NP-MRD: Showing NP-Card for palmadorin Q (NP0041780)

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Record Information

Version

2.0

Created at

2021-06-20 23:36:39 UTC

Updated at

2021-06-30 00:16:30 UTC

NP-MRD ID

NP0041780

Secondary Accession Numbers

None

Natural Product Identification

Common Name

palmadorin Q

Provided By

JEOL Database JEOL Logo

Description

(2R)-2,3-dihydroxypropyl (2E)-5-[(1R,2R,4aS,8aS)-2-hydroxy-2,5,5,8a-tetramethyl-decahydronaphthalen-1-yl]-3-methylpent-2-enoate belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. palmadorin Q is found in Austrodoris kerguelenensis. palmadorin Q was first documented in 2012 (Maschek, J. A., et al.). Based on a literature review very few articles have been published on (2R)-2,3-dihydroxypropyl (2E)-5-[(1R,2R,4aS,8aS)-2-hydroxy-2,5,5,8a-tetramethyl-decahydronaphthalen-1-yl]-3-methylpent-2-enoate.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306212101363D          

 68 69  0  0  0  0            999 V2000
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   -1.8535    2.7104   -4.4431 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652306212101363D          

 68 69  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0041780

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]([H])(O[H])C([H])([H])OC(=O)C(\[H])=C(/C([H])([H])[H])C([H])([H])C([H])([H])[C@@]1([H])[C@@](O[H])(C([H])([H])[H])C([H])([H])C([H])([H])[C@@]2([H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])[C@]12C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C23H40O5/c1-16(13-20(26)28-15-17(25)14-24)7-8-19-22(4)11-6-10-21(2,3)18(22)9-12-23(19,5)27/h13,17-19,24-25,27H,6-12,14-15H2,1-5H3/b16-13+/t17-,18+,19-,22+,23-/m1/s1

> <INCHI_KEY>
MKRXBTPWEZWRSX-MYTCBAEWSA-N

> <FORMULA>
C23H40O5

> <MOLECULAR_WEIGHT>
396.568

> <EXACT_MASS>
396.287574388

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
46.299897554637944

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R)-2,3-dihydroxypropyl (2E)-5-[(1R,2R,4aS,8aS)-2-hydroxy-2,5,5,8a-tetramethyl-decahydronaphthalen-1-yl]-3-methylpent-2-enoate

> <ALOGPS_LOGP>
3.28

> <JCHEM_LOGP>
3.5708140056666666

> <ALOGPS_LOGS>
-4.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.561635819540221

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.618691472007402

> <JCHEM_PKA_STRONGEST_BASIC>
-0.43544863158583913

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
110.84969999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.10e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2,3-dihydroxypropyl (2E)-5-[(1R,2R,4aS,8aS)-2-hydroxy-2,5,5,8a-tetramethyl-hexahydro-1H-naphthalen-1-yl]-3-methylpent-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 68 69  0  0  0  0  0  0  0  0999 V2000
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 28 68  1  0
M  END

