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Human Metabolome Database Version 3.5

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Showing metabocard for UDP-D-apiose (HMDB12301)

Record Information
Version 3.5
Creation Date 2009-04-06 10:22:36 -0600
Update Date 2013-02-08 17:28:45 -0700
HMDB ID HMDB12301
Secondary Accession Numbers None
Metabolite Identification
Common Name UDP-D-apiose
Description D-apiose is a plant-specific branched-chain monosaccharide found in rhamnogalacturonan II (RG-II), apiogalacturonan, and several apioglycosides. Within RG-II, d-apiose serves as the binding site for borate, which leads to the formation of cross-links within the wall. Biochemical studies in duckweed and parsley have established that uridine 5'-diphospho-d-apiose (UDP-d-apiose) is formed from UDP-d-glucuronate by decarboxylation and re-arrangement of the carbon skeleton, leading to ring contraction and branch formation. The enzyme catalyzing this reaction also forms UDP-d-xylose by decarboxylation of UDP-d-glucuronate, and has therefore been named UDP-d-apiose/UDP-d-xylose synthase. (PMID: 12969423 Link_out).
Structure Thumb
Download: MOL | SDF | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. UDP-Apiose
  2. Uridine 5'-(alpha-D-apio-D-furanosyl pyrophosphate)
Chemical Formula C14H22N2O16P2
Average Molecular Weight 536.2758
Monoisotopic Molecular Weight 536.04445569
IUPAC Name [({[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}(hydroxy)phosphoryl)oxy]({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy})phosphinic acid
Traditional IUPAC Name {[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy(hydroxy)phosphoryl}oxy[(2R,3S,4R,5R)-5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxyphosphinic acid
CAS Registry Number 20230-91-5
SMILES OC[C@@]1(O)CO[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]1O
InChI Identifier InChI=1S/C14H22N2O16P2/c17-4-14(23)5-28-12(10(14)21)31-34(26,27)32-33(24,25)29-3-6-8(19)9(20)11(30-6)16-2-1-7(18)15-13(16)22/h1-2,6,8-12,17,19-21,23H,3-5H2,(H,24,25)(H,26,27)(H,15,18,22)/t6-,8-,9-,10+,11-,12+,14-/m1/s1
InChI Key SYVORCSTSYHSPN-VPPDZDBCSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Nucleosides, Nucleotides, and Analogues
Class Pyrimidine Nucleotides
Sub Class Pyrimidine Ribonucleotides
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
Substituents
  • 1,2 Diol
  • Disaccharide Phosphate
  • Glycosyl Compound
  • Hydropyrimidine
  • N Glycosyl Compound
  • Organic Hypophosphite
  • Organic Phosphite
  • Organic Pyrophosphate
  • Oxolane
  • Pentose Disaccharide
  • Phosphoric Acid Ester
  • Primary Alcohol
  • Pyrimidine
  • Pyrimidone
  • Saccharide
  • Secondary Alcohol
  • Tertiary Alcohol
Direct Parent Pyrimidine Ribonucleoside Diphosphates
Ontology
Status Expected and Not 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
Water Solubility 12.2 g/L ALOGPS
LogP -1.05 ALOGPS
LogP -4.5 ChemAxon
LogS -1.64 ALOGPS
pKa (strongest acidic) 1.73 ChemAxon
pKa (strongest basic) -3.1 ChemAxon
Hydrogen Acceptor Count 13 ChemAxon
Hydrogen Donor Count 8 ChemAxon
Polar Surface Area 271.31 A2 ChemAxon
Rotatable Bond Count 9 ChemAxon
Refractivity 100.71 ChemAxon
Polarizability 43.5 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -2 ChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations Not Available
Biofluid Locations Not Available
Tissue Location Not Available
Pathways Not Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID FDB028924
KNApSAcK ID Not Available
Chemspider ID Not Available
KEGG Compound ID C01623 Link_out
BioCyc ID UDP-APIOSE Link_out
BiGG ID Not Available
Wikipedia Link Not Available
NuGOwiki Link HMDB12301 Link_out
Metagene Link HMDB12301 Link_out
METLIN ID Not Available
PubChem Compound 25202307 Link_out
PDB ID Not Available
ChEBI ID 15933 Link_out
References
Synthesis Reference Not Available
Material Safety Data Sheet (MSDS) Not Available
General References Not Available