NP-MRD: Showing NP-Card for (1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate (NP0319580)

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Record Information

Version

2.0

Created at

2022-09-11 20:41:31 UTC

Updated at

2022-09-11 20:41:31 UTC

NP-MRD ID

NP0319580

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate

Description

Ryanodine belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. (1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate is found in Ryania speciosa. (1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate was first documented in 2022 (PMID: 36122240). Based on a literature review a small amount of articles have been published on ryanodine (PMID: 36117698) (PMID: 36114707) (PMID: 36106241) (PMID: 36104752).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112222412D          

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M  END

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  Mrv1652309112222412D          

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 13 14  1  0  0  0  0
 10 14  1  0  0  0  0
  6 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
  4 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 15 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
 26 27  1  6  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  0  0  0  0
 17 34  1  0  0  0  0
 26 34  1  0  0  0  0
 34 35  1  1  0  0  0
 21 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0319580

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@]1(O)[C@H](OC(=O)C2=CC=CN2)[C@]2(O)[C@]3(C)C[C@@]4(O)O[C@]5([C@@H](O)[C@H](C)CC[C@@]35O)[C@]2(O)[C@]14C

> <INCHI_IDENTIFIER>
InChI=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+/m1/s1

> <INCHI_KEY>
JJSYXNQGLHBRRK-BOEHKCAMSA-N

> <FORMULA>
C25H35NO9

> <MOLECULAR_WEIGHT>
493.553

> <EXACT_MASS>
493.231181711

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
42.26645618039031

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,3R,6R,7R,9R,10S,11S,12S,13R,14S)-2,6,9,11,13,14-hexahydroxy-3,7,10-trimethyl-11-(propan-2-yl)-15-oxapentacyclo[7.5.1.0^{1,6}.0^{7,13}.0^{10,14}]pentadecan-12-yl 1H-pyrrole-2-carboxylate

> <JCHEM_LOGP>
0.10185210766666547

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.852682060247172

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.223243679962478

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4100629455048983

> <JCHEM_POLAR_SURFACE_AREA>
172.7

> <JCHEM_REFRACTIVITY>
119.0629

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,3R,6R,7R,9R,10S,11S,12S,13R,14S)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0^{1,6}.0^{7,13}.0^{10,14}]pentadecan-12-yl 1H-pyrrole-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.201   1.109   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.691   0.810   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.676   1.968   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.195  -0.648   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.689  -1.019   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.946  -2.203   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.114  -3.206   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -3.567  -2.695   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -3.851  -1.181   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -4.736  -3.698   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.611  -5.233   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.032  -5.826   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -7.035  -4.657   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -6.234  -3.342   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       0.691  -2.729   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.071  -4.138   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.457  -1.239   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.465  -2.402   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.235  -0.022   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.518   1.491   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.039  -1.154   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.466  -1.480   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.080  -3.104   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.747  -3.331   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.103  -4.829   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.132  -2.403   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       3.321  -3.932   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       4.591  -2.927   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.731  -1.887   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.451  -0.357   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.625   0.639   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.989   0.169   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       3.753   1.690   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       2.722  -0.802   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       1.457   0.313   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6   19                                             
CONECT    5    4                                                            
CONECT    6    4    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   14                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   10                                                       
CONECT   15    6   16   17   24                                             
CONECT   16   15                                                            
CONECT   17   15   18   19   34                                             
CONECT   18   17                                                            
CONECT   19   17    4   20   21                                             
CONECT   20   19                                                            
CONECT   21   19   22   23   35                                             
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   15   25   26                                             
CONECT   25   24                                                            
CONECT   26   24   27   28   34                                             
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   17   26   35                                             
CONECT   35   34   21                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₅NO₉

Average Mass

493.5530 Da

Monoisotopic Mass

493.23118 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(C)[C@@]1(O)[C@H](OC(=O)C2=CC=CN2)[C@]2(O)[C@]3(C)C[C@@]4(O)O[C@]5([C@@H](O)[C@H](C)CC[C@@]35O)[C@]2(O)[C@]14C

InChI Identifier

InChI=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+/m1/s1

InChI Key

JJSYXNQGLHBRRK-BOEHKCAMSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Ryania speciosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Ryanodane diterpenoid
Diterpenoid
Pyrrole-2-carboxylic acid or derivatives
Oxepane
Substituted pyrrole
Oxane
Monosaccharide
Heteroaromatic compound
Tetrahydrofuran
Tertiary alcohol
Pyrrole
Cyclic alcohol
Secondary alcohol
Hemiacetal
Carboxylic acid ester
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00001661

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Ryanodine

METLIN ID

Not Available

PubChem Compound

139593370

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Arige V, Terry LE, Wagner LE 2nd, Malik S, Baker MR, Fan G, Joseph SK, Serysheva II, Yule DI: Functional determination of calcium-binding sites required for the activation of inositol 1,4,5-trisphosphate receptors. Proc Natl Acad Sci U S A. 2022 Sep 27;119(39):e2209267119. doi: 10.1073/pnas.2209267119. Epub 2022 Sep 19. [PubMed:36122240 ]
Bolanos P, Calderon JC: Excitation-contraction coupling in mammalian skeletal muscle: Blending old and last-decade research. Front Physiol. 2022 Sep 2;13:989796. doi: 10.3389/fphys.2022.989796. eCollection 2022. [PubMed:36117698 ]
Zhang X, Smith CER, Morotti S, Edwards AG, Sato D, Louch WE, Ni H, Grandi E: Mechanisms of spontaneous Ca(2+) release-mediated arrhythmia in a novel 3D human atrial myocyte model: II. Ca(2+) -handling protein variation. J Physiol. 2023 Jul;601(13):2685-2710. doi: 10.1113/JP283602. Epub 2022 Sep 29. [PubMed:36114707 ]
Acharya S, Devkota P, Shrestha R, Bajracharya AK, Jesmajian S: Catecholaminergic Polymorphic Ventricular Tachycardia Presented As Generalized Tonic-Clonic Seizure: A Case Report. Cureus. 2022 Aug 9;14(8):e27806. doi: 10.7759/cureus.27806. eCollection 2022 Aug. [PubMed:36106241 ]
Xu B, Wang Y, Bahriz SMFM, Zhao M, Zhu C, Xiang YK: Probing spatiotemporal PKA activity at the ryanodine receptor and SERCA2a nanodomains in cardomyocytes. Cell Commun Signal. 2022 Sep 14;20(1):143. doi: 10.1186/s12964-022-00947-8. [PubMed:36104752 ]
LOTUS database [Link]

Showing NP-Card for (1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate (NP0319580)

MOL for NP0319580 ((1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate)

3D MOL for NP0319580 ((1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate)

3D SDF for NP0319580 ((1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate)

3D-SDF for NP0319580 ((1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate)

PDB for NP0319580 ((1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate)

3D PDB for NP0319580 ((1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate)

SMILES for NP0319580 ((1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate)

INCHI for NP0319580 ((1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate)

Structure for NP0319580 ((1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate)

3D Structure for NP0319580 ((1s,2s,3r,6r,7r,9r,10s,11s,12s,13r,14s)-2,6,9,11,13,14-hexahydroxy-11-isopropyl-3,7,10-trimethyl-15-oxapentacyclo[7.5.1.0¹,⁶.0⁷,¹³.0¹⁰,¹⁴]pentadecan-12-yl 1h-pyrrole-2-carboxylate)