You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 21:43:07 UTC
Update Date2021-09-14 15:44:31 UTC
HMDB IDHMDB0036562
Secondary Accession Numbers
  • HMDB36562
Metabolite Identification
Common NameAucubin
DescriptionAucubin is found in common verbena. Aucubin is a monoterpenoid based compound. Aucubin, like all iridoids, has a cyclopentan-[C]-pyran skeleton. Iridoids can consist of ten, nine, or rarely eight carbons in which C11 is more frequently missing than C10. Aucubin has 10 carbons with the C11 carbon missing. The stereochemical configurations at C5 and C9 lead to cis fused rings, which are common to all iridoids containing carbocylclic- or seco-skeleton in non-rearranged form. Oxidative cleavage at C7-C8 bond affords secoiridoids. The last steps in the biosynthesis of iridoids usually consist of O-glycosylation and O-alkylation. Aucubin, a glycoside iridoid, has an O-linked glucose moiety. Aucubin is an iridoid glycoside. Iridoids are commonly found in plants and function as defensive compounds. Irioids decrease the growth rates of many generalist herbivores. Aucubin is found in the leaves of Aucuba japonica (Cornaceae), Eucommia ulmoides (Eucommiaceae), and Plantago asiatic (Plantaginaceae), etc, plants used in traditional Chinese and folk medicine. Aucubin was found to protect against liver damage induced by carbon tetrachloride or alpha-amanitin in mice and rats when 80 mg/kg was dosed intraperitoneally. Geranyl pyrophosphate is the precursor for iridoids. Geranyl phosphate is generated through the mevalonate pathway or the methylerythritol phosphate pathway. The initial steps of the pathway involve the fusion of three molecules of acetyl-CoA to produce the C6 compound 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA). HMG-CoA is then reduced in two steps by the enzyme HMG-CoA reductase. The resulting mevalonate is then sequentially phosphorylated by two separate kinases, mevalonate kinase and phosphomevalonate kinase, to form 5-pyrophosphomevalonate. Phosphosphomevalonate decarboxylase through a concerted decarboxylation reaction affords isopentenyl pyrophosphate (IPP). IPP is the basic C5 building block that is added to prenyl phosphate cosubstrates to form longer chains. IPP is isomerized to the allylic ester dimethylallyl pyrophosphate (DMAPP) by IPP isomerase. Through a multistep process, including the dephosphorylation DMAPP, IPP and DMAPP are combinded to from the C10 compound geranyl pyrophosphate (GPP). Geranyl pyrophosphate is a major branch point for terpenoid synthesis. The cyclizaton reaction to form the iridoid pyrane ring may result from one of two routes: route 1 - a hydride nucleophillic attack on C1 will lead to 1-O-carbonyl atom attack on C3, yielding the lactone ring; route 2 - loss of proton from carbon 4 leads to the formation of a double bond C3-C4; consequently the 3-0-carbonyl atom will attach to C1
Structure
Data?1563862889
Synonyms
ValueSource
AucubosideHMDB
RhimantinHMDB
RhinanthinHMDB
Chemical FormulaC15H22O9
Average Molecular Weight346.3298
Monoisotopic Molecular Weight346.126382302
IUPAC Name2-{[5-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Nameaucubin
CAS Registry Number479-98-1
SMILES
OCC1OC(OC2OC=CC3C(O)C=C(CO)C23)C(O)C(O)C1O
InChI Identifier
InChI=1S/C15H22O9/c16-4-6-3-8(18)7-1-2-22-14(10(6)7)24-15-13(21)12(20)11(19)9(5-17)23-15/h1-3,7-21H,4-5H2
InChI KeyRJWJHRPNHPHBRN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene glycosides
Direct ParentIridoid O-glycosides
Alternative Parents
Substituents
  • Iridoid o-glycoside
  • Hexose monosaccharide
  • Glycosyl compound
  • Iridoid-skeleton
  • O-glycosyl compound
  • Bicyclic monoterpenoid
  • Monoterpenoid
  • Monosaccharide
  • Oxane
  • Secondary alcohol
  • Acetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Alcohol
  • Hydrocarbon derivative
  • Primary alcohol
  • Organic oxygen compound
  • Organooxygen compound
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Route of exposure:

Biological location:

Source:

Process

Naturally occurring process:

Role

Industrial application:

Biological role:

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point181 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility356 mg/mL at 20 °CNot Available
LogPNot AvailableNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility50 g/LALOGPS
logP-2.1ALOGPS
logP-3.2ChemAxon
logS-0.84ALOGPS
pKa (Strongest Acidic)12.2ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area149.07 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity79.18 m³·mol⁻¹ChemAxon
Polarizability33.65 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Collision Cross Sections

NameAdductTypeData SourceValueReference
DarkChem[M+H]+PredictedNot Available178.74831661259
DarkChem[M-H]-PredictedNot Available169.88331661259