HEADER    PROTEIN                                 21-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JUN-21         0                                  
HETATM    1  C   UNK     0      -2.866   4.386  -0.570  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.282   3.035  -0.910  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.121   2.578  -2.169  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.535   3.270  -3.413  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.337   4.183  -3.508  0.00  0.00           O+0
HETATM    6  O   UNK     0      -1.853   2.710  -4.443  0.00  0.00           O+0
HETATM    7  C   UNK     0      -2.168   3.197  -5.769  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.609   4.611  -6.006  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.569   5.610  -5.617  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.319   4.851  -7.489  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.525   4.748  -8.244  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.895   2.237   0.334  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.213   0.875   0.120  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.654   0.201   1.417  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.378  -0.977   1.089  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.263  -2.034   0.157  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.608  -0.363   0.332  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.973  -0.953   0.693  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.904  -2.432   1.035  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.014  -2.708   2.273  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.920  -2.658   3.533  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.475  -4.151   2.179  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.891  -1.612   2.429  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.269  -2.053   3.338  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.150  -0.868   3.695  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.751  -0.151   2.478  0.00  0.00           C+0
HETATM   27  C   UNK     0      -2.963  -0.918   1.935  0.00  0.00           C+0
HETATM   28  O   UNK     0      -2.267   1.093   2.989  0.00  0.00           O+0
HETATM   29  H   UNK     0      -2.308   4.845   0.254  0.00  0.00           H+0
HETATM   30  H   UNK     0      -2.818   5.101  -1.394  0.00  0.00           H+0
HETATM   31  H   UNK     0      -3.909   4.277  -0.257  0.00  0.00           H+0
HETATM   32  H   UNK     0      -1.678   1.605  -2.353  0.00  0.00           H+0
HETATM   33  H   UNK     0      -3.252   3.149  -5.922  0.00  0.00           H+0
HETATM   34  H   UNK     0      -1.698   2.482  -6.453  0.00  0.00           H+0
HETATM   35  H   UNK     0      -0.702   4.774  -5.415  0.00  0.00           H+0
HETATM   36  H   UNK     0      -2.953   5.335  -4.755  0.00  0.00           H+0
HETATM   37  H   UNK     0      -0.598   4.127  -7.881  0.00  0.00           H+0
HETATM   38  H   UNK     0      -0.921   5.859  -7.646  0.00  0.00           H+0
HETATM   39  H   UNK     0      -3.152   5.349  -7.791  0.00  0.00           H+0
HETATM   40  H   UNK     0      -1.227   2.861   0.942  0.00  0.00           H+0
HETATM   41  H   UNK     0      -2.821   2.091   0.901  0.00  0.00           H+0
HETATM   42  H   UNK     0      -1.918   0.203  -0.381  0.00  0.00           H+0
HETATM   43  H   UNK     0      -0.381   1.029  -0.575  0.00  0.00           H+0
HETATM   44  H   UNK     0      -0.047   0.985   1.898  0.00  0.00           H+0
HETATM   45  H   UNK     0       0.477  -2.723  -0.256  0.00  0.00           H+0
HETATM   46  H   UNK     0      -0.743  -1.579  -0.714  0.00  0.00           H+0
HETATM   47  H   UNK     0      -1.008  -2.648   0.662  0.00  0.00           H+0
HETATM   48  H   UNK     0       1.461  -0.463  -0.752  0.00  0.00           H+0
HETATM   49  H   UNK     0       1.677   0.716   0.517  0.00  0.00           H+0
HETATM   50  H   UNK     0       3.394  -0.401   1.542  0.00  0.00           H+0
HETATM   51  H   UNK     0       3.665  -0.796  -0.143  0.00  0.00           H+0
HETATM   52  H   UNK     0       3.921  -2.809   1.203  0.00  0.00           H+0
HETATM   53  H   UNK     0       2.540  -2.980   0.158  0.00  0.00           H+0
HETATM   54  H   UNK     0       3.393  -1.677   3.648  0.00  0.00           H+0
HETATM   55  H   UNK     0       2.354  -2.865   4.447  0.00  0.00           H+0
HETATM   56  H   UNK     0       3.722  -3.403   3.474  0.00  0.00           H+0
HETATM   57  H   UNK     0       0.970  -4.458   3.101  0.00  0.00           H+0
HETATM   58  H   UNK     0       0.769  -4.277   1.355  0.00  0.00           H+0
HETATM   59  H   UNK     0       2.294  -4.861   2.014  0.00  0.00           H+0
HETATM   60  H   UNK     0       1.371  -0.775   2.963  0.00  0.00           H+0
HETATM   61  H   UNK     0       0.121  -2.473   4.272  0.00  0.00           H+0
HETATM   62  H   UNK     0      -0.870  -2.839   2.871  0.00  0.00           H+0
HETATM   63  H   UNK     0      -1.948  -1.196   4.374  0.00  0.00           H+0
HETATM   64  H   UNK     0      -0.561  -0.150   4.284  0.00  0.00           H+0
HETATM   65  H   UNK     0      -2.714  -1.905   1.548  0.00  0.00           H+0
HETATM   66  H   UNK     0      -3.711  -1.060   2.726  0.00  0.00           H+0
HETATM   67  H   UNK     0      -3.480  -0.355   1.152  0.00  0.00           H+0
HETATM   68  H   UNK     0      -2.914   0.891   3.687  0.00  0.00           H+0
CONECT    1    2   29   30   31                                             
CONECT    2    1    3   12                                                  
CONECT    3    2    4   32                                                  
CONECT    4    3    6    5                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   33   34                                             
CONECT    8    9    7   10   35                                             
CONECT    9    8   36                                                       
CONECT   10    8   11   37   38                                             
CONECT   11   10   39                                                       
CONECT   12   13    2   40   41                                             
CONECT   13   14   12   42   43                                             
CONECT   14   13   26   15   44                                             
CONECT   15   17   16   23   14                                             
CONECT   16   15   45   46   47                                             
CONECT   17   15   18   48   49                                             
CONECT   18   17   19   50   51                                             
CONECT   19   20   18   52   53                                             
CONECT   20   21   23   19   22                                             
CONECT   21   20   54   55   56                                             
CONECT   22   20   57   58   59                                             
CONECT   23   24   20   60   15                                             
CONECT   24   23   25   61   62                                             
CONECT   25   24   26   63   64                                             
CONECT   26   25   27   14   28                                             
CONECT   27   26   65   66   67                                             
CONECT   28   26   68                                                       
CONECT   29    1                                                            
CONECT   30    1                                                            
CONECT   31    1                                                            
CONECT   32    3                                                            
CONECT   33    7                                                            
CONECT   34    7                                                            
CONECT   35    8                                                            
CONECT   36    9                                                            
CONECT   37   10                                                            
CONECT   38   10                                                            
CONECT   39   11                                                            
CONECT   40   12                                                            
CONECT   41   12                                                            
CONECT   42   13                                                            
CONECT   43   13                                                            
CONECT   44   14                                                            
CONECT   45   16                                                            
CONECT   46   16                                                            
CONECT   47   16                                                            
CONECT   48   17                                                            
CONECT   49   17                                                            
CONECT   50   18                                                            
CONECT   51   18                                                            
CONECT   52   19                                                            
CONECT   53   19                                                            
CONECT   54   21                                                            
CONECT   55   21                                                            
CONECT   56   21                                                            
CONECT   57   22                                                            
CONECT   58   22                                                            
CONECT   59   22                                                            
CONECT   60   23                                                            
CONECT   61   24                                                            
CONECT   62   24                                                            
CONECT   63   25                                                            
CONECT   64   25                                                            
CONECT   65   27                                                            
CONECT   66   27                                                            
CONECT   67   27                                                            
CONECT   68   28                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  138    0
END

