Cannabis Compound Database: Showing Compound Card for UDP-L-rhamnose (CDB005035)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (1) Show 2 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 19:02:43 UTC

Updated at

2020-11-18 16:39:14 UTC

CannabisDB ID

CDB005035

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

UDP-L-rhamnose

Description

UDP-L-rhamnose, also known as UDP-gal or GDU, belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. UDP-L-rhamnose is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, UDP-L-rhamnose is found, on average, in the highest concentration within milk (cow). UDP-L-rhamnose has also been detected, but not quantified in, several different foods, such as winter savories, spelts, cherry tomato, chayotes, and cornmints. This could make UDP-L-rhamnose a potential biomarker for the consumption of these foods. UDP-L-rhamnose 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
Uridine 5'-(trihydrogen diphosphate), mono(6-deoxy-beta-L-mannopyranosyl) ester	ChEBI
Uridine 5'-(trihydrogen diphosphate), mono(6-deoxy-b-L-mannopyranosyl) ester	Generator
Uridine 5'-(trihydrogen diphosphate), mono(6-deoxy-β-L-mannopyranosyl) ester	Generator
Uridine 5'-(trihydrogen diphosphoric acid), mono(6-deoxy-b-L-mannopyranosyl) ester	Generator
Uridine 5'-(trihydrogen diphosphoric acid), mono(6-deoxy-beta-L-mannopyranosyl) ester	Generator
Uridine 5'-(trihydrogen diphosphoric acid), mono(6-deoxy-β-L-mannopyranosyl) ester	Generator
Galactose-uridine-5'-diphosphate	HMDB
GDU	HMDB
Glucose-uridine-C1,5'-diphosphate	HMDB
UDP Galactose	HMDB
UDP-alpha-D-Galactose	HMDB
UDP-D-Galactopyranose	HMDB
UDP-D-Galactose	HMDB
UDP-Gal	HMDB
UDP-Galactopyranose	HMDB
UDP-Galactose	HMDB
Udpgal	HMDB
UPG	HMDB
Uridine 5'-diphosphate galactose	HMDB
Uridine 5'-diphosphogalactose	HMDB
Uridine diphosphate galactose	HMDB
Uridine diphosphate-D-galactose	HMDB
Uridine diphosphogalactose	HMDB
Uridine pyrophosphogalactose	HMDB
Uridine-5'-diphosphate-mannose	HMDB
Uridine-5'-monophosphate glucopyranosyl-monophosphateester	HMDB
Uridinediphosphate galactose	HMDB
Uridinediphosphogalactose	HMDB
UDP-beta-L-Rhamnose	MeSH, HMDB
UDP-b-L-Rhamnose	Generator
UDP-Β-L-rhamnose	Generator
UDP-Rha	MeSH
UDP-Rhamnose	MeSH

Chemical Formula

C₁₅H₂₄N₂O₁₆P₂

Average Molecular Weight

550.3

Monoisotopic Molecular Weight

550.0601

IUPAC Name

{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({[hydroxy({[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy})phosphoryl]oxy})phosphinic acid

Traditional Name

[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy([hydroxy([(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy)phosphoryl]oxy)phosphinic acid

CAS Registry Number

1955-26-6

SMILES

C[C@@H]1O[C@H](OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N2C=CC(=O)NC2=O)[C@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C15H24N2O16P2/c1-5-8(19)10(21)12(23)14(30-5)32-35(27,28)33-34(25,26)29-4-6-9(20)11(22)13(31-6)17-3-2-7(18)16-15(17)24/h2-3,5-6,8-14,19-23H,4H2,1H3,(H,25,26)(H,27,28)(H,16,18,24)/t5-,6+,8-,9+,10+,11+,12+,13+,14+/m0/s1

InChI Key

DRDCJEIZVLVWNC-SLBWPEPYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine nucleotide sugars

Direct Parent

Pyrimidine nucleotide sugars

Alternative Parents

Substituents

Pyrimidine nucleotide sugar
Pyrimidine ribonucleoside diphosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Organic pyrophosphate
Monoalkyl phosphate
Pyrimidone
Hydropyrimidine
Alkyl phosphate
Monosaccharide
Organic phosphoric acid derivative
Pyrimidine
Oxane
Phosphoric acid ester
Vinylogous amide
Tetrahydrofuran
Heteroaromatic compound
Lactam
Urea
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Alcohol
Organic oxygen compound
Organopnictogen compound
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

UDP-L-rhamnose (CHEBI:84725 )

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Animal

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	-1.2	ALOGPS
logP	-3.6	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	274.8 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	105.23 m³·mol⁻¹	ChemAxon
Polarizability	45.7 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
Predicted GC-MS	UDP-L-rhamnose, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-057l-4933450000-9b68de4de326b7782ff3	Spectrum
Predicted GC-MS	UDP-L-rhamnose, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-004j-7354219000-9fc893b0c5397f725ee6	Spectrum
Predicted GC-MS	UDP-L-rhamnose, "UDP-L-rhamnose,1TMS,#1" TMS, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_1_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_1_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_1_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_1_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_1_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_9, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_10, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_11, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_12, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_13, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_14, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	UDP-L-rhamnose, TMS_2_15, 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 32V, negative	splash10-052b-5614390000-8207db0554e68840adca	2020-07-21	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0901110000-7af2d5ab14e05545288f	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4911000000-07a3ee7bed9a9e59aa87	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-5900000000-74f891c988bc2c098848	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0lyn-5502290000-504031de82fe382cb81c	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ox-9604010000-1bdfc26f473d183f5612	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-06tf-4901000000-149a648e41231773f1fc	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fk9-0000960000-eeec69d4e41830f15305	2021-09-23	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0r90-5653950000-3e93cf6653d30c282fce	2021-09-23	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01ox-9531000000-f9dcc8cd87e605b25ce2	2021-09-23	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0000090000-2c0643b44b5b1f646668	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056v-9503430000-17e241cf1089b9364116	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-2419000000-1e0a5bbc494bdb18a07a	2021-09-24	View Spectrum

NMR

Not Available

Pathways

Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
Beta-1,4-galactosyltransferase 6	B4GALT6	18q11	Q9UBX8	details

Transporters

Not Available

Metal Bindings

Protein Name	Gene Name	Locus	Uniprot ID	Details
Beta-1,4-galactosyltransferase 6	B4GALT6	18q11	Q9UBX8	details

Receptors

Not Available

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0012305

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB028928

KNApSAcK ID

Not Available

Chemspider ID

167268

KEGG Compound ID

C02199

BioCyc ID

UDP-L-RHAMNOSE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

192751

PDB ID

Not Available

ChEBI ID

84725

References

General References

Not Available

Enzymes

Enzyme Details

1. Beta-1,4-galactosyltransferase 6

General function:: Involved in transferase activity, transferring glycosyl groups
Specific function:: Required for the biosynthesis of glycosphingolipids.
Gene Name:: B4GALT6
Uniprot ID:: Q9UBX8
Molecular weight:: 44913.315

Showing Compound Card for UDP-L-rhamnose (CDB005035)

Structure for CDB005035 (UDP-L-rhamnose)

Enzymes