NP-MRD: Showing NP-Card for (2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one (NP0324831)

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Record Information

Version

2.0

Created at

2022-09-12 05:08:48 UTC

Updated at

2022-09-12 05:08:48 UTC

NP-MRD ID

NP0324831

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one

Description

Herbasterol belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Thus, herbasterol is considered to be a sterol. (2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one is found in Lamellodysidea herbacea. (2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one was first documented in 2019 (PMID: 30853340). Based on a literature review very few articles have been published on Herbasterol (PMID: 33265937).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122207082D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309122207082D          

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   12.2326   -4.3213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9859   -5.1085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  9  7  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 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
 17 24  1  0  0  0  0
 24 25  1  1  0  0  0
 25 26  1  0  0  0  0
 24 27  1  0  0  0  0
 13 27  1  0  0  0  0
 27 28  2  0  0  0  0
 12 29  1  0  0  0  0
  9 29  1  0  0  0  0
 29 30  1  1  0  0  0
 29 31  1  6  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0324831

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]([C@@H]2C[C@@H](O)[C@@H]3C[C@H](O)[C@@H](O)C[C@]3(CO)C2=O)[C@]1(C)CCO

> <INCHI_IDENTIFIER>
InChI=1S/C27H48O6/c1-16(2)6-5-7-17(3)19-8-9-20(26(19,4)10-11-28)18-12-22(30)21-13-23(31)24(32)14-27(21,15-29)25(18)33/h16-24,28-32H,5-15H2,1-4H3/t17-,18+,19-,20+,21+,22-,23+,24+,26-,27-/m1/s1

> <INCHI_KEY>
UWPWCNUBZQKCGV-YJJKLKRJSA-N

> <FORMULA>
C27H48O6

> <MOLECULAR_WEIGHT>
468.675

> <EXACT_MASS>
468.345089266

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
54.23206806207658

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4R,4aR,6S,7S,8aS)-4,6,7-trihydroxy-2-[(1S,2R,3R)-2-(2-hydroxyethyl)-2-methyl-3-[(2R)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-decahydronaphthalen-1-one

> <JCHEM_LOGP>
2.627309626666664

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.589981851075983

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.805644613917686

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7228673711807025

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
128.99759999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4R,4aR,6S,7S,8aS)-4,6,7-trihydroxy-2-[(1S,2R,3R)-2-(2-hydroxyethyl)-2-methyl-3-[(2R)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      12.843  -4.837   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.177  -5.607   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.177  -7.147   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.511  -4.837   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.844  -5.607   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.178  -4.837   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      19.512  -5.607   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      19.512  -7.147   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      20.846  -4.837   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.006  -3.305   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      22.513  -2.985   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      23.283  -4.319   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      24.814  -4.480   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      25.720  -3.234   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      27.251  -3.395   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      28.156  -2.149   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      27.878  -4.802   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      29.409  -4.963   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      30.035  -6.370   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      31.567  -6.531   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      29.130  -7.615   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      29.757  -9.022   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      27.599  -7.455   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      26.972  -6.048   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      26.067  -7.294   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      26.694  -8.700   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      25.441  -5.887   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      24.536  -7.133   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      22.252  -5.463   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      23.271  -6.618   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      21.792  -6.933   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      22.834  -8.066   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      22.374  -9.536   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   29                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   29                                                  
CONECT   13   12   14   27                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   24                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   17   25   27                                             
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27   24   13   28                                                  
CONECT   28   27                                                            
CONECT   29   12    9   30   31                                             
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₈O₆

Average Mass

468.6750 Da

Monoisotopic Mass

468.34509 Da

IUPAC Name

(2S,4R,4aR,6S,7S,8aS)-4,6,7-trihydroxy-2-[(1S,2R,3R)-2-(2-hydroxyethyl)-2-methyl-3-[(2R)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-decahydronaphthalen-1-one

Traditional Name

(2S,4R,4aR,6S,7S,8aS)-4,6,7-trihydroxy-2-[(1S,2R,3R)-2-(2-hydroxyethyl)-2-methyl-3-[(2R)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one

CAS Registry Number

Not Available

SMILES

CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]([C@@H]2C[C@@H](O)[C@@H]3C[C@H](O)[C@@H](O)C[C@]3(CO)C2=O)[C@]1(C)CCO

InChI Identifier

InChI=1S/C27H48O6/c1-16(2)6-5-7-17(3)19-8-9-20(26(19,4)10-11-28)18-12-22(30)21-13-23(31)24(32)14-27(21,15-29)25(18)33/h16-24,28-32H,5-15H2,1-4H3/t17-,18+,19-,20+,21+,22-,23+,24+,26-,27-/m1/s1

InChI Key

UWPWCNUBZQKCGV-YJJKLKRJSA-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
Lamellodysidea herbacea	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Cyclopentane sesquiterpenoid
Sesquiterpenoid
Cyclic alcohol
Secondary alcohol
Ketone
Polyol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Cholesterol and derivatives (LMST01010292 )

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	2.63	ChemAxon
pKa (Strongest Acidic)	13.81	ChemAxon
pKa (Strongest Basic)	-1.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	118.22 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	129 m³·mol⁻¹	ChemAxon
Polarizability	54.23 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

10280906

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21671289

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yamazaki H, Ohte S, Rotinsulu H, Wewengkang DS, Sumilat DA, Abdjul DB, Maarisit W, Kapojos MM, Namikoshi M, Katagiri T, Tomoda H, Uchida R: Screening for Small Molecule Inhibitors of BMP-Induced Osteoblastic Differentiation from Indonesian Marine Invertebrates. Mar Drugs. 2020 Nov 30;18(12). pii: md18120606. doi: 10.3390/md18120606. [PubMed:33265937 ]
Gao Y, Wu S: Comprehensive analysis of the phospholipids and phytosterols in Schisandra chinensis oil by UPLC-Q/TOF- MS(E). Chem Phys Lipids. 2019 Jul;221:15-23. doi: 10.1016/j.chemphyslip.2019.03.003. Epub 2019 Mar 7. [PubMed:30853340 ]
LOTUS database [Link]

Showing NP-Card for (2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one (NP0324831)

MOL for NP0324831 ((2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one)

3D MOL for NP0324831 ((2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one)

3D SDF for NP0324831 ((2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one)

3D-SDF for NP0324831 ((2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one)

PDB for NP0324831 ((2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one)

3D PDB for NP0324831 ((2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one)

SMILES for NP0324831 ((2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one)

INCHI for NP0324831 ((2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one)

Structure for NP0324831 ((2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one)

3D Structure for NP0324831 ((2s,4r,4ar,6s,7s,8as)-4,6,7-trihydroxy-2-[(1s,2r,3r)-2-(2-hydroxyethyl)-2-methyl-3-[(2r)-6-methylheptan-2-yl]cyclopentyl]-8a-(hydroxymethyl)-octahydronaphthalen-1-one)