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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-04-23 20:55:48 UTC
HMDB IDHMDB0001018
Secondary Accession Numbers
  • HMDB01018
Metabolite Identification
Common NameUDP-D-Xylose
DescriptionUDP-D-Xylose, also known as UDP xylose or UDP-alpha, 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 is an extremely weak basic (essentially neutral) compound (based on its pKa). UDP-D-xylose can be biosynthesized from uridine diphosphate glucuronic acid through the action of the enzyme UDP-glucuronic acid decarboxylase 1. In humans, UDP-D-xylose is involved in the metabolic disorder called galactosemia II (galk). Outside of the human body, UDP-D-xylose has been detected, but not quantified in, soy beans. This could make UDP-D-xylose a potential biomarker for the consumption of these foods.
Structure
Data?1582752171
Synonyms
ValueSource
alpha-D-Xylopyranosyl esterHMDB
alpha-delta-Xylopyranosyl esterHMDB
UDP XyloseHMDB
UDP-alphaHMDB
UDP-delta-XyloseHMDB
Uridine diphosphate xyloseHMDB
Chemical FormulaC14H22N2O16P2
Average Molecular Weight536.2758
Monoisotopic Molecular Weight536.04445569
IUPAC Name{[(2R,3S,4R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[hydroxy({[(3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy})phosphoryl]oxy})phosphinic acid
Traditional Name[(2R,3S,4R)-5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy({hydroxy[(3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyphosphoryl}oxy)phosphinic acid
CAS Registry Number3616-06-6
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 KeyDQQDLYVHOTZLOR-QDHANXEVSA-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
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Oxane
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Vinylogous amide
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Lactam
  • Urea
  • Secondary alcohol
  • Oxacycle
  • Polyol
  • Organoheterocyclic compound
  • Azacycle
  • Alcohol
  • Organic nitrogen compound
  • Organic oxide
  • Organonitrogen compound
  • Organooxygen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point144.5 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-0.96NARURKAR,MM & MITRA,AK (1988)
Predicted Properties
PropertyValueSource
Water Solubility13.6 g/LALOGPS
logP-1.3ALOGPS
logP-4.4ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area271.31 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity100.49 m³·mol⁻¹ChemAxon
Polarizability42.52 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-016r-4936760000-00f37a38fe624376e23dSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0690-5941635000-1aa68e9b8684d9615e1eSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0901110000-8ae0db777cff3d445c4cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4910000000-67006286cf564f62ff42Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-5900000000-da262c67a1973399a755Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000f-8713790000-946e0081f7ad1a09d3d6Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ox-9622010000-7089747eea74980128f4Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-06tf-4900000000-53eebd3beb66a7fd8d3fSpectrum
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 IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB005661
KNApSAcK IDNot Available
Chemspider ID388324
KEGG Compound IDC00190
BioCyc IDNot Available
BiGG ID34192
Wikipedia LinkNot Available
METLIN ID5948
PubChem Compound439179
PDB IDNot Available
ChEBI ID16082
Food Biomarker OntologyNot Available
VMH 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
  1. Okuyama A, Koh E, Kondoh N, Nakamura M, Namiki M, Fujioka H, Mizutani S, Kiyohara H, Sonoda T: In vitro temperature sensitivity of DNA, RNA, and protein syntheses throughout puberty in human testis. Arch Androl. 1991 Jan-Feb;26(1):7-13. [PubMed:1706913 ]
  2. Ostergaard M, Hansen GA, Vorum H, Honore B: Proteomic profiling of fibroblasts reveals a modulating effect of extracellular calumenin on the organization of the actin cytoskeleton. Proteomics. 2006 Jun;6(12):3509-19. [PubMed:16691550 ]
  3. Pal'tsyn AA, Pobedina VG, Chervonskaia NV, Badikova AK, Sanovich EIa: [Method of electron-autoradiographic study of nucleic acid biosynthesis in bacteria during phagocytosis]. Biull Eksp Biol Med. 1981 Jun;91(6):763-5. [PubMed:6168317 ]
  4. Sterling JD, Atmodjo MA, Inwood SE, Kumar Kolli VS, Quigley HF, Hahn MG, Mohnen D: Functional identification of an Arabidopsis pectin biosynthetic homogalacturonan galacturonosyltransferase. Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5236-41. Epub 2006 Mar 15. [PubMed:16540543 ]
  5. Nakamura M, Nonomura N, Namiki M, Okuyama A, Koh E, Kondoh N, Fujioka H, Nishimune Y, Matsumoto K, Matsuda M: DNA and RNA synthesis by postpubertal undescended testis in vitro. Arch Androl. 1989;22(1):91-4. [PubMed:2469403 ]
  6. Yong J, Wan L, Dreyfuss G: Why do cells need an assembly machine for RNA-protein complexes? Trends Cell Biol. 2004 May;14(5):226-32. [PubMed:15130578 ]
  7. Moore A, Findlay K, Morris ID: In-vitro DNA synthesis in Leydig and other interstitial cells of the rat testis. J Endocrinol. 1992 Aug;134(2):247-55. [PubMed:1402535 ]
  8. Saliba F, Hagipantelli R, Misset JL, Bastian G, Vassal G, Bonnay M, Herait P, Cote C, Mahjoubi M, Mignard D, Cvitkovic E: Pathophysiology and therapy of irinotecan-induced delayed-onset diarrhea in patients with advanced colorectal cancer: a prospective assessment. J Clin Oncol. 1998 Aug;16(8):2745-51. [PubMed:9704727 ]
  9. Molina JM, Tourneur M, Sarfati C, Chevret S, de Gouvello A, Gobert JG, Balkan S, Derouin F: Fumagillin treatment of intestinal microsporidiosis. N Engl J Med. 2002 Jun 20;346(25):1963-9. [PubMed:12075057 ]
  10. Yamamoto T, Moriwaki Y, Cheng J, Takahashi S, Tsutsumi Z, Ka T, Hada T: Effect of inosine on the plasma concentration of uridine and purine bases. Metabolism. 2002 Apr;51(4):438-42. [PubMed:11912550 ]
  11. Kost S, Keinert K, Glaser FH: [D-xylose test of resorption as a method to determine radiation side effects in the small intestine]. Strahlenther Onkol. 1998 Sep;174(9):462-7. [PubMed:9765687 ]
  12. Kucera O, Lotkova H, Kand'ar R, Hezova R, Muzakova V, Cervinkova Z: The model of D-galactosamine-induced injury of rat hepatocytes in primary culture. Acta Medica (Hradec Kralove). 2006;49(1):59-65. [PubMed:16696445 ]
  13. Pierard-Franchimont C, Damseaux M, Melotte P, Pierard GE: The fate of hypodermis after liposuction surgery. J Am Acad Dermatol. 1988 Oct;19(4):723-8. [PubMed:3183095 ]
  14. Nakamura M, Namiki M, Okuyama A, Koh E, Kondoh N, Takeyama M, Fujioka H, Nishimune Y, Matsumoto K, Matsuda M: Optimal temperature for synthesis of DNA, RNA, and protein by human testis in vitro. Arch Androl. 1988;20(1):41-4. [PubMed:2455487 ]
  15. Chilov D, Fux C, Joch H, Fussenegger M: Identification of a novel proliferation-inducing determinant using lentiviral expression cloning. Nucleic Acids Res. 2003 Sep 15;31(18):e113. [PubMed:12954789 ]
  16. Nasrallah SM, Al-Khalidi UA: Clinical value of 14C-phenylacetic oil as a fat absorption test. Lancet. 1980 Feb 2;1(8162):229-31. [PubMed:6101679 ]
  17. Thorell L, Sjoberg LB, Hernell O: Nucleotides in human milk: sources and metabolism by the newborn infant. Pediatr Res. 1996 Dec;40(6):845-52. [PubMed:8947961 ]
  18. Bjarnason I, Smethurst P, Macpherson A, Walker F, McElnay JC, Passmore AP, Menzies IS: Glucose and citrate reduce the permeability changes caused by indomethacin in humans. Gastroenterology. 1992 May;102(5):1546-50. [PubMed:1568563 ]
  19. Cherwinski HM, Cohn RG, Cheung P, Webster DJ, Xu YZ, Caulfield JP, Young JM, Nakano G, Ransom JT: The immunosuppressant leflunomide inhibits lymphocyte proliferation by inhibiting pyrimidine biosynthesis. J Pharmacol Exp Ther. 1995 Nov;275(2):1043-9. [PubMed:7473131 ]
  20. Gallai V, Mazzotta G, Montesi S, Sarchielli P, Del Gatto F: Effects of uridine in the treatment of diabetic neuropathy: an electrophysiological study. Acta Neurol Scand. 1992 Jul;86(1):3-7. [PubMed:1325728 ]

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