Cannabis Compound Database: Showing Compound Card for Xanthosine (CDB004842)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (9) Show 17 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 18:42:25 UTC

Updated at

2020-12-07 19:11:05 UTC

CannabisDB ID

CDB004842

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

Xanthosine

Description

Xanthosine, also known as xanthine riboside, belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety. Xanthosine is an extremely weak basic (essentially neutral) compound (based on its pKa). Xanthosine exists in all living species, ranging from bacteria to humans. Within humans, xanthosine participates in a number of enzymatic reactions. In particular, xanthosine can be biosynthesized from xanthylic acid through the action of the enzyme cytosolic purine 5'-nucleotidase. In addition, xanthosine can be converted into xanthine and ribose 1-phosphate; which is mediated by the enzyme purine nucleoside phosphorylase. A purine nucleoside in which xanthine is attached to ribofuranose via a beta-N(9)-glycosidic bond. In humans, xanthosine is involved in the metabolic disorder called the lesch-nyhan syndrome (lns) pathway. Xanthosine 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
9-beta-D-Ribofuranosyl-3,9-dihydro-1H-purine-2,6-dione	ChEBI
9-beta-D-Ribofuranosylxanthine	ChEBI
Xanthine 9-beta-D-ribofuranoside	ChEBI
Xanthine riboside	ChEBI
9-b-D-Ribofuranosyl-3,9-dihydro-1H-purine-2,6-dione	Generator
9-Β-D-ribofuranosyl-3,9-dihydro-1H-purine-2,6-dione	Generator
9-b-D-Ribofuranosylxanthine	Generator
9-Β-D-ribofuranosylxanthine	Generator
Xanthine 9-b-D-ribofuranoside	Generator
Xanthine 9-β-D-ribofuranoside	Generator
3,9-Dihydro-9-b-D-ribofuranosyl-1H-purine-2,6-dione	HMDB
3,9-Dihydro-9-beta-delta-ribofuranosyl-1H-purine-2,6-dione	HMDB
3,9-Dihydro-9-D-ribofuranosyl-1H-purine-2,6-dione	HMDB
3,9-Dihydro-9-delta-ribofuranosyl-1H-purine-2,6-dione	HMDB
9-beta-delta-Ribofuranosylxanthine	HMDB
9-D-Ribofuranosylxanthine	HMDB
9-delta-Ribofuranosylxanthine	HMDB
9 beta-D-Ribofuranosylxanthine	HMDB

Chemical Formula

C₁₀H₁₂N₄O₆

Average Molecular Weight

284.23

Monoisotopic Molecular Weight

284.0757

IUPAC Name

9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-9H-purine-2,6-diol

Traditional Name

9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purine-2,6-diol

CAS Registry Number

146-80-5

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=C(O)N=C2O

InChI Identifier

InChI=1S/C10H12N4O6/c15-1-3-5(16)6(17)9(20-3)14-2-11-4-7(14)12-10(19)13-8(4)18/h2-3,5-6,9,15-17H,1H2,(H2,12,13,18,19)/t3-,5-,6-,9-/m1/s1

InChI Key

UBORTCNDUKBEOP-UUOKFMHZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Not Available

Direct Parent

Purine nucleosides

Alternative Parents

Substituents

Purine nucleoside
Glycosyl compound
N-glycosyl compound
Xanthine
6-oxopurine
Purinone
Pentose monosaccharide
Purine
Imidazopyrimidine
Alkaloid or derivatives
Pyrimidone
Pyrimidine
Monosaccharide
N-substituted imidazole
Imidazole
Heteroaromatic compound
Tetrahydrofuran
Azole
Vinylogous amide
Lactam
Urea
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

xanthosines (CHEBI:18107 )
Purine alkaloids (C01762 )

Ontology

Physiological effect

Health effect:

Health condition:

Uremia

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Animal

Plant:

Biological location:

Tissue and substructures:

