Bovine Metabolome Database: Showing metabocard for UDP-L-rhamnose (BMDB0012305)

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

Record Information

Version

1.0

Creation Date

2016-10-03 18:35:47 UTC

Update Date

2020-06-04 18:58:17 UTC

BMDB ID

BMDB0012305

Secondary Accession Numbers

BMDB12305

Metabolite Identification

Common Name

UDP-L-rhamnose

Description

UDP-L-rhamnose 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. Based on a literature review a significant number of articles have been published on UDP-L-rhamnose.

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

550.3024

Monoisotopic Molecular Weight

550.060105754

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

Status

Detected and Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

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	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
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-057l-4933450000-9b68de4de326b7782ff3	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-004j-7354219000-9fc893b0c5397f725ee6	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS ("UDP-L-rhamnose,1TMS,#1" TMS) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 32V, negative	splash10-052b-5614390000-8207db0554e68840adca	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0901110000-7af2d5ab14e05545288f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4911000000-07a3ee7bed9a9e59aa87	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-5900000000-74f891c988bc2c098848	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0lyn-5502290000-504031de82fe382cb81c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ox-9604010000-1bdfc26f473d183f5612	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-06tf-4901000000-149a648e41231773f1fc	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fk9-0000960000-eeec69d4e41830f15305	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0r90-5653950000-3e93cf6653d30c282fce	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01ox-9531000000-f9dcc8cd87e605b25ce2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0000090000-2c0643b44b5b1f646668	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056v-9503430000-17e241cf1089b9364116	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-2419000000-1e0a5bbc494bdb18a07a	View in MoNA
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Milk

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Milk	Detected and Quantified	0 - 134.700 uM	Not Specified	Not Specified	Normal	PMID: 7196410	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0012305

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB 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

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Gil A, Sanchez-Medina F: Acid-soluble nucleotides of cow's, goat's and sheep's milks, at different stages of lactation. J Dairy Res. 1981 Feb;48(1):35-44. [PubMed:7196410 ]

Enzymes

Enzyme Details

1. Polypeptide N-acetylgalactosaminyltransferase 6

General function:: Cell wall/membrane/envelope biogenesis
Specific function:: Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. May participate in synthesis of oncofetal fibronectin. Has activity toward Muc1a, Muc2, EA2 and fibronectin peptides (By similarity).
Gene Name:: GALNT6
Uniprot ID:: Q5EA41
Molecular weight:: 71138.0

Enzyme Details

2. Polypeptide N-acetylgalactosaminyltransferase 1

General function:: Involved in calcium ion binding
Specific function:: Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b and Muc7.
Gene Name:: GALNT1
Uniprot ID:: Q07537
Molecular weight:: 64192.0

Enzyme Details

3. Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1

General function:: Involved in glycoprotein-N-acetylgalactosamine 3-beta-g
Specific function:: Glycosyltransferase that generates the core 1 O-glycan Gal-beta1-3GalNAc-alpha1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in glycoproteins. Plays a central role in many processes, such as angiogenesis, thrombopoiesis and kidney homeostasis development (By similarity).
Gene Name:: C1GALT1
Uniprot ID:: Q0VC84
Molecular weight:: 43041.0

Enzyme Details

4. Beta-1,4-galactosyltransferase 1

General function:: Involved in alpha-tubulin binding
Specific function:: The Golgi complex form catalyzes the production of lactose in the lactating mammary gland and could also be responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids.
Gene Name:: B4GALT1
Uniprot ID:: P08037
Molecular weight:: 44843.0

Enzyme Details

5. Beta-1,4-galactosyltransferase 3

General function:: Involved in beta-N-acetylglucosaminylglycopeptide beta-
Specific function:: Responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids.
Gene Name:: B4GALT3
Uniprot ID:: Q5EA87
Molecular weight:: 44371.0

Enzyme Details

6. N-acetyllactosaminide alpha-1,3-galactosyltransferase

General function:: Involved in manganese ion binding
Specific function:: Synthesizes the galactose-alpha(1,3)-galactose group by catalyzing the transfer of a galactose residue, with an alpha-1,3 linkage, on terminal lactosaminide (Gal-beta-1,4-GlcNAc-R) disaccharide borne by a glycoprotein or a glycolipid. Preferentially glycosylates proteins, can synthesize galactose-alpha(1,3)-galactose on glycoproteins but cannot synthesize the glycolipid called isoglobotrihexosylceramide or isogloboside 3 (iGb3).
Gene Name:: GGTA1
Uniprot ID:: P14769
Molecular weight:: 43247.0

Enzyme Details

7. Galactose-1-phosphate uridylyltransferase

General function:: Energy production and conversion
Specific function:: Not Available
Gene Name:: GALT
Uniprot ID:: Q0V7N7
Molecular weight:: 37812.0

Enzyme Details

8. Galactose-1-phosphate uridylyltransferase

General function:: Energy production and conversion
Specific function:: Not Available
Gene Name:: GALT
Uniprot ID:: Q58CX1
Molecular weight:: 41288.0

Enzyme Details

9. UDP-galactose translocator

General function:: Carbohydrate transport and metabolism
Specific function:: Transports nucleotide sugars from the cytosol into Golgi vesicles where glycosyltransferases function.
Gene Name:: SLC35A2
Uniprot ID:: Q58DA6
Molecular weight:: 41180.0

Showing metabocard for UDP-L-rhamnose (BMDB0012305)

Structure for BMDB0012305 (UDP-L-rhamnose)

Enzymes