Bovine Metabolome Database: Showing metabocard for UDP-D-Xylose (BMDB0001018)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (5) Show 5 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:39:58 UTC

Update Date

2020-05-21 16:26:58 UTC

BMDB ID

BMDB0001018

Secondary Accession Numbers

BMDB01018

Metabolite Identification

Common Name

UDP-D-Xylose

Description

UDP-D-Xylose belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. UDP-D-Xylose exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. UDP-D-Xylose can be biosynthesized from uridine diphosphate glucuronic acid; which is catalyzed by the enzyme UDP-glucuronic acid decarboxylase 1. In cattle, UDP-D-xylose is involved in the metabolic pathway called the nucleotide sugars metabolism pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
alpha-D-Xylopyranosyl ester	HMDB
alpha-delta-Xylopyranosyl ester	HMDB
UDP Xylose	HMDB
UDP-alpha	HMDB
UDP-delta-Xylose	HMDB
Uridine diphosphate xylose	HMDB

Chemical Formula

C₁₄H₂₂N₂O₁₆P₂

Average Molecular Weight

536.2758

Monoisotopic Molecular Weight

536.04445569

IUPAC Name

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

Traditional Name

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

CAS Registry Number

3616-06-6

SMILES

O[C@@H]1[C@@H](COP(O)(=O)OP(O)(=O)OC2OC[C@@H](O)[C@H](O)[C@H]2O)OC([C@@H]1O)N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C14H22N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/t5-,6-,8+,9-,10-,11-,12?,13?/m1/s1

InChI Key

DQQDLYVHOTZLOR-QDHANXEVSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as methionine and derivatives. Methionine and derivatives are compounds containing methionine or a derivative thereof resulting from reaction of methionine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Methionine and derivatives

Alternative Parents

Substituents

Methionine or derivatives
N-acyl-l-alpha-amino acid
N-formyl-alpha-amino acid
N-formyl-alpha amino acid or derivatives
Thia fatty acid
Fatty acid
Fatty acyl
Carboxamide group
Secondary carboxylic acid amide
Dialkylthioether
Sulfenyl compound
Thioether
Monocarboxylic acid or derivatives
Carboxylic acid
Hydrocarbon derivative
Organic oxide
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

proteinogenic amino acid (CHEBI:16552 )
L-methionine derivative (CHEBI:16552 )
N-formyl amino acid (CHEBI:16552 )
Other amino acids (C03145 )

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm
Endoplasmic reticulum
Golgi
Mitochondria

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	144.5 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	-0.96	NARURKAR,MM & MITRA,AK (1988)

Predicted Properties

Property	Value	Source
logP	-1.2	ALOGPS
logP	-4	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.5	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	100.82 m³·mol⁻¹	ChemAxon
Polarizability	43.53 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	splash10-016r-4936760000-00f37a38fe624376e23d	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0690-5941635000-1aa68e9b8684d9615e1e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0901110000-8ae0db777cff3d445c4c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4910000000-67006286cf564f62ff42	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-5900000000-da262c67a1973399a755	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000f-8713790000-946e0081f7ad1a09d3d6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ox-9622010000-7089747eea74980128f4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-06tf-4900000000-53eebd3beb66a7fd8d3f	View in MoNA

Biological Properties

Cellular Locations

Cytoplasm
Endoplasmic reticulum
Golgi
Mitochondria

Biospecimen Locations

Adipose Tissue
Epidermis
Fibroblasts
Intestine
Kidney
Liver
Neuron
Spleen
Testis

Pathways

Name	SMPDB/Pathwhiz	KEGG
Nucleotide Sugars Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Adipose Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Testis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0001018

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB005661

KNApSAcK ID

Not Available

Chemspider ID

388324

KEGG Compound ID

C00190

BioCyc ID

Not Available

BiGG ID

34192

Wikipedia Link

Not Available

METLIN ID

5948

PubChem Compound

439179

PDB ID

Not Available

ChEBI ID

16082

References

Synthesis Reference

Ernst, Christiane; Klaffke, Werner. Chemical Synthesis of Uridine Diphospho-D-xylose and UDP-L-arabinose. Journal of Organic Chemistry (2003), 68(14), 5780-5783.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. dTDP-D-glucose 4,6-dehydratase

General function:: Cell wall/membrane/envelope biogenesis
Specific function:: Not Available
Gene Name:: TGDS
Uniprot ID:: A6QLW2
Molecular weight:: 40666.0

Reactions

Uridine diphosphate glucuronic acid → UDP-D-Xylose + Carbon dioxide	details

Enzyme Details

2. Xylosyltransferase 2

General function:: Involved in acetylglucosaminyltransferase activity
Specific function:: Catalyzes the first step in the biosynthesis of chondroitin sulfate, heparan sulfate and dermatan sulfate proteoglycans, such as DCN (By similarity). Transfers D-xylose from UDP-D-xylose to specific serine residues of the core protein (By similarity).
Gene Name:: XYLT2
Uniprot ID:: Q5QQ49
Molecular weight:: 97189.0

Enzyme Details

3. Exostosin-2

General function:: Involved in glucuronosyl-N-acetylglucosaminyl-proteogly
Specific function:: Glycosyltransferase required for the biosynthesis of heparan-sulfate. The EXT1/EXT2 complex possesses substantially higher glycosyltransferase activity than EXT1 or EXT2 alone. Appears to be a tumor suppressor. Required for the exosomal release of SDCBP, CD63 and syndecan.
Gene Name:: EXT2
Uniprot ID:: O77783
Molecular weight:: 81887.0

Enzyme Details

4. Hyaluronan synthase 2

General function:: Cell wall/membrane/envelope biogenesis
Specific function:: Catalyzes the addition of GlcNAc or GlcUA monosaccharides to the nascent hyaluronan polymer. Therefore, it is essential to hyaluronan synthesis a major component of most extracellular matrices that has a structural role in tissues architectures and regulates cell adhesion, migration and differentiation. This is one of the isozymes catalyzing that reaction and it is particularly responsible for the synthesis of high molecular mass hyaluronan. Required for the transition of endocardial cushion cells into mesenchymal cells, a process crucial for heart development. May also play a role in vasculogenesis. High molecular mass hyaluronan also play a role in early contact inhibition a process which stops cell growth when cells come into contact with each other or the extracellular matrix (By similarity).
Gene Name:: HAS2
Uniprot ID:: O97711
Molecular weight:: 63459.0

Enzyme Details

5. Exostosin-1

General function:: Involved in glucuronosyl-N-acetylglucosaminyl-proteogly
Specific function:: Glycosyltransferase required for the biosynthesis of heparan-sulfate. The EXT1/EXT2 complex possesses substantially higher glycosyltransferase activity than EXT1 or EXT2 alone. Required for the exosomal release of SDCBP, CD63 and syndecan (By similarity).
Gene Name:: EXT1
Uniprot ID:: A5D7I4
Molecular weight:: 86299.0

Showing metabocard for UDP-D-Xylose (BMDB0001018)

Structure for BMDB0001018 (UDP-D-Xylose)

Enzymes

Reactions