Placenta

Biofluid and excreta:

Subcellular:

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	-1.6	ALOGPS
logP	-1.2	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	11.33	ChemAxon
pKa (Strongest Basic)	0.078	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	153.98 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	62.4 m³·mol⁻¹	ChemAxon
Polarizability	25.55 Å³	ChemAxon
Number of Rings	3	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	Xanthosine, non-derivatized, GC-MS Spectrum	splash10-0032-0963000000-08e48347b76242e521e6	Spectrum
GC-MS	Xanthosine, non-derivatized, GC-MS Spectrum	splash10-0032-0963000000-08e48347b76242e521e6	Spectrum
Predicted GC-MS	Xanthosine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-05fu-9250000000-9694fd3e1c7370e27866	Spectrum
Predicted GC-MS	Xanthosine, 5 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0059-2110049000-cbeec0d3159947f31d5f	Spectrum
Predicted GC-MS	Xanthosine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_1_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_1_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_2_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_2_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_2_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_2_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_2_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_2_9, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_2_10, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_3_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_3_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_3_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_3_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Xanthosine, TMS_3_5, 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)	splash10-0udi-0900000000-e3e76f5bf26f34680c35	Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0udi-7900000000-6e1f70509da5adf99678	Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0a4r-9500000000-3cce63949eec45fa9204	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0udi-0910000000-b2c7e01e9105bba310aa	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0udi-0910000000-e6e1d21c0d22b3ad2821	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0udi-0910000000-b2c7e01e9105bba310aa	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0udi-0910000000-e6e1d21c0d22b3ad2821	Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0uk9-8900000000-b0f93d77cf447ada9ed9	Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-1900000000-19c92745c311f6435fd3	Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-0udi-2910000000-6f97748a645ffb972e67	Spectrum
MS/MS	LC-MS/MS Spectrum - 0V, Positive	splash10-03di-0900000000-a999e0e022115ec9ec7a	Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0910000000-63959f162289e268a620	Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-0zg0-8900000000-f8aa72afbf821cfb2cf2	Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-4900000000-943b0d3fbe3cd8345d54	Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-06rl-9400000000-3072bed88bbdca66de69	Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0udi-0900000000-f3b10c4bf03522fbd1ff	Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0940000000-f59c82b81d81cd9c6b68	Spectrum
MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-0udi-0900000000-e0cf07456bb1d35aec56	Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-0900000000-6189db27589e05c3f039	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0940000000-2394018b58d040767e06	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-fec1dd4fe1f5f7e56482	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0f79-1900000000-850759ea222062877fa9	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f8c-1590000000-4fdccf755ee2b8b75ac6	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0f6x-6910000000-308e886a8ecec5d8cd09	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9500000000-af861bef2f6b2f10296c	Spectrum

NMR

Type	Description	View
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	13C NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	13C NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	13C NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	13C NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	13C NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	13C NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	13C NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	13C NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	13C NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
1D NMR	13C NMR Spectrum	Spectrum
1D NMR	1H NMR Spectrum	Spectrum
2D NMR	[1H,1H] 2D NMR Spectrum	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Spectrum

Pathways

Name	SMPDB/Pathwhiz	KEGG
Purine Metabolism
Adenosine Deaminase Deficiency		Not Available
Adenylosuccinate Lyase Deficiency		Not Available
Gout or Kelley-Seegmiller Syndrome		Not Available
Lesch-Nyhan Syndrome (LNS)		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
5'-nucleotidase	NT5E	6q14-q21	P21589	details
Cytosolic 5'-nucleotidase 1B	NT5C1B	2p24.2	Q96P26	details
Cytosolic 5'-nucleotidase 1A	NT5C1A	1p34.3-p33	Q9BXI3	details
5'(3')-deoxyribonucleotidase, cytosolic type	NT5C		Q8TCD5	details
5'(3')-deoxyribonucleotidase, mitochondrial	NT5M		Q9NPB1	details
Inosine triphosphate pyrophosphatase	ITPA	20p	Q9BY32	details
Cytosolic 5'-nucleotidase 3	NT5C3	7p14.3	Q9H0P0	details
Cytosolic purine 5'-nucleotidase	NT5C2	10q24.32	P49902	details
Purine nucleoside phosphorylase	PNP	14q13.1	P00491	details