Retention Indices

Underivatized

Not Available

Derivatized

DerivativeValueReference
Aucubin,1TMS,#13036.7227https://arxiv.org/abs/1905.12712
Aucubin,1TMS,#23045.2007https://arxiv.org/abs/1905.12712
Aucubin,1TMS,#33030.1677https://arxiv.org/abs/1905.12712
Aucubin,1TMS,#43004.2454https://arxiv.org/abs/1905.12712
Aucubin,1TMS,#52986.2153https://arxiv.org/abs/1905.12712
Aucubin,1TMS,#62991.8835https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#13002.5835https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#22978.989https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#32981.5864https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#42976.9753https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#52979.7012https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#62988.7144https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#72978.7417https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#82970.8452https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#92994.601https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#102953.1394https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#112948.319https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#122955.079https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#132947.3628https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#142962.5645https://arxiv.org/abs/1905.12712
Aucubin,2TMS,#152956.5935https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#12918.0293https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#22945.5647https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#32934.1438https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#42948.6648https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#52916.5232https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#62901.1333https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#72907.0337https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#82902.6938https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#92926.8877https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#102923.0623https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#112946.9922https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#122935.522https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#132927.9253https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#142944.3865https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#152940.4084https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#162938.6982https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#172900.1306https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#182897.574https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#192886.9873https://arxiv.org/abs/1905.12712
Aucubin,3TMS,#202915.9976https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#12893.6362https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#22857.5166https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#32870.7996https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#42866.8252https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#52891.977https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#62893.9746https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#72846.0627https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#82837.6655https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#92809.5256https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#102878.5403https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#112877.252https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#122886.5635https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#132848.0183https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#142884.2773https://arxiv.org/abs/1905.12712
Aucubin,4TMS,#152834.509https://arxiv.org/abs/1905.12712
Aucubin,5TMS,#12772.2888https://arxiv.org/abs/1905.12712
Aucubin,5TMS,#22774.8127https://arxiv.org/abs/1905.12712
Aucubin,5TMS,#32736.2896https://arxiv.org/abs/1905.12712
Aucubin,5TMS,#42791.3545https://arxiv.org/abs/1905.12712
Aucubin,5TMS,#52747.941https://arxiv.org/abs/1905.12712
Aucubin,5TMS,#62736.0425https://arxiv.org/abs/1905.12712
Aucubin,6TMS,#12682.2375https://arxiv.org/abs/1905.12712
Aucubin,1TBDMS,#13261.0803https://arxiv.org/abs/1905.12712
Aucubin,1TBDMS,#23308.8447https://arxiv.org/abs/1905.12712
Aucubin,1TBDMS,#33265.729https://arxiv.org/abs/1905.12712
Aucubin,1TBDMS,#43266.023https://arxiv.org/abs/1905.12712
Aucubin,1TBDMS,#53258.5977https://arxiv.org/abs/1905.12712
Aucubin,1TBDMS,#63254.9717https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#13437.5005https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#23420.4788https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#33412.7197https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#43420.2852https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#53404.5144https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#63483.8044https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#73442.5815https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#83453.399https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#93446.057https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#103425.0198https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#113428.6074https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#123421.5664https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#133405.8088https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#143416.1045https://arxiv.org/abs/1905.12712
Aucubin,2TBDMS,#153408.3037https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#13613.3887https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#23581.3164https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#33607.481https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#43582.28https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#53570.8406https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#63585.5999https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#73572.3936https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#83564.5857https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#93558.5493https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#103574.3423https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#113632.4385https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#123639.13https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#133626.5151https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#143594.015https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#153583.1633https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#163589.3462https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#173565.3564https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#183560.4163https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#193562.6216https://arxiv.org/abs/1905.12712
Aucubin,3TBDMS,#203537.4543https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#13784.6802https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#23807.9521https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#33785.4111https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#43758.0884https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#53757.166https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#63771.688https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#73753.154https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#83743.5037https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#93747.7854https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#103733.888https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#113770.0935https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#123756.201https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#133765.72https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#143715.3315https://arxiv.org/abs/1905.12712
Aucubin,4TBDMS,#153692.763https://arxiv.org/abs/1905.12712
Spectra

GC-MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00or-4719000000-a03c5ea19b82d7991f352017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-01b9-2252049000-fb4fdbe14aa2fef93db32017-10-06View Spectrum

LC-MS/MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-02vr-0904000000-0dc8cc1fee5ec1d7b66a2015-04-24View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014i-0901000000-23ae99445d0f902ebb102015-04-24View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014i-1900000000-0197bf91c00175908c8f2015-04-24View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00nb-0917000000-5b5a2c303dee5ed5b7782015-04-25View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0159-1901000000-dcbc777e43693cc64c6f2015-04-25View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001l-5900000000-66eed55623a37e730cdc2015-04-25View Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
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 IDFDB015466
KNApSAcK IDC00003073
Chemspider ID308989
KEGG Compound IDC09771
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkAucubin
METLIN IDNot Available
PubChem Compound348157
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Hung JY, Yang CJ, Tsai YM, Huang HW, Huang MS: Antiproliferative activity of aucubin is through cell cycle arrest and apoptosis in human non-small cell lung cancer A549 cells. Clin Exp Pharmacol Physiol. 2008 Sep;35(9):995-1001. doi: 10.1111/j.1440-1681.2008.04935.x. Epub 2008 Apr 21. [PubMed:18430063 ]
  2. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  3. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  4. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  5. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  6. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  7. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.