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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:53:16 UTC
Update Date2022-03-07 02:53:59 UTC
HMDB IDHMDB0034095
Secondary Accession Numbers
  • HMDB34095
Metabolite Identification
Common NameGambogic acid
DescriptionGambogic acid, also known as gambogate, belongs to the class of organic compounds known as pyranoxanthones. These are organic aromatic compounds containing a pyran or a hydrogenated derivative fused to a xanthone ring system. Gambogic acid has been detected, but not quantified in, fruits and herbs and spices. This could make gambogic acid a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on Gambogic acid.
Structure
Data?1563862509
Synonyms
ValueSource
GambogateGenerator
Gamboge acidMeSH
Gambogoic acidMeSH
a-Gambogic acidHMDB
b-GuttiferinHMDB
b-GuttilactoneHMDB
Guttatic acidHMDB
Guttic acidHMDB
(2Z)-4-[12-Hydroxy-8,21,21-trimethyl-5-(3-methylbut-2-en-1-yl)-8-(4-methylpent-3-en-1-yl)-14,18-dioxo-3,7,20-trioxahexacyclo[15.4.1.0²,¹⁵.0²,¹⁹.0⁴,¹³.0⁶,¹¹]docosa-4(13),5,9,11,15-pentaen-19-yl]-2-methylbut-2-enoateGenerator
Gambogic acidMeSH
Chemical FormulaC38H44O8
Average Molecular Weight628.7512
Monoisotopic Molecular Weight628.303618384
IUPAC Name(2Z)-4-[12-hydroxy-8,21,21-trimethyl-5-(3-methylbut-2-en-1-yl)-8-(4-methylpent-3-en-1-yl)-14,18-dioxo-3,7,20-trioxahexacyclo[15.4.1.0²,¹⁵.0²,¹⁹.0⁴,¹³.0⁶,¹¹]docosa-4,6(11),9,12,15-pentaen-19-yl]-2-methylbut-2-enoic acid
Traditional Name(2Z)-4-[12-hydroxy-8,21,21-trimethyl-5-(3-methylbut-2-en-1-yl)-8-(4-methylpent-3-en-1-yl)-14,18-dioxo-3,7,20-trioxahexacyclo[15.4.1.0²,¹⁵.0²,¹⁹.0⁴,¹³.0⁶,¹¹]docosa-4,6(11),9,12,15-pentaen-19-yl]-2-methylbut-2-enoic acid
CAS Registry Number2752-65-0
SMILES
CC(C)=CCCC1(C)OC2=C(C=C1)C(O)=C1C(=O)C3=CC4CC5C(C)(C)OC(C\C=C(\C)C(O)=O)(C4=O)C35OC1=C2CC=C(C)C
InChI Identifier
InChI=1S/C38H44O8/c1-20(2)10-9-15-36(8)16-14-24-29(39)28-30(40)26-18-23-19-27-35(6,7)46-37(33(23)41,17-13-22(5)34(42)43)38(26,27)45-32(28)25(31(24)44-36)12-11-21(3)4/h10-11,13-14,16,18,23,27,39H,9,12,15,17,19H2,1-8H3,(H,42,43)/b22-13-
InChI KeyGEZHEQNLKAOMCA-XKZIYDEJSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyranoxanthones. These are organic aromatic compounds containing a pyran or a hydrogenated derivative fused to a xanthone ring system.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzopyrans
Sub Class1-benzopyrans
Direct ParentPyranoxanthones
Alternative Parents
Substituents
  • Pyranoxanthone
  • Pyranochromene
  • Chromone
  • Aromatic monoterpenoid
  • Monoterpenoid
  • Aryl ketone
  • Alkyl aryl ether
  • Cyclohexenone
  • Oxepane
  • Benzenoid
  • Vinylogous acid
  • Tetrahydrofuran
  • Ketone
  • Monocarboxylic acid or derivatives
  • Oxacycle
  • Ether
  • Dialkyl ether
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Organic oxygen compound
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point86 - 91 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.00071 g/LALOGPS
logP5.57ALOGPS
logP7.78ChemAxon
logS-6ALOGPS
pKa (Strongest Acidic)3.76ChemAxon
pKa (Strongest Basic)-4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area119.36 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity179.16 m³·mol⁻¹ChemAxon
Polarizability68.1 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+240.67931661259
DarkChem[M-H]-232.49731661259
DeepCCS[M-2H]-277.64930932474
DeepCCS[M+Na]+251.83830932474
AllCCS[M+H]+246.032859911
AllCCS[M+H-H2O]+244.832859911
AllCCS[M+NH4]+247.132859911
AllCCS[M+Na]+247.432859911
AllCCS[M-H]-248.532859911
AllCCS[M+Na-2H]-251.832859911
AllCCS[M+HCOO]-255.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.7.26 minutes32390414
Predicted by Siyang on May 30, 202217.1845 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.92 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid48.2 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4310.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid158.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid257.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid142.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid102.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid929.9 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid779.2 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)93.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1635.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid752.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1385.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid638.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid502.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate136.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA268.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water9.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Gambogic acidCC(C)=CCCC1(C)OC2=C(C=C1)C(O)=C1C(=O)C3=CC4CC5C(C)(C)OC(C\C=C(\C)C(O)=O)(C4=O)C35OC1=C2CC=C(C)C6134.6Standard polar33892256
Gambogic acidCC(C)=CCCC1(C)OC2=C(C=C1)C(O)=C1C(=O)C3=CC4CC5C(C)(C)OC(C\C=C(\C)C(O)=O)(C4=O)C35OC1=C2CC=C(C)C4227.5Standard non polar33892256
