Cannabis Compound Database: Showing Compound Card for D-Ribose 5-phosphate (CDB004923)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (16)transporters (1) Show 28 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 18:50:55 UTC

Updated at

2020-11-18 16:39:00 UTC

CannabisDB ID

CDB004923

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

D-Ribose 5-phosphate

Description

D-Ribose 5-phosphate, also known as R-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). A D-Ribose 5-phosphate with an alpha-configuration at anomeric position. D-Ribose 5-phosphate exists in all eukaryotes, ranging from yeast 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 through the action of the enzyme ribokinase. In humans, D-ribose 5-phosphate is involved in the metabolic disorder called the ribose-5-phosphate isomerase deficiency pathway. D-Ribose 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
5-O-Phosphono-alpha-D-ribofuranose	ChEBI
alpha-D-Ribose 5-phosphate	ChEBI
5-O-Phosphono-a-D-ribofuranose	Generator
5-O-Phosphono-α-D-ribofuranose	Generator
a-D-Ribose 5-phosphate	Generator
a-D-Ribose 5-phosphoric acid	Generator
alpha-D-Ribose 5-phosphoric acid	Generator
Α-D-ribose 5-phosphate	Generator
Α-D-ribose 5-phosphoric acid	Generator
D-Ribose 5-phosphoric acid	Generator
D-Ribofuranose 5-phosphate	HMDB
R-5-p	HMDB
Ribose 5-(dihydrogen phosphate)	HMDB
Ribose 5-monophosphate	HMDB
Ribose 5-phosphate	HMDB
alpha-D-Ribose-5-phosphate	HMDB
Α-D-ribose-5-phosphate	HMDB
D-Ribose 5-phosphate	HMDB

Chemical Formula

C₅H₁₁O₈P

Average Molecular Weight

230.11

Monoisotopic Molecular Weight

230.0192

IUPAC Name

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

Traditional Name

α-D-ribose 5-phosphate

CAS Registry Number

34980-65-9

SMILES

O[C@H]1O[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-AIHAYLRMSA-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-ribofuranose 5-phosphate (CHEBI:18189 )

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Poaceae

Biological location:

Biofluid and excreta:

Subcellular:

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	-2.1	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	18.25 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

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
GC-MS	D-Ribose 5-phosphate, 5 TMS, GC-MS Spectrum	splash10-014j-1942000000-8c3468eabd202324a3ae	Spectrum
GC-MS	D-Ribose 5-phosphate, 5 TMS, GC-MS Spectrum	splash10-0fr2-1943000000-b5d1468f33c224a23bd3	Spectrum
GC-MS	D-Ribose 5-phosphate, 5 TMS; 1 MEOX, GC-MS Spectrum	splash10-00di-9532000000-693524b08b2ccd6179c5	Spectrum
GC-MS	D-Ribose 5-phosphate, 5 TMS; 1 MEOX, GC-MS Spectrum	splash10-00di-9421000000-dbcd94d0a73f35716059	Spectrum
GC-MS	D-Ribose 5-phosphate, non-derivatized, GC-MS Spectrum	splash10-014j-1942000000-8c3468eabd202324a3ae	Spectrum
GC-MS	D-Ribose 5-phosphate, non-derivatized, GC-MS Spectrum	splash10-0fr2-1943000000-b5d1468f33c224a23bd3	Spectrum
GC-MS	D-Ribose 5-phosphate, non-derivatized, GC-MS Spectrum	splash10-00di-9532000000-693524b08b2ccd6179c5	Spectrum
GC-MS	D-Ribose 5-phosphate, non-derivatized, GC-MS Spectrum	splash10-00di-9421000000-dbcd94d0a73f35716059	Spectrum
Predicted GC-MS	D-Ribose 5-phosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0002-9320000000-9b5fdcbd0e9ea3ece549	Spectrum
Predicted GC-MS	D-Ribose 5-phosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-Ribose 5-phosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0002-9320000000-7f3d980d223a6b9f5f3f	2020-03-06	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0002-9000000000-a5df0614f5cbd8b55405	2020-03-06	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-056r-0090700000-ea86961dacc666b5fc7d	2020-03-06	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0002-9100000000-6cbb3e84820a37a47fbb	2020-03-06	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-004i-0090000000-10949588537786dbae1e	2020-03-06	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0a4i-0000900000-10d8b4fd09ed514cc12e	2020-03-06	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-002b-9000000000-49264a7584727750bd70	2020-03-06	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0002-9100000000-6cbb3e84820a37a47fbb	2020-03-06	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-004i-0090000000-10949588537786dbae1e	2020-03-06	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0a4i-0000900000-10d8b4fd09ed514cc12e	2020-03-06	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-002b-9000000000-340deaecb0169ce2acd3	2020-03-06	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-1790000000-a3ced14cd6c2537c6d8f	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-5940000000-8bcb763477232ce1dd2c	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00y1-9300000000-ff5bd2489969fca00eb7	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-7190000000-184075252146923d2684	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-917b1eb059131caa49ac	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-579393c266ea056c9e74	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0159-1900000000-c7b876b70c54c880bdf3	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01c1-9600000000-649e860a529bc7f5b4f8	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-053s-9000000000-f9d938955d2446665511	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004j-9040000000-9ee7ba6767ffa3f356db	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-22	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)	Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Spectrum

