NP-MRD: Showing NP-Card for 8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one (NP0227306)

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Record Information

Version

1.0

Created at

2022-09-06 06:35:34 UTC

Updated at

2022-09-06 06:35:34 UTC

NP-MRD ID

NP0227306

Secondary Accession Numbers

None

Natural Product Identification

Common Name

8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one

Description

Gargalol B belongs to the class of organic compounds known as ergostane steroids. These are steroids with a structure based on the ergostane skeleton, which arises from the methylation of cholestane at the 24-position. 8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one is found in Grifola gargal. It was first documented in 2022 (PMID: 36088043). Based on a literature review a significant number of articles have been published on Gargalol B (PMID: 36087927) (PMID: 36087886) (PMID: 36087866) (PMID: 36087840).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062208352D          

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M  END

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  Mrv1652309062208352D          

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M  END
> <DATABASE_ID>
NP0227306

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C(C)C=CC(C)C1CCC2=C3C(=O)CC45CC(O)CCC4(C)C3(CCC12C)OO5

> <INCHI_IDENTIFIER>
InChI=1S/C28H42O4/c1-17(2)18(3)7-8-19(4)21-9-10-22-24-23(30)16-27-15-20(29)11-12-26(27,6)28(24,32-31-27)14-13-25(21,22)5/h7-8,17-21,29H,9-16H2,1-6H3

> <INCHI_KEY>
LJBJXGTWGWODIW-UHFFFAOYSA-N

> <FORMULA>
C28H42O4

> <MOLECULAR_WEIGHT>
442.64

> <EXACT_MASS>
442.308309832

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
51.306311396202126

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0^{1,13}.0^{4,12}.0^{5,9}]nonadec-4-en-3-one

> <JCHEM_LOGP>
5.5933398369999985

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.797995429796533

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.13506790167865

> <JCHEM_PKA_STRONGEST_BASIC>
-2.729200427477008

> <JCHEM_POLAR_SURFACE_AREA>
55.760000000000005

> <JCHEM_REFRACTIVITY>
126.98409999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0^{1,13}.0^{4,12}.0^{5,9}]nonadec-4-en-3-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      16.938   1.165   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      15.409   1.348   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.486   0.115   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.802   2.763   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.725   3.996   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.273   2.946   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.666   4.361   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.137   4.544   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.531   5.959   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.215   3.311   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.670   1.840   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.412   0.952   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.179   1.875   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.651   1.575   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.300  -0.009   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       7.398  -1.089   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.747  -0.382   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.621   0.782   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.146   1.224   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.791   2.722   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.316   3.164   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.912   3.779   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.575   3.227   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.741   1.838   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.864   0.784   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.506   2.758   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.140   4.219   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.669   4.513   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.675   3.332   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       9.330   4.726   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       3.950   3.387   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       2.837   2.194   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   29                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   29                                                  
CONECT   14   13   15   26                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   24   32                                             
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   18   25   26                                             
CONECT   25   24                                                            
CONECT   26   24   14   27   31                                             
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   13   10   30                                             
CONECT   30   29                                                            
CONECT   31   26   32                                                       
CONECT   32   31   18                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₂O₄

Average Mass

442.6400 Da

Monoisotopic Mass

442.30831 Da

IUPAC Name

8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0^{1,13}.0^{4,12}.0^{5,9}]nonadec-4-en-3-one

Traditional Name

8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0^{1,13}.0^{4,12}.0^{5,9}]nonadec-4-en-3-one

CAS Registry Number

Not Available

SMILES

CC(C)C(C)C=CC(C)C1CCC2=C3C(=O)CC45CC(O)CCC4(C)C3(CCC12C)OO5

InChI Identifier

InChI=1S/C28H42O4/c1-17(2)18(3)7-8-19(4)21-9-10-22-24-23(30)16-27-15-20(29)11-12-26(27,6)28(24,32-31-27)14-13-25(21,22)5/h7-8,17-21,29H,9-16H2,1-6H3

InChI Key

LJBJXGTWGWODIW-UHFFFAOYSA-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
Grifola gargal	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ergostane steroids. These are steroids with a structure based on the ergostane skeleton, which arises from the methylation of cholestane at the 24-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Ergostane steroids

Direct Parent

Ergostane steroids

Alternative Parents

Substituents

Ergostane-skeleton
Cyclic alcohol
Ortho-dioxolane
Dialkyl peroxide
Secondary alcohol
Ketone
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
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
logP	5.59	ChemAxon
pKa (Strongest Acidic)	15.14	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	55.76 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	126.98 m³·mol⁻¹	ChemAxon
Polarizability	51.31 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

76155746

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Motahari Rad H, Mowla SJ, Ramazanali F, Rezazadeh Valojerdi M: Characterization of altered microRNAs related to different phenotypes of polycystic ovarian syndrome (PCOS) in serum, follicular fluid, and cumulus cells. Taiwan J Obstet Gynecol. 2022 Sep;61(5):768-779. doi: 10.1016/j.tjog.2022.05.013. [PubMed:36088043 ]
Pontrelli G, Huscher C, Scioscia M, Brusca F, Tedeschi U, Greco P, Mancarella M, Biglia N, Novara L: End-to-end versus side-to-end anastomosis after bowel resection for deep infiltrating endometriosis: a retrospective study. J Gynecol Obstet Hum Reprod. 2022 Sep 7:102472. doi: 10.1016/j.jogoh.2022.102472. [PubMed:36087927 ]
Qi H, Cai H, Liu X, Liu S, Ding C, Xu M: The cytokinin type-B response regulator PeRR12 is a negative regulator of adventitious rooting and salt tolerance in poplar. Plant Sci. 2022 Sep 7:111456. doi: 10.1016/j.plantsci.2022.111456. [PubMed:36087886 ]
Shah L, Latif A, Williams KJ, Tirella A: Role of stiffness and physico-chemical properties of tumour microenvironment on breast cancer cell stemness. Acta Biomater. 2022 Sep 7. pii: S1742-7061(22)00557-8. doi: 10.1016/j.actbio.2022.08.074. [PubMed:36087866 ]
Temme JS, Crainic JA, Walker LM, Yang W, Tan Z, Huang X, Gildersleeve JC: Microarray-guided evaluation of the frequency, B cell origins, and selectivity of human glycan-binding antibodies reveals new insights and novel antibodies. J Biol Chem. 2022 Sep 7:102468. doi: 10.1016/j.jbc.2022.102468. [PubMed:36087840 ]
LOTUS database [Link]

Showing NP-Card for 8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one (NP0227306)

MOL for NP0227306 (8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one)

3D MOL for NP0227306 (8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one)

3D SDF for NP0227306 (8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one)

3D-SDF for NP0227306 (8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one)

PDB for NP0227306 (8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one)

3D PDB for NP0227306 (8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one)

SMILES for NP0227306 (8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one)

INCHI for NP0227306 (8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one)

Structure for NP0227306 (8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one)

3D Structure for NP0227306 (8-(5,6-dimethylhept-3-en-2-yl)-16-hydroxy-9,13-dimethyl-18,19-dioxapentacyclo[10.5.2.0¹,¹³.0⁴,¹².0⁵,⁹]nonadec-4-en-3-one)