Gambogic acidCC(C)=CCCC1(C)OC2=C(C=C1)C(O)=C1C(=O)C3=CC4CC5C(C)(C)OC(C\C=C(\C)C(O)=O)(C4=O)C35OC1=C2CC=C(C)C4305.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Gambogic acid,1TMS,isomer #1CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5CC3C(C)(C)OC4(C/C=C(/C)C(=O)O)C5=O)C(=O)C1=C2O[Si](C)(C)C4379.1Semi standard non polar33892256
Gambogic acid,1TMS,isomer #2CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5CC3C(C)(C)OC4(C/C=C(/C)C(=O)O[Si](C)(C)C)C5=O)C(=O)C1=C2O4324.7Semi standard non polar33892256
Gambogic acid,1TMS,isomer #3CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5=C(O[Si](C)(C)C)C3(C/C=C(/C)C(=O)O)OC(C)(C)C4C5)C(=O)C1=C2O4252.4Semi standard non polar33892256
Gambogic acid,2TMS,isomer #1CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5CC3C(C)(C)OC4(C/C=C(/C)C(=O)O[Si](C)(C)C)C5=O)C(=O)C1=C2O[Si](C)(C)C4266.3Semi standard non polar33892256
Gambogic acid,2TMS,isomer #2CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5=C(O[Si](C)(C)C)C3(C/C=C(/C)C(=O)O)OC(C)(C)C4C5)C(=O)C1=C2O[Si](C)(C)C4191.7Semi standard non polar33892256
Gambogic acid,2TMS,isomer #3CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5=C(O[Si](C)(C)C)C3(C/C=C(/C)C(=O)O[Si](C)(C)C)OC(C)(C)C4C5)C(=O)C1=C2O4148.5Semi standard non polar33892256
Gambogic acid,3TMS,isomer #1CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5=C(O[Si](C)(C)C)C3(C/C=C(/C)C(=O)O[Si](C)(C)C)OC(C)(C)C4C5)C(=O)C1=C2O[Si](C)(C)C4112.2Semi standard non polar33892256
Gambogic acid,3TMS,isomer #1CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5=C(O[Si](C)(C)C)C3(C/C=C(/C)C(=O)O[Si](C)(C)C)OC(C)(C)C4C5)C(=O)C1=C2O[Si](C)(C)C4212.5Standard non polar33892256
Gambogic acid,1TBDMS,isomer #1CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5CC3C(C)(C)OC4(C/C=C(/C)C(=O)O)C5=O)C(=O)C1=C2O[Si](C)(C)C(C)(C)C4630.9Semi standard non polar33892256
Gambogic acid,1TBDMS,isomer #2CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5CC3C(C)(C)OC4(C/C=C(/C)C(=O)O[Si](C)(C)C(C)(C)C)C5=O)C(=O)C1=C2O4576.8Semi standard non polar33892256
Gambogic acid,1TBDMS,isomer #3CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5=C(O[Si](C)(C)C(C)(C)C)C3(C/C=C(/C)C(=O)O)OC(C)(C)C4C5)C(=O)C1=C2O4503.1Semi standard non polar33892256
Gambogic acid,2TBDMS,isomer #1CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5CC3C(C)(C)OC4(C/C=C(/C)C(=O)O[Si](C)(C)C(C)(C)C)C5=O)C(=O)C1=C2O[Si](C)(C)C(C)(C)C4707.6Semi standard non polar33892256
Gambogic acid,2TBDMS,isomer #2CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5=C(O[Si](C)(C)C(C)(C)C)C3(C/C=C(/C)C(=O)O)OC(C)(C)C4C5)C(=O)C1=C2O[Si](C)(C)C(C)(C)C4637.3Semi standard non polar33892256
Gambogic acid,2TBDMS,isomer #3CC(C)=CCCC1(C)C=CC2=C(O1)C(CC=C(C)C)=C1OC34C(=CC5=C(O[Si](C)(C)C(C)(C)C)C3(C/C=C(/C)C(=O)O[Si](C)(C)C(C)(C)C)OC(C)(C)C4C5)C(=O)C1=C2O4588.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9000057000-19abde6d758101a01ef72017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-10-17Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gambogic acid GC-MS ("Gambogic acid,1TMS,#1" TMS) - 70eV, PositiveNot Available2021-11-02Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 10V, Positive-QTOFsplash10-01t9-0000096000-e56a0ec531207df34ab62016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 20V, Positive-QTOFsplash10-0o6r-3001591000-411cf0af71ea4c9389ec2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 40V, Positive-QTOFsplash10-016r-7153941000-92579129327c5702bfb82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 10V, Negative-QTOFsplash10-004i-1001039000-9c55dff29165d33866d82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 20V, Negative-QTOFsplash10-057i-1014095000-77a8e0d8dca00f9672ef2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 40V, Negative-QTOFsplash10-0ab9-2794313000-d45dab05ad38be7aee922016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 10V, Negative-QTOFsplash10-004i-0000009000-312b00b9e28384b5d53e2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 20V, Negative-QTOFsplash10-004i-0000059000-d354ba3ab7fc6d3f14622021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 40V, Negative-QTOFsplash10-02t9-2100391000-dcdb58e0da6ce0fbbe962021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 10V, Positive-QTOFsplash10-004i-0000079000-d5501837c889acaa50342021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 20V, Positive-QTOFsplash10-004r-0000093000-23942b0217f9c03ee8782021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gambogic acid 40V, Positive-QTOFsplash10-00kg-2000951000-5ee22b87ea31bfe4e09e2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • 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 IDFDB012358
KNApSAcK IDC00002950
Chemspider ID4510165
KEGG Compound IDC10062
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGambogic acid
METLIN IDNot Available
PubChem Compound5353639
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1525961
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .