000-ae4da5853e1b24392d1d	Spectrum
GC-MS	D-Ribulose 5-phosphate, non-derivatized, GC-MS Spectrum	splash10-0a4j-1935000000-dfb75754c9a7045f108f	Spectrum
GC-MS	D-Ribulose 5-phosphate, non-derivatized, GC-MS Spectrum	splash10-0a4j-1935000000-31be2cabeeebc480c1b8	Spectrum
GC-MS	D-Ribulose 5-phosphate, non-derivatized, GC-MS Spectrum	splash10-0pba-1924000000-11aca642135096a8e378	Spectrum
GC-MS	D-Ribulose 5-phosphate, non-derivatized, GC-MS Spectrum	splash10-014j-1943000000-34588179b9bd7796e907	Spectrum
GC-MS	D-Ribulose 5-phosphate, non-derivatized, GC-MS Spectrum	splash10-0pbj-2914000000-d91b422c677fd9231297	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0592-9800000000-d336b0e2eff1402939d8	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-029t-9327100000-10a5d90f15e25f16925c	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_1_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_1_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_1_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_2_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_2_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_2_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_2_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_2_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribulose 5-phosphate, TMS_2_9, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-004j-9010000000-49c14e85e3a3dee61721	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - QTOF 10V, positive	splash10-00ec-0970000000-6e833fd34cda3327e6ae	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - QTOF 15V, positive	splash10-007o-0930000000-72bf0b63618d4b200421	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - QTOF 17V, positive	splash10-007o-0920000000-fe7037f21876801587ec	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - QTOF 20V, positive	splash10-007o-0910000000-5dacb5e16b8a32f079c0	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - QTOF 23V, positive	splash10-007o-0900000000-1d35981b82e13d258d9d	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - QTOF 25V, positive	splash10-00ec-0900000000-23938808d1a77a77203d	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - QTOF 27V, positive	splash10-00dl-0900000000-abc2b8be05c39eef69e6	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, positive	splash10-00di-0190000000-f09b49c51cfa01814ef3	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, positive	splash10-00di-0490000000-acd1f6a33bd147e29ac3	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, positive	splash10-00ec-0980000000-e8070ccdca137f841520	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 7V, positive	splash10-007o-0940000000-0e8aaff469756dafc2ee	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 8V, positive	splash10-000x-0920000000-bef5b5a1a6528a057748	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 9V, positive	splash10-000x-0910000000-7a57ccc066185b618224	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 11V, positive	splash10-007o-0900000000-0412a8fa5b22fb04ec87	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 12V, positive	splash10-007o-0900000000-e655723668ec0397d76e	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 14V, positive	splash10-00dl-0900000000-4d7aa68ec0ea7a05fe8b	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 18V, positive	splash10-00di-1900000000-ef58c4a909999b72f8fa	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 22V, positive	splash10-0229-4900000000-6c4c40d2771cf3aec25f	2020-07-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-3790000000-6f5913e9948fa7667e41	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btd-9710000000-3724bb9f611bbdc1fe11	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-8bc9cecb2dddad8ca5e3	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-9520000000-c36fdbcc1d3b19b2fafd	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-b67b8ea484aa4ddb40e3	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-82b17cf4f5a8c927fe64	2015-09-15	View Spectrum

NMR

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Pentose Phosphate Pathway
Glucose-6-phosphate dehydrogenase deficiency		Not Available
Ribose-5-phosphate isomerase deficiency		Not Available
Transaldolase deficiency		Not Available
Warburg Effect		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
Ribose-phosphate pyrophosphokinase 3	PRPS1L1	7p21.1	P21108	details
ADP-sugar pyrophosphatase	NUDT5	10p14	Q9UKK9	details
Ribose-phosphate pyrophosphokinase 1	PRPS1	Xq21.32-q24	P60891	details
Ribose-phosphate pyrophosphokinase 2	PRPS2	Xp22.2	P11908	details
Transketolase-like protein 1	TKTL1	Xq28	P51854	details
Transketolase	TKT	3p14.3	P29401	details
6-phosphogluconate dehydrogenase, decarboxylating	PGD	1p36.22	P52209	details
Ribokinase	RBKS	2p23.3	Q9H477	details
Phosphoglucomutase-1	PGM1	1p31	P36871	details
Phosphoacetylglucosamine mutase	PGM3	6q14.1-q15	O95394	details
Ribose-5-phosphate isomerase	RPIA	2p11.2	P49247	details
Putative uncharacterized protein RPE	RPE	2q32-q33.3	Q53TV9	details
Ribulose-phosphate 3-epimerase	RPE	2q32-q33.3	Q96AT9	details
Transketolase-like protein 2	TKTL2	4q32.2	Q9H0I9	details
Putative uncharacterized protein PGD	PGD	1p36.3-p36.13	A9Z1X1	details

