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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:38:59 UTC
HMDB IDHMDB0001018
Secondary Accession Numbers
  • HMDB01018
Metabolite Identification
Common NameUDP-D-Xylose
DescriptionUDP-alpha-D-xylose, also known as UDP xylose or UDP-α-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-alpha-D-xylose is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
Synonyms
Chemical FormulaC14H22N2O16P2
Average Molecular Weight536.2758
Monoisotopic Molecular Weight536.04445569
IUPAC Name[({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy})phosphinic acid
Traditional Nameudp-xylose
CAS Registry Number3616-06-6
SMILES
O[C@@H]1[C@@H](COP(O)(=O)OP(O)(=O)O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2O)O[C@H]([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 KeyDQQDLYVHOTZLOR-OCIMBMBZSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct ParentPyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Hydroxypyrimidine
  • Hydropyrimidine
  • Monosaccharide
  • Alkyl phosphate
  • Organic phosphoric acid derivative
  • Pyrimidine
  • Oxane
  • Phosphoric acid ester
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Polyol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Alcohol
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point144.5 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-0.96NARURKAR,MM & MITRA,AK (1988)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Endoplasmic reticulum
  • Golgi apparatus
Biospecimen LocationsNot Available
Tissue Locations
  • Adipose Tissue
  • Epidermis
  • Fibroblasts
  • Intestine
  • Kidney
  • Liver
  • Neuron
  • Spleen
  • Testis
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01713
Phenol Explorer Compound IDNot Available
FooDB IDFDB005661
KNApSAcK IDNot Available
Chemspider ID18152
KEGG Compound IDC00190
BioCyc IDUDP-D-XYLOSE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5948
PubChem Compound19235
PDB IDNot Available
ChEBI ID16082
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceErnst, 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

Enzymes

General function:
Involved in acetylglucosaminyltransferase activity
Specific function:
Catalyzes the first step in biosynthesis of glycosaminoglycan. Transfers D-xylose from UDP-D-xylose to specific serine residues of the core protein. Initial enzyme in the biosynthesis of chondroitin sulfate and dermatan sulfate proteoglycans in fibroblasts and chondrocytes
Gene Name:
XYLT1
Uniprot ID:
Q86Y38
Molecular weight:
107568.4
General function:
Involved in acetylglucosaminyltransferase activity
Specific function:
Probably catalyzes the first step in biosynthesis of glycosaminoglycan. Transfers D-xylose from UDP-D-xylose to specific serine residues of the core protein. Initial enzyme in the biosynthesis of chondroitin sulfate and dermatan sulfate proteoglycans in fibroblasts and chondrocytes. Its enzyme activity has not been demonstrated
Gene Name:
XYLT2
Uniprot ID:
Q9H1B5
Molecular weight:
96766.3
General function:
Involved in catalytic activity
Specific function:
Catalyzes the NAD-dependent decarboxylation of UDP-glucuronic acid to UDP-xylose. Necessary for the biosynthesis of the core tetrasaccharide in glycosaminoglycan biosynthesis.
Gene Name:
UXS1
Uniprot ID:
Q8NBZ7
Molecular weight:
48151.17
Reactions
Uridine diphosphate glucuronic acid → UDP-D-Xylose + CO(2)details
Uridine diphosphate glucuronic acid → UDP-D-Xylose + Carbon dioxidedetails
General function:
Not Available
Specific function:
Glycosyltransferase which elongates the O-linked glucose attached to EGF-like repeats in the extracellular domain of Notch proteins by catalyzing the addition of xylose.
Gene Name:
GXYLT1
Uniprot ID:
Q4G148
Molecular weight:
46799.87
Reactions
UDP-D-Xylose + beta-D-glucosyl-R → Uridine 5'-diphosphate + alpha-D-xylose-(1->3)-beta-D-glucosyl-Rdetails
General function:
Not Available
Specific function:
Glycosyltransferase which elongates the O-linked glucose attached to EGF-like repeats in the extracellular domain of Notch proteins by catalyzing the addition of xylose.
Gene Name:
GXYLT2
Uniprot ID:
A0PJZ3
Molecular weight:
51055.05
Reactions
UDP-D-Xylose + beta-D-glucosyl-R → Uridine 5'-diphosphate + alpha-D-xylose-(1->3)-beta-D-glucosyl-Rdetails
General function:
Not Available
Specific function:
Alpha-1,3-xylosyltransferase, which elongates the O-linked xylose-glucose disaccharide attached to EGF-like repeats in the extracellular domain of Notch proteins by catalyzing the addition of the second xylose.
Gene Name:
XXYLT1
Uniprot ID:
Q8NBI6
Molecular weight:
43806.33
Reactions
UDP-D-Xylose + alpha-D-xylose-(1->3)-beta-D-glucosyl-R → Uridine 5'-diphosphate + alpha-D-xylose-(1->3)-alpha-D-xylose-(1->3)-beta-D-glucosyl-Rdetails