Pathways

Name	SMPDB/Pathwhiz	KEGG
Purine Metabolism
Pentose Phosphate Pathway
Glucose-6-phosphate dehydrogenase deficiency		Not Available
Ribose-5-phosphate isomerase deficiency		Not Available
Transaldolase deficiency		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
ADP-ribose pyrophosphatase, mitochondrial	NUDT9	4q22.1	Q9BW91	details
Transketolase-like protein 1	TKTL1	Xq28	P51854	details
Transketolase	TKT	3p14.3	P29401	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
Phosphoglucomutase-2	PGM2	4p14	Q96G03	details
Transketolase-like protein 2	TKTL2	4q32.2	Q9H0I9	details
Putative uncharacterized protein PRPS2	PRPS2		A6NMS2	details
Ribose-phosphate pyrophosphokinase			Q53FW2	details
Manganese-dependent ADP-ribose/CDP-alcohol diphosphatase	ADPRM	17p13.1	Q3LIE5	details

Transporters

Protein Name	Gene Name	Locus	Uniprot ID	Details
Transient receptor potential cation channel subfamily M member 2	TRPM2	21q22.3	O94759	details

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
Phosphoglucomutase-2	PGM2	4p14	Q96G03	details
Transketolase-like protein 2	TKTL2	4q32.2	Q9H0I9	details
Ribose-phosphate pyrophosphokinase			Q53FW2	details
Manganese-dependent ADP-ribose/CDP-alcohol diphosphatase	ADPRM	17p13.1	Q3LIE5	details

Receptors

Protein Name	Gene Name	Locus	Uniprot ID	Details
Transient receptor potential cation channel subfamily M member 2	TRPM2	21q22.3	O94759	details

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0001548

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB001615

KNApSAcK ID

Not Available

Chemspider ID

389102

KEGG Compound ID

C03736

BioCyc ID

RIBOSE-5P

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440101

PDB ID

Not Available

ChEBI ID

18189

References

General References

Not Available

Only showing the first 10 proteins. There are 28 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. ADP-ribose pyrophosphatase, mitochondrial

General function:: Involved in hydrolase activity
Specific function:: Hydrolyzes ADP-ribose (ADPR) to AMP and ribose 5'-phosphate.
Gene Name:: NUDT9
Uniprot ID:: Q9BW91
Molecular weight:: 35448.725

Enzyme Details

6. 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

7. 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

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

Transporters

Enzyme Details

1. Transient receptor potential cation channel subfamily M member 2

General function:: Involved in ion channel activity
Specific function:: Nonselective, voltage-independent cation channel mediating sodium and calcium ion influx in response to oxidative stress. Extracellular calcium passes through the channel and acts from the intracellular side as a positive regulator in channel activation. Activated by ADP-ribose, nicotinamide adenine dinucleotide (NAD(+)), reactive nitrogen species and arachidonic acid. Inactivated by intracellular ATP. Confers susceptibility to cell death following oxidative stress. Isoform 2 does not seem to be regulated by ADPR. Has ADP-ribose pyrophosphatase activity.
Gene Name:: TRPM2
Uniprot ID:: O94759
Molecular weight:: 171224.9

Only showing the first 10 proteins. There are 28 proteins in total.

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Showing Compound Card for D-Ribose 5-phosphate (CDB004923)

Structure for CDB004923 (D-Ribose 5-phosphate)

Enzymes

Transporters