Transporters

Not Available

Metal Bindings

Protein Name	Gene Name	Locus	Uniprot ID	Details
Ribose-phosphate pyrophosphokinase 3	PRPS1L1	7p21.1	P21108	details
Ribose-phosphate pyrophosphokinase 1	PRPS1	Xq21.32-q24	P60891	details
Ribose-phosphate pyrophosphokinase 2	PRPS2	Xp22.2	P11908	details
Transketolase-like protein 1	TKTL1	Xq28	P51854	details
Phosphoglucomutase-1	PGM1	1p31	P36871	details
Phosphoacetylglucosamine mutase	PGM3	6q14.1-q15	O95394	details
Ribulose-phosphate 3-epimerase	RPE	2q32-q33.3	Q96AT9	details
Transketolase-like protein 2	TKTL2	4q32.2	Q9H0I9	details

Receptors

Not Available

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0000618

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022145

KNApSAcK ID

Not Available

Chemspider ID

388327

KEGG Compound ID

C00199

BioCyc ID

RIBULOSE-5P

BiGG ID

Not Available

Wikipedia Link

Ribulose_5-phosphate

METLIN ID

Not Available

PubChem Compound

439184

PDB ID

Not Available

ChEBI ID

17363

References

General References

Not Available

Only showing the first 10 proteins. There are 23 proteins in total.

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Enzymes

Enzyme Details

1. Ribose-phosphate pyrophosphokinase 3

General function:: Involved in magnesium ion binding
Specific function:: Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
Gene Name:: PRPS1L1
Uniprot ID:: P21108
Molecular weight:: 34838.915

Enzyme Details

2. ADP-sugar pyrophosphatase

General function:: Involved in hydrolase activity
Specific function:: Hydrolyzes with similar activities ADP-ribose ADP-mannose, ADP-glucose, 8-oxo-GDP and 8-oxo-dGDP. Can also hydrolyze other nucleotide sugars with low activity.
Gene Name:: NUDT5
Uniprot ID:: Q9UKK9
Molecular weight:: 24327.41

Enzyme Details

3. Ribose-phosphate pyrophosphokinase 1

General function:: Involved in magnesium ion binding
Specific function:: Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
Gene Name:: PRPS1
Uniprot ID:: P60891
Molecular weight:: 12324.195

Enzyme Details

4. Ribose-phosphate pyrophosphokinase 2

General function:: Involved in magnesium ion binding
Specific function:: Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
Gene Name:: PRPS2
Uniprot ID:: P11908
Molecular weight:: 35054.06

Enzyme Details

5. Transketolase-like protein 1

General function:: Involved in catalytic activity
Specific function:: Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate (By similarity).
Gene Name:: TKTL1
Uniprot ID:: P51854
Molecular weight:: 59302.195

Enzyme Details

6. Transketolase

General function:: Involved in catalytic activity
Specific function:: Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.
Gene Name:: TKT
Uniprot ID:: P29401
Molecular weight:: 67876.95

Enzyme Details

7. 6-phosphogluconate dehydrogenase, decarboxylating

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH (By similarity).
Gene Name:: PGD
Uniprot ID:: P52209
Molecular weight:: 53139.56

Enzyme Details

8. Ribokinase

General function:: Involved in ribokinase activity
Specific function:: Not Available
Gene Name:: RBKS
Uniprot ID:: Q9H477
Molecular weight:: 34142.685

Enzyme Details

9. Phosphoglucomutase-1

General function:: Involved in intramolecular transferase activity, phosphotransferases
Specific function:: This enzyme participates in both the breakdown and synthesis of glucose.
Gene Name:: PGM1
Uniprot ID:: P36871
Molecular weight:: 63789.985

Enzyme Details

10. Phosphoacetylglucosamine mutase

General function:: Involved in intramolecular transferase activity, phosphotransferases
Specific function:: Interconverts GlcNAc-6-P and GlcNAc-1-P.
Gene Name:: PGM3
Uniprot ID:: O95394
Molecular weight:: 62940.905

Only showing the first 10 proteins. There are 23 proteins in total.

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Showing Compound Card for D-Ribulose 5-phosphate (CDB004850)

Structure for CDB004850 (D-Ribulose 5-phosphate)

Enzymes