NP-MRD: Showing NP-Card for [(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate (NP0178951)

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Record Information

Version

1.0

Created at

2022-09-03 17:03:21 UTC

Updated at

2022-09-03 17:03:21 UTC

NP-MRD ID

NP0178951

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate

Description

Scabronine H belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. [(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate is found in Sarcodon scabrosus. It was first documented in 2011 (PMID: 21530015). Based on a literature review a significant number of articles have been published on Scabronine H (PMID: 36057450) (PMID: 36057449) (PMID: 36057448) (PMID: 33281604).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032219032D          

 32 35  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309032219032D          

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M  END
> <DATABASE_ID>
NP0178951

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](CO)C1=C2[C@H]3C[C@H](O)C(COC(=O)C4=CC=CC=C4)=C[C@H](O)[C@]3(C)CC[C@@]2(C)CC1

> <INCHI_IDENTIFIER>
InChI=1S/C27H36O5/c1-17(15-28)20-9-10-26(2)11-12-27(3)21(24(20)26)14-22(29)19(13-23(27)30)16-32-25(31)18-7-5-4-6-8-18/h4-8,13,17,21-23,28-30H,9-12,14-16H2,1-3H3/t17-,21+,22-,23-,26+,27+/m0/s1

> <INCHI_KEY>
QZEMMWXYJUKIBS-GIXUWZPISA-N

> <FORMULA>
C27H36O5

> <MOLECULAR_WEIGHT>
440.58

> <EXACT_MASS>
440.256274259

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
49.38287168644867

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[(3aR,5aR,6S,9S,10aR)-6,9-dihydroxy-1-[(2R)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2H,3H,3aH,4H,5H,5aH,6H,9H,10H,10aH-cyclohepta[e]inden-8-yl]methyl benzoate

> <JCHEM_LOGP>
3.2673037680000006

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.734998829500292

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.085557933533043

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6679231567233495

> <JCHEM_POLAR_SURFACE_AREA>
86.99

> <JCHEM_REFRACTIVITY>
125.55579999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(3aR,5aR,6S,9S,10aR)-6,9-dihydroxy-1-[(2R)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2H,3H,4H,5H,6H,9H,10H,10aH-cyclohepta[e]inden-8-yl]methyl benzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       2.741  -0.579   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.251  -0.969   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.169   0.127   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.321  -0.263   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.844  -2.454   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.806  -3.656   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.343  -3.746   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.988  -2.348   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.484  -1.981   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.802  -0.474   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.703  -2.921   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.080  -2.230   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.366  -3.077   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      10.743  -2.386   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      10.832  -0.848   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      12.029  -3.232   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      13.405  -2.541   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.692  -3.388   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      14.602  -4.925   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      13.226  -5.616   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      11.939  -4.770   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.729  -4.461   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.541  -5.441   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.908  -6.936   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       4.034  -5.123   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.620  -6.547   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.187  -6.409   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.650  -6.319   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.959  -4.943   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -0.017  -6.134   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.526  -4.535   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -0.597  -2.997   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6   32                                                  
CONECT    6    5    7   29                                                  
CONECT    7    6    8   25                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   22                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   16                                                       
CONECT   22   11   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23    7   26   27                                             
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28    6   30   31                                             
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31    5                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₆O₅

Average Mass

440.5800 Da

Monoisotopic Mass

440.25627 Da

IUPAC Name

[(3aR,5aR,6S,9S,10aR)-6,9-dihydroxy-1-[(2R)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2H,3H,3aH,4H,5H,5aH,6H,9H,10H,10aH-cyclohepta[e]inden-8-yl]methyl benzoate

Traditional Name

[(3aR,5aR,6S,9S,10aR)-6,9-dihydroxy-1-[(2R)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2H,3H,4H,5H,6H,9H,10H,10aH-cyclohepta[e]inden-8-yl]methyl benzoate

