Gymnodimine (T3D4051)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationXML
Record Information
Version2.0
Creation Date2014-08-29 04:58:27 UTC
Update Date2014-12-24 20:26:36 UTC
Accession NumberT3D4051
Identification
Common NameGymnodimine
ClassSmall Molecule
DescriptionGymnodimine is found in mollusks. Gymnodimine is isolated from New Zealand oysters (Tiostrea chilensis) and the dinoflagellate Gymnodinium cf. mikimotoi.
Compound Type
  • Animal Toxin
  • Ester
  • Ether
  • Food Toxin
  • Marine Toxin
  • Metabolite
  • Natural Compound
  • Organic Compound
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Synonym
(5S)-5-[(1R,2E,11R,16S,17E,19S,22R,24R)-19-Hydroxy-2,15,18,24-tetramethyl-25-oxa-7-azatetracyclo[20.2.1.06,11.011,16]pentacosa-2,6,14,17-tetraen-14-yl]-3-methyl-2(5H)-furanone
(−)-Gymnodimine A
Chemical FormulaC32H45NO4
Average Molecular Mass507.704 g/mol
Monoisotopic Mass507.335 g/mol
CAS Registry Number173792-58-0
IUPAC Name5-[(2E)-19-hydroxy-2,15,18,24-tetramethyl-25-oxa-7-azatetracyclo[20.2.1.0⁶,¹¹.0¹¹,¹⁶]pentacosa-2,6,14,17-tetraen-14-yl]-3-methyl-2,5-dihydrofuran-2-one
Traditional Name5-[(2E)-19-hydroxy-2,15,18,24-tetramethyl-25-oxa-7-azatetracyclo[20.2.1.0⁶,¹¹.0¹¹,¹⁶]pentacosa-2,6,14,17-tetraen-14-yl]-3-methyl-5H-furan-2-one
SMILES[H]\C1=C(C)/C2OC(CC2C)CCC(O)\C(C)=C([H])\C2C(C)=C(CCC22CCCN=C2CC1)C1OC(=O)C(C)=C1
InChI IdentifierInChI=1/C32H45NO4/c1-19-8-6-9-29-32(13-7-15-33-29)14-12-25(28-18-22(4)31(35)37-28)23(5)26(32)17-20(2)27(34)11-10-24-16-21(3)30(19)36-24/h8,17-18,21,24,26-28,30,34H,6-7,9-16H2,1-5H3/b19-8+,20-17+
InChI KeyInChIKey=DVXZVCNEGRKLMW-DCJZOFSYNA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as tetrahydropyridines. These are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassHydropyridines
Direct ParentTetrahydropyridines
Alternative Parents
Substituents
  • Tetrahydropyridine
  • 2-furanone
  • Dihydrofuran
  • Tetrahydrofuran
  • Enoate ester
  • Alpha,beta-unsaturated carboxylic ester
  • Carboxylic acid ester
  • Ketimine
  • Lactone
  • Secondary alcohol
  • Carboxylic acid derivative
  • Dialkyl ether
  • Ether
  • Monocarboxylic acid or derivatives
  • Oxacycle
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic oxide
  • Imine
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organonitrogen compound
  • Organooxygen compound
  • Alcohol
  • Organic oxygen compound
  • Organopnictogen compound
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Extracellular
  • Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot Available
LogPNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.0023 g/LALOGPS
logP5.35ALOGPS
logP5.75ChemAxon
logS-5.3ALOGPS
pKa (Strongest Acidic)14.56ChemAxon
pKa (Strongest Basic)7.19ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area68.12 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity150.03 m³·mol⁻¹ChemAxon
Polarizability58.06 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-1000900000-b82637757d6a834777902017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0hb9-5000390000-fee203e839b6cb58df1b2017-10-06View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0536-0000920000-a3f628705e2e6a0e2a462016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00yu-0000900000-9df5c5e06bee3a748b6c2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004r-7109700000-10d898778adbd4ed830c2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0000790000-47d22a5a77d06aeed9a02016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0bt9-2000940000-56e4a3edbcde7f3df5012016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-000x-2015900000-843815d7349a6995ca312016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4l-0002980000-04328292a60ad2c1c5aa2021-09-24View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0bt9-0000940000-ccbf9796bdaa2ac405d42021-09-24View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-1004900000-ed2558f11fcccc20e1c22021-09-24View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0000290000-f29567e802fbf48154c82021-09-24View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-0000910000-9376a4fbf77032e3293a2021-09-24View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0udr-5001940000-ee51e656106fa49d70582021-09-24View Spectrum
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityGymnodimine exerts its toxic effects via binding to nicotinic acetylcholine receptors with picomolar affinities with no sign of apparent reversibility in short time frames. The toxicity of gymnodimine has been attributed, at least in part, to the imine functionality as its reduction leads to a non-toxic derivative. Gymnodimine and 13-desmethyl spirolide C bound to acetylcholine binding proteins. (1)
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesGymnodimine is found in mollusks. Gymnodimine is isolated from New Zealand oysters (Tiostrea chilensis) and the dinoflagellate Gymnodinium cf.
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsNot Available
TreatmentNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDNot Available
HMDB IDHMDB41430
PubChem Compound ID10436276
ChEMBL IDNot Available
ChemSpider ID8611700
KEGG IDC20025
UniProt IDNot Available
OMIM ID
ChEBI IDNot Available
BioCyc IDNot Available
CTD IDNot Available
Stitch IDNot Available
PDB IDNot Available
ACToR IDNot Available
Wikipedia LinkNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General References
  1. Kong K, Moussa Z, Lee C, Romo D: Total synthesis of the spirocyclic imine marine toxin (-)-gymnodimine and an unnatural C4-epimer. J Am Chem Soc. 2011 Dec 14;133(49):19844-56. doi: 10.1021/ja207385y. Epub 2011 Nov 16. [22023219 ]
  2. Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.
Gene Regulation
Up-Regulated GenesNot Available
Down-Regulated GenesNot Available