Udp-xylose (CHEM025921)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-05-25 22:40:51 UTC
Update Date2016-11-09 01:18:10 UTC
Accession NumberCHEM025921
Identification
Common NameUdp-xylose
ClassSmall Molecule
DescriptionUDP-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.
Contaminant Sources
  • FooDB Chemicals
Contaminant TypeNot Available
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
alpha-D-Xylopyranosyl esterHMDB
alpha-delta-Xylopyranosyl esterHMDB
UDP XyloseHMDB
UDP-alphaHMDB
UDP-delta-XyloseHMDB
Uridine diphosphate xyloseHMDB
Chemical FormulaC14H20N2O16P2
Average Molecular Mass534.260 g/mol
Monoisotopic Mass534.029 g/mol
CAS Registry NumberNot Available
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
SMILESO[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP([O-])(=O)OP([O-])(=O)O[C@H]1OC[C@@H](O)[C@H](O)[C@H]1O)N1C=CC(=O)NC1=O
InChI IdentifierInChI=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)/p-2/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1
InChI KeyDQQDLYVHOTZLOR-OCIMBMBZSA-L
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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentMethionine 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 FrameworkAliphatic acyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginNot Available
Cellular LocationsNot Available
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateNot Available
AppearanceNot Available
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot Available
Predicted Properties
PropertyValueSource
Water Solubility21.8 g/LALOGPS
logP-1.2ALOGPS
logP-4ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area274.8 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity100.82 m³·mol⁻¹ChemAxon
Polarizability43.53 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
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
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityNot Available
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)Not Available
Uses/SourcesNot Available
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsNot Available
TreatmentNot Available
Concentrations
Not Available
DrugBank IDNot Available
HMDB IDHMDB0001018
FooDB IDFDB005661
Phenol Explorer IDNot Available
KNApSAcK IDNot Available
BiGG ID34192
BioCyc IDNot Available
METLIN ID5948
PDB IDNot Available
Wikipedia LinkNot Available
Chemspider ID388324
ChEBI ID16082
PubChem Compound ID439179
Kegg Compound IDC00190
YMDB IDNot Available
ECMDB IDNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General References
1. Ernst, Christiane; Klaffke, Werner. Chemical Synthesis of Uridine Diphospho-D-xylose and UDP-L-arabinose. Journal of Organic Chemistry (2003), 68(14), 5780-5783.
2. Ernst, Christiane; Klaffke, Werner. Chemical Synthesis of Uridine Diphospho-D-xylose and UDP-L-arabinose. Journal of Organic Chemistry (2003), 68(14), 5780-5783.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. Nasrallah SM, Al-Khalidi UA: Clinical value of 14C-phenylacetic oil as a fat absorption test. Lancet. 1980 Feb 2;1(8162):229-31.
19. 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.
20. 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.
21. 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.
22. 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.