RDKit          3D

68 69  0  0  0  0  0  0  0  0999 V2000
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 28 68  1  0
M  END

View in JSmol

Synonyms

Value	Source
(2R)-2,3-Dihydroxypropyl (2E)-5-[(1R,2R,4as,8as)-2-hydroxy-2,5,5,8a-tetramethyl-decahydronaphthalen-1-yl]-3-methylpent-2-enoic acid	Generator

Chemical Formula

C₂₃H₄₀O₅

Average Mass

396.5680 Da

Monoisotopic Mass

396.28757 Da

IUPAC Name

(2R)-2,3-dihydroxypropyl (2E)-5-[(1R,2R,4aS,8aS)-2-hydroxy-2,5,5,8a-tetramethyl-decahydronaphthalen-1-yl]-3-methylpent-2-enoate

Traditional Name

(2R)-2,3-dihydroxypropyl (2E)-5-[(1R,2R,4aS,8aS)-2-hydroxy-2,5,5,8a-tetramethyl-hexahydro-1H-naphthalen-1-yl]-3-methylpent-2-enoate

CAS Registry Number

Not Available

SMILES

[H]OC([H])([H])[C@@]([H])(O[H])C([H])([H])OC(=O)C(\[H])=C(/C([H])([H])[H])C([H])([H])C([H])([H])[C@@]1([H])[C@@](O[H])(C([H])([H])[H])C([H])([H])C([H])([H])[C@@]2([H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])[C@]12C([H])([H])[H]

InChI Identifier

InChI=1S/C23H40O5/c1-16(13-20(26)28-15-17(25)14-24)7-8-19-22(4)11-6-10-21(2,3)18(22)9-12-23(19,5)27/h13,17-19,24-25,27H,6-12,14-15H2,1-5H3/b16-13+/t17-,18+,19-,22+,23-/m1/s1

InChI Key

MKRXBTPWEZWRSX-MYTCBAEWSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Doris kerguelenensis	JEOL database	Maschek, J. A., et al, Tetrahedron 68, 9095 (2012)

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
Labdane diterpenoid
Monoradylglycerol
Monoacylglycerol
1-acyl-sn-glycerol
Glycerolipid
Fatty acid ester
Fatty acyl
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic 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	3.28	ALOGPS
logP	3.57	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	13.62	ChemAxon
pKa (Strongest Basic)	-0.44	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	8	ChemAxon
Refractivity	110.85 m³·mol⁻¹	ChemAxon
Polarizability	46.3 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

29215217

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71475092

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Maschek, J. A., et al. (2012). Maschek, J. A., et al, Tetrahedron 68, 9095 (2012). Tetrahedron.

Showing NP-Card for palmadorin Q (NP0041780)

MOL for NP0041780 (palmadorin Q)

3D MOL for NP0041780 (palmadorin Q)

3D SDF for NP0041780 (palmadorin Q)

3D-SDF for NP0041780 (palmadorin Q)

PDB for NP0041780 (palmadorin Q)

3D PDB for NP0041780 (palmadorin Q)

SMILES for NP0041780 (palmadorin Q)

INCHI for NP0041780 (palmadorin Q)

Structure for NP0041780 (palmadorin Q)

3D Structure for NP0041780 (palmadorin Q)