Ryanodine (T3D4066)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationTargets (1)XML
Targets (1)
Record Information
Version2.0
Creation Date2014-08-29 05:01:22 UTC
Update Date2014-12-24 20:26:37 UTC
Accession NumberT3D4066
Identification
Common NameRyanodine
ClassSmall Molecule
DescriptionRyanodine is a poisonous alkaloid found in the South American plant Ryania speciosa (Flacourtiaceae). It was originally used as an insecticide. The compound has extremely high affinity to the open-form ryanodine receptor, a group of calcium channels found in skeletal muscle, smooth muscle, and heart muscle cells. It binds with such high affinity to the receptor that it was used as a label for the first purification of that class of ion channels and gave its name to it.
Compound Type
  • Ester
  • Insecticide
  • Natural Compound
  • Organic Compound
  • Pesticide
  • Plant Toxin
Chemical Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
Synonym
Ryania
Chemical FormulaC25H35NO9
Average Molecular Mass493.547 g/mol
Monoisotopic Mass493.231 g/mol
CAS Registry Number15662-33-6
IUPAC Name(1R,2R,3S,6S,7S,9S,10S,11S,12R,13S,14R)-2,6,9,11,13,14-hexahydroxy-3,7,10-trimethyl-11-(propan-2-yl)-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1H-pyrrole-2-carboxylate
Traditional Nameryania
SMILES[H][C@@]1(OC(=O)C2=CC=CN2)[C@](O)(C(C)C)[C@]2(C)[C@]3(O)C[C@@]4(C)[C@@]5(O)CC[C@]([H])(C)[C@@]([H])(O)[C@]5(O3)[C@]2(O)[C@@]14O
InChI IdentifierInChI=1S/C25H35NO9/c1-12(2)22(31)17(34-16(28)14-7-6-10-26-14)23(32)18(4)11-21(30)19(22,5)25(23,33)24(35-21)15(27)13(3)8-9-20(18,24)29/h6-7,10,12-13,15,17,26-27,29-33H,8-9,11H2,1-5H3/t13-,15+,17+,18-,19-,20-,21-,22+,23+,24+,25+/m0/s1
InChI KeyInChIKey=JJSYXNQGLHBRRK-YSOSZROBSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassDiterpenoids
Direct ParentDiterpenoids
Alternative Parents
Substituents
  • Diterpenoid
  • Ryanodane diterpenoid
  • Pyrrole-2-carboxylic acid or derivatives
  • Oxepane
  • Monosaccharide
  • Oxane
  • Substituted pyrrole
  • Cyclic alcohol
  • Heteroaromatic compound
  • Pyrrole
  • Tetrahydrofuran
  • Tertiary alcohol
  • Carboxylic acid ester
  • Hemiacetal
  • Secondary alcohol
  • Polyol
  • Oxacycle
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Actin Cytoskeleton
  • Actin Filament
  • Caveolae
  • Cell junction
  • Cell surface
  • Cytoplasm
  • Cytoskeleton
  • Cytosol
  • Endoplasmic reticulum
  • Endoplasmic reticulum membrane
  • Endosome
  • Extracellular
  • Golgi apparatus
  • Membrane Fraction
  • Microsome
  • Mitochondrial Matrix
  • Mitochondrion
  • Nuclear Membrane
  • Perinuclear region
  • Plasma Membrane
  • Sarcoplasm
  • Sarcoplasmic Reticulum
  • Secretory vesicle
  • Synaptic Vesicle
Biofluid LocationsNot Available
Tissue LocationsNot Available
Pathways
NameSMPDB LinkKEGG Link
ApoptosisNot Availablemap04210
Insulin secretionNot Availablemap04911
Cardiac muscle contractionNot Availablemap04260
Oxidative phosphorylationNot Availablemap00190
Circadian rhythmNot Availablemap04710
Long-term potentiationNot Availablemap04720
Long-term depressionNot Availablemap04730
PhototransductionNot Availablemap04744
Renin-angiotensin systemNot Availablemap04614
Cholinergic synapseNot Availablemap04725
Calcium signaling pathwayNot Availablemap04020
Antiarrhythmic DrugsNot AvailableNot Available
Applications
Biological Roles
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 Solubility9.18 g/LALOGPS
logP0.39ALOGPS
logP0.1ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)11.22ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area172.7 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity119.06 m³·mol⁻¹ChemAxon
Polarizability50.56 ųChemAxon
Number of Rings6ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-1002900000-c715042aa215c115e2ed2016-06-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000x-8004900000-d44f709b09d0431bc6752016-06-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014l-9005000000-412616ac99f603b759232016-06-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-1105900000-7da3ccb64cfebdd8793a2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-029y-3309300000-40f8eb8ad8754e0a40632016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-090u-9206000000-1ef5662142d2f16415302016-08-03View Spectrum
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityRyanodine has extremely high affinity to the open-form ryanodine receptor, a group of calcium channels found in skeletal muscle, smooth muscle, and heart muscle cells. It binds with such high affinity to the receptor that it was used as a label for the first purification of that class of ion channels and gave its name to it. At nanomolar concentrations, ryanodine locks the receptor in a half-open state, whereas it fully closes them at micromolarconcentration. The effect of the nanomolar-level binding is that ryanodine causes release of calcium from calcium stores as thesarcoplasmic reticulum in the cytoplasm, leading to massive muscular contractions. (Wikipedia)
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesThis is a natural compound that is used as a pesticide.
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsNot Available
TreatmentNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDNot Available
HMDB IDNot Available
PubChem Compound ID441753
ChEMBL IDNot Available
ChemSpider ID390355
KEGG IDC08705
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
MSDST3D4066.pdf
General ReferencesNot Available
Gene Regulation
Up-Regulated GenesNot Available
Down-Regulated GenesNot Available

Targets

Target Details
1. Ryanodine receptor 1
General Function:
Voltage-gated calcium channel activity
Specific Function:
Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules. Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm. Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity).
Gene Name:
RYR1
Uniprot ID:
P21817
Molecular Weight:
565170.715 Da
References
  1. Ahn KC, Zhao B, Chen J, Cherednichenko G, Sanmarti E, Denison MS, Lasley B, Pessah IN, Kultz D, Chang DP, Gee SJ, Hammock BD: In vitro biologic activities of the antimicrobials triclocarban, its analogs, and triclosan in bioassay screens: receptor-based bioassay screens. Environ Health Perspect. 2008 Sep;116(9):1203-10. doi: 10.1289/ehp.11200. [18795164 ]