CAS Registry Number

Not Available

SMILES

C[C@@H](CO)C1=C2[C@H]3C[C@H](O)C(COC(=O)C4=CC=CC=C4)=C[C@H](O)[C@]3(C)CC[C@@]2(C)CC1

InChI Identifier

InChI=1S/C27H36O5/c1-17(15-28)20-9-10-26(2)11-12-27(3)21(24(20)26)14-22(29)19(13-23(27)30)16-32-25(31)18-7-5-4-6-8-18/h4-8,13,17,21-23,28-30H,9-12,14-16H2,1-3H3/t17-,21+,22-,23-,26+,27+/m0/s1

InChI Key

QZEMMWXYJUKIBS-GIXUWZPISA-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
Sarcodon scabrosus	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

Diterpenoid
Benzoate ester
Benzoic acid or derivatives
Benzoyl
Benzenoid
Monocyclic benzene moiety
Secondary alcohol
Carboxylic acid ester
Carboxylic acid derivative
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organic oxygen compound
Alcohol
Organic oxide
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic 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	3.27	ChemAxon
pKa (Strongest Acidic)	14.09	ChemAxon
pKa (Strongest Basic)	-1.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	125.56 m³·mol⁻¹	ChemAxon
Polarizability	49.38 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

26631958

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

56683329

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Shi XW, Liu L, Gao JM, Zhang AL: Cyathane diterpenes from Chinese mushroom Sarcodon scabrosus and their neurite outgrowth-promoting activity. Eur J Med Chem. 2011 Jul;46(7):3112-7. doi: 10.1016/j.ejmech.2011.04.006. Epub 2011 Apr 9. [PubMed:21530015 ]
Micalizzi E, Vaudano AE, Ballerini A, Talami F, Giovannini G, Turchi G, Cioclu MC, Giunta L, Meletti S: Ictal Apnea: a prospective monocentric study in patients with epilepsy. Eur J Neurol. 2022 Sep 3. doi: 10.1111/ene.15547. [PubMed:36057450 ]
Jiang S, Guo P, Heo HY, Zhang Y, Wu J, Jin Y, Laterra J, Eberhart CG, Lim M, Blakeley JO: Radiomics analysis of amide proton transfer-weighted and structural MR images for treatment response assessment in malignant gliomas. NMR Biomed. 2022 Sep 3:e4824. doi: 10.1002/nbm.4824. [PubMed:36057449 ]
Agarwal K, Saikia P, Podder I: Metabolic syndrome and Dyslipidemia in xanthelasma palpebrarum and associated risk-factors- a case-control study. J Cosmet Dermatol. 2022 Sep 3. doi: 10.1111/jocd.15353. [PubMed:36057448 ]
Nakagawasai O, Lin JR, Odaira T, Takahashi K, Nemoto W, Moriguchi S, Yabuki Y, Kobayakawa Y, Fukunaga K, Nakada M, Tan-No K: Scabronine G Methyl Ester Improves Memory-Related Behavior and Enhances Hippocampal Cell Proliferation and Long-Term Potentiation via the BDNF-CREB Pathway in Olfactory Bulbectomized Mice. Front Pharmacol. 2020 Nov 12;11:583291. doi: 10.3389/fphar.2020.583291. eCollection 2020. [PubMed:33281604 ]
LOTUS database [Link]

Showing NP-Card for [(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate (NP0178951)

MOL for NP0178951 ([(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate)

3D MOL for NP0178951 ([(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate)

3D SDF for NP0178951 ([(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate)

3D-SDF for NP0178951 ([(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate)

PDB for NP0178951 ([(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate)

3D PDB for NP0178951 ([(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate)

SMILES for NP0178951 ([(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate)

INCHI for NP0178951 ([(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate)

Structure for NP0178951 ([(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate)

3D Structure for NP0178951 ([(3ar,5ar,6s,9s,10ar)-6,9-dihydroxy-1-[(2r)-1-hydroxypropan-2-yl]-3a,5a-dimethyl-2h,3h,4h,5h,6h,9h,10h,10ah-cyclohepta[e]inden-8-yl]methyl benzoate)