NP-MRD: Showing NP-Card for (3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one (NP0236450)

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Record Information

Version

2.0

Created at

2022-09-06 19:21:11 UTC

Updated at

2022-09-06 19:21:11 UTC

NP-MRD ID

NP0236450

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one

Description

Yibeissine belongs to the class of organic compounds known as jerveratrum-type alkaloids. These are steroidal alkaloids with a structure that is based on the jervane ring system. Jerveratrum alkaloids have alkamines with 1-3 oxygen atoms, and occur as such or as monoglycosides. (3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one is found in Fritillaria pallidiflora. (3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one was first documented in 2021 (PMID: 35011398). Based on a literature review very few articles have been published on Yibeissine.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062221212D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309062221212D          

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 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  1  0  0  0
  9 15  1  0  0  0  0
 15 16  1  0  0  0  0
  7 16  1  0  0  0  0
 16 17  1  1  0  0  0
  4 18  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 22 20  1  1  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  1  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 22 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 30 18  1  1  0  0  0
 30 31  1  0  0  0  0
  3 31  1  0  0  0  0
 31 32  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0236450

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1[C@@H]2NC[C@@H](C)C[C@H]2O[C@]11CC[C@H]2[C@@H]3CC(=O)[C@H]4C[C@@H](O)CC[C@]4(C)[C@H]3[C@@H](O)C2=C1C

> <INCHI_IDENTIFIER>
InChI=1S/C27H41NO4/c1-13-9-21-24(28-12-13)15(3)27(32-21)8-6-17-18-11-20(30)19-10-16(29)5-7-26(19,4)23(18)25(31)22(17)14(27)2/h13,15-19,21,23-25,28-29,31H,5-12H2,1-4H3/t13-,15+,16-,17-,18-,19+,21+,23+,24-,25-,26-,27-/m0/s1

> <INCHI_KEY>
NURPXYQPDMVKOY-RUKZUWONSA-N

> <FORMULA>
C27H41NO4

> <MOLECULAR_WEIGHT>
443.628

> <EXACT_MASS>
443.303558804

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
51.959276546921195

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'S,2R,2'R,3R,3aS,5'S,6S,7'S,7aR,10'S,11'S,17'R)-5',17'-dihydroxy-2',3,6,15'-tetramethyl-3a,4,5,6,7,7a-hexahydro-3H-spiro[furo[3,2-b]pyridine-2,14'-tetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadecan]-15'-en-8'-one

> <JCHEM_LOGP>
2.125938211333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.281550418373627

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.249500774500891

> <JCHEM_PKA_STRONGEST_BASIC>
9.93400524201199

> <JCHEM_POLAR_SURFACE_AREA>
78.79

> <JCHEM_REFRACTIVITY>
123.4249

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1'S,2R,2'R,3R,3aS,5'S,6S,7'S,7aR,10'S,11'S,17'R)-5',17'-dihydroxy-2',3,6,15'-tetramethyl-3a,4,5,6,7,7a-hexahydro-3H-spiro[furo[3,2-b]pyridine-2,14'-tetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadecan]-15'-en-8'-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       8.739   2.357   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.351   0.867   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.866   0.458   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.479  -1.032   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.575  -2.113   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.060  -1.704   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.448  -0.214   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       9.989   1.228   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      11.528   1.158   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.609   2.255   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.099   1.867   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      15.181   2.963   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.509   0.382   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      13.427  -0.715   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      11.937  -0.327   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.651  -1.175   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.582  -2.713   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.941  -1.124   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.981  -2.328   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.458  -2.097   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.497  -3.301   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.896  -0.664   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.373  -0.434   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.189   1.000   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -1.712   1.230   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       0.772   2.204   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.294   1.974   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.856   0.540   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.817   1.744   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.379   0.310   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.569   1.288   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.477   2.825   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   31                                                  
CONECT    4    3    5   18                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8   16                                             
CONECT    8    7    9                                                       
CONECT    9    8   10   15                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    9   16                                                  
CONECT   16   15    7   17                                                  
CONECT   17   16                                                            
CONECT   18    4   19   30                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   28                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   22   29   30                                             
CONECT   29   28                                                            
CONECT   30   28   18   31                                                  
CONECT   31   30    3   32                                                  
CONECT   32   31                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₁NO₄

Average Mass

443.6280 Da

Monoisotopic Mass

443.30356 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@@H]1[C@@H]2NC[C@@H](C)C[C@H]2O[C@]11CC[C@H]2[C@@H]3CC(=O)[C@H]4C[C@@H](O)CC[C@]4(C)[C@H]3[C@@H](O)C2=C1C

InChI Identifier

InChI=1S/C27H41NO4/c1-13-9-21-24(28-12-13)15(3)27(32-21)8-6-17-18-11-20(30)19-10-16(29)5-7-26(19,4)23(18)25(31)22(17)14(27)2/h13,15-19,21,23-25,28-29,31H,5-12H2,1-4H3/t13-,15+,16-,17-,18-,19+,21+,23+,24-,25-,26-,27-/m0/s1

InChI Key

NURPXYQPDMVKOY-RUKZUWONSA-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
Fritillaria pallidiflora	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as jerveratrum-type alkaloids. These are steroidal alkaloids with a structure that is based on the jervane ring system. Jerveratrum alkaloids have alkamines with 1-3 oxygen atoms, and occur as such or as monoglycosides.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal alkaloids

Direct Parent

Jerveratrum-type alkaloids

Alternative Parents

Substituents

Jerveratrum-type alkaloid
Azasteroid
Alkaloid or derivatives
Piperidine
Cyclic alcohol
Tetrahydrofuran
Ketone
Secondary alcohol
Dialkyl ether
Secondary aliphatic amine
Ether
Oxacycle
Secondary amine
Azacycle
Organoheterocyclic compound
Organic oxide
Organopnictogen compound
Amine
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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

C00029250

Chemspider ID

2340608

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3083381

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Shim KS, Gu DR, Hwang YH, Yang H, Ryuk JA, Ha H: Water Extract of Fritillariae thunbergii Bulbus Inhibits RANKL-Mediated Osteoclastogenesis and Ovariectomy-Induced Trabecular Bone Loss. Molecules. 2021 Dec 28;27(1). pii: molecules27010169. doi: 10.3390/molecules27010169. [PubMed:35011398 ]
LOTUS database [Link]

Showing NP-Card for (3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one (NP0236450)

MOL for NP0236450 ((3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one)

3D MOL for NP0236450 ((3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one)

3D SDF for NP0236450 ((3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one)

3D-SDF for NP0236450 ((3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one)

PDB for NP0236450 ((3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one)

3D PDB for NP0236450 ((3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one)

SMILES for NP0236450 ((3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one)

INCHI for NP0236450 ((3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one)

Structure for NP0236450 ((3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one)

3D Structure for NP0236450 ((3s,3'r,3'as,4as,6's,6as,6bs,7'ar,9r,11r,11as,11br)-3,11-dihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5',6,6',6a,6b,7,7',7'a,8,11,11a-octadecahydro-3'h-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridin]-5-one)