Transporters

Not Available

Metal Bindings

Protein Name	Gene Name	Locus	Uniprot ID	Details
5'-nucleotidase	NT5E	6q14-q21	P21589	details
Cytosolic 5'-nucleotidase 1B	NT5C1B	2p24.2	Q96P26	details
Cytosolic 5'-nucleotidase 1A	NT5C1A	1p34.3-p33	Q9BXI3	details
5'(3')-deoxyribonucleotidase, cytosolic type	NT5C		Q8TCD5	details
5'(3')-deoxyribonucleotidase, mitochondrial	NT5M		Q9NPB1	details
Inosine triphosphate pyrophosphatase	ITPA	20p	Q9BY32	details
Cytosolic 5'-nucleotidase 3	NT5C3	7p14.3	Q9H0P0	details
Cytosolic purine 5'-nucleotidase	NT5C2	10q24.32	P49902	details

Receptors

Not Available

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0000299

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

18107

References

General References

Not Available

Only showing the first 10 proteins. There are 17 proteins in total.

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Enzymes

Enzyme Details

1. 5'-nucleotidase

General function:: Involved in hydrolase activity
Specific function:: Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:: NT5E
Uniprot ID:: P21589
Molecular weight:: 57948.125

Enzyme Details

2. Cytosolic 5'-nucleotidase 1B

General function:: Involved in nucleotide binding
Specific function:: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:: NT5C1B
Uniprot ID:: Q96P26
Molecular weight:: 68803.055

Enzyme Details

3. Cytosolic 5'-nucleotidase 1A

General function:: Involved in nucleotide binding
Specific function:: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:: NT5C1A
Uniprot ID:: Q9BXI3
Molecular weight:: 41020.145

Enzyme Details

4. 5'(3')-deoxyribonucleotidase, cytosolic type

General function:: Involved in metal ion binding
Specific function:: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:: NT5C
Uniprot ID:: Q8TCD5
Molecular weight:: Not Available

Enzyme Details

5. 5'(3')-deoxyribonucleotidase, mitochondrial

General function:: Involved in phosphatase activity
Specific function:: Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:: NT5M
Uniprot ID:: Q9NPB1
Molecular weight:: Not Available

Enzyme Details

6. Inosine triphosphate pyrophosphatase

General function:: Involved in hydrolase activity
Specific function:: Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) and xanthosine 5'-triphosphate (XTP) to their respective monophosphate derivatives. The enzyme does not distinguish between the deoxy- and ribose forms. Probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.
Gene Name:: ITPA
Uniprot ID:: Q9BY32
Molecular weight:: 16833.23

Enzyme Details

7. Cytosolic 5'-nucleotidase 3

General function:: Involved in magnesium ion binding
Specific function:: Can act both as nucleotidase and as phosphotransferase.
Gene Name:: NT5C3
Uniprot ID:: Q9H0P0
Molecular weight:: 33914.91

Enzyme Details

8. Cytosolic purine 5'-nucleotidase

General function:: Involved in 5'-nucleotidase activity
Specific function:: May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:: NT5C2
Uniprot ID:: P49902
Molecular weight:: 64969.2

Enzyme Details

9. Purine nucleoside phosphorylase

General function:: Involved in purine-nucleoside phosphorylase activity
Specific function:: The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.
Gene Name:: PNP
Uniprot ID:: P00491
Molecular weight:: 32117.69

Only showing the first 10 proteins. There are 17 proteins in total.

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Showing Compound Card for Xanthosine (CDB004842)

Structure for CDB004842 (Xanthosine)

Enzymes