NP-MRD: Showing NP-Card for [(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate (NP0305356)

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Record Information

Version

2.0

Created at

2022-09-10 21:07:31 UTC

Updated at

2022-09-10 21:07:32 UTC

NP-MRD ID

NP0305356

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate

Description

[(1R,2R,4S,4aR,8aR)-4-hydroxy-1-[(3S)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-2-yl]methyl 2-phenylacetate belongs to the class of organic compounds known as colensane and clerodane diterpenoids. These are diterpenoids with a structure based on the clerodane or the colensane skeleton. Clerodanes arise from labdanes by two methyl migrations. [(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate is found in Moquiniastrum paniculatum. Based on a literature review very few articles have been published on [(1R,2R,4S,4aR,8aR)-4-hydroxy-1-[(3S)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-2-yl]methyl 2-phenylacetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102223072D          

 33 35  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309102223072D          

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 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 16 21  1  0  0  0  0
 10 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 27 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 33 32  1  6  0  0  0
 25 33  1  0  0  0  0
  8 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0305356

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CCO)CC[C@@]1(C)[C@H](COC(=O)CC2=CC=CC=C2)C[C@H](O)[C@]2(C)[C@@H]1CCC=C2CO

> <INCHI_IDENTIFIER>
InChI=1S/C28H42O5/c1-20(13-15-29)12-14-27(2)23(19-33-26(32)16-21-8-5-4-6-9-21)17-25(31)28(3)22(18-30)10-7-11-24(27)28/h4-6,8-10,20,23-25,29-31H,7,11-19H2,1-3H3/t20-,23-,24+,25-,27-,28-/m0/s1

> <INCHI_KEY>
KVDRBIDXUWTEJH-NYCRRLSRSA-N

> <FORMULA>
C28H42O5

> <MOLECULAR_WEIGHT>
458.639

> <EXACT_MASS>
458.303224452

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
53.187087051406664

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1R,2R,4S,4aR,8aR)-4-hydroxy-1-[(3S)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-2-yl]methyl 2-phenylacetate

> <JCHEM_LOGP>
3.7562069170000005

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.261336184877614

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.507378493924467

> <JCHEM_PKA_STRONGEST_BASIC>
-1.8759716394992227

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
131.4456

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(1R,2R,4S,4aR,8aR)-4-hydroxy-1-[(3S)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl phenylacetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0      13.198   2.327   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.198   0.787   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.864   0.017   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.531   0.787   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       9.197   0.017   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      14.532   0.017   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      15.865   0.787   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      17.199   0.017   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      16.209  -1.163   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      17.726   1.464   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      16.736   2.644   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      17.263   4.091   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      18.779   4.359   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      19.769   3.179   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      19.306   5.806   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      20.822   6.073   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      21.349   7.520   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      22.866   7.788   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      23.856   6.608   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      23.329   5.161   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      21.812   4.893   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      19.242   1.732   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      20.232   0.552   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      21.749   0.819   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      19.706  -0.895   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      21.222  -0.628   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      20.695  -2.075   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      22.212  -1.807   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      23.202  -2.987   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      20.169  -3.522   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      18.652  -3.789   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      17.662  -2.610   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      18.189  -1.163   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    2    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   33                                             
CONECT    9    8                                                            
CONECT   10    8   11   22                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   16                                                       
CONECT   22   10   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   27   33                                             
CONECT   26   25                                                            
CONECT   27   25   28   30                                                  
CONECT   28   27   29                                                       
CONECT   29   28                                                            
CONECT   30   27   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   25    8                                                  
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Value	Source
[(1R,2R,4S,4AR,8ar)-4-hydroxy-1-[(3S)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-2-yl]methyl 2-phenylacetic acid	Generator

Chemical Formula

C₂₈H₄₂O₅

Average Mass

458.6390 Da

Monoisotopic Mass

458.30322 Da

IUPAC Name

[(1R,2R,4S,4aR,8aR)-4-hydroxy-1-[(3S)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-2-yl]methyl 2-phenylacetate

Traditional Name

[(1R,2R,4S,4aR,8aR)-4-hydroxy-1-[(3S)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl phenylacetate

CAS Registry Number

Not Available

SMILES

C[C@H](CCO)CC[C@@]1(C)[C@H](COC(=O)CC2=CC=CC=C2)C[C@H](O)[C@]2(C)[C@@H]1CCC=C2CO

InChI Identifier

InChI=1S/C28H42O5/c1-20(13-15-29)12-14-27(2)23(19-33-26(32)16-21-8-5-4-6-9-21)17-25(31)28(3)22(18-30)10-7-11-24(27)28/h4-6,8-10,20,23-25,29-31H,7,11-19H2,1-3H3/t20-,23-,24+,25-,27-,28-/m0/s1

InChI Key

KVDRBIDXUWTEJH-NYCRRLSRSA-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
Gochnatia paniculata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as colensane and clerodane diterpenoids. These are diterpenoids with a structure based on the clerodane or the colensane skeleton. Clerodanes arise from labdanes by two methyl migrations.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Colensane and clerodane diterpenoids

Alternative Parents

Substituents

Clerodane diterpenoid
Fatty alcohol
Monocyclic benzene moiety
Fatty acyl
Benzenoid
Cyclic alcohol
Carboxylic acid ester
Secondary alcohol
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Primary alcohol
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
Organooxygen compound
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	3.76	ChemAxon
pKa (Strongest Acidic)	14.51	ChemAxon
pKa (Strongest Basic)	-1.9	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	11	ChemAxon
Refractivity	131.45 m³·mol⁻¹	ChemAxon
Polarizability	53.19 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

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

163078493

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate (NP0305356)

MOL for NP0305356 ([(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate)

3D MOL for NP0305356 ([(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate)

3D SDF for NP0305356 ([(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate)

3D-SDF for NP0305356 ([(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate)

PDB for NP0305356 ([(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate)

3D PDB for NP0305356 ([(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate)

SMILES for NP0305356 ([(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate)

INCHI for NP0305356 ([(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate)

Structure for NP0305356 ([(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate)

3D Structure for NP0305356 ([(1r,2r,4s,4ar,8ar)-4-hydroxy-1-[(3s)-5-hydroxy-3-methylpentyl]-5-(hydroxymethyl)-1,4a-dimethyl-2,3,4,7,8,8a-hexahydronaphthalen-2-yl]methyl 2-phenylacetate)