NP-MRD: Showing NP-Card for 6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one (NP0159550)

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Record Information

Version

2.0

Created at

2022-09-02 17:19:29 UTC

Updated at

2022-09-02 17:19:29 UTC

NP-MRD ID

NP0159550

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one

Description

12-Hydroxydaphnetoxin belongs to the class of organic compounds known as rhamnofolane and daphnane diterpenoids. These are diterpenoids with a structure based on one the rhamnofolane or daphnane skeleton. The rhamnofolane and daphnane skeletons are closely related, being formally derived from casbane by two cyclizations (6,10 and 5,14) followed by cleavage of the 1,15 (daphnane) or 2,15 (rhamnofolane) cyclopropane bonds. 6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one is found in Daphne acutiloba and Daphne mezereum. 12-Hydroxydaphnetoxin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171505042D          

 36 42  0  0  0  0            999 V2000
    2.9476   -0.3377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.0169    0.7591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5286    1.3666    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0620    0.9752    0.0000 C   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


  Mrv1533004171505042D          

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 22 24  1  0  0  0  0
 18 24  1  0  0  0  0
 24 25  2  0  0  0  0
 20 26  1  0  0  0  0
  2 26  1  0  0  0  0
 10 26  1  0  0  0  0
 26 27  1  0  0  0  0
  7 27  1  0  0  0  0
  7 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 28 33  1  0  0  0  0
  5 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0159550

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1C(O)C2(OC3(OC2C2C4OC4(CO)C(O)C4(O)C(C=C(C)C4=O)C12O3)C1=CC=CC=C1)C(C)=C

> <INCHI_IDENTIFIER>
InChI=1S/C27H30O9/c1-12(2)25-19(30)14(4)26-16-10-13(3)18(29)24(16,32)22(31)23(11-28)20(33-23)17(26)21(25)34-27(35-25,36-26)15-8-6-5-7-9-15/h5-10,14,16-17,19-22,28,30-32H,1,11H2,2-4H3

> <INCHI_KEY>
ATCCMDINGQUBOE-UHFFFAOYSA-N

> <FORMULA>
C27H30O9

> <MOLECULAR_WEIGHT>
498.528

> <EXACT_MASS>
498.188982546

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
50.433379263893016

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one

> <ALOGPS_LOGP>
1.20

> <JCHEM_LOGP>
1.302064356333336

> <ALOGPS_LOGS>
-2.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.125963397173837

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.640847760772793

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1497130859340547

> <JCHEM_POLAR_SURFACE_AREA>
138.21

> <JCHEM_REFRACTIVITY>
123.82059999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.74e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       5.502  -0.630   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.971  -0.464   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.604  -1.449   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.992  -2.621   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.778  -0.054   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.169  -0.099   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -0.032   1.417   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.987   2.551   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.454   1.894   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.849   1.820   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.371   1.588   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.911   1.585   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.139   0.253   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.525  -0.418   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.799   0.447   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       5.573  -1.180   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.619  -2.311   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       4.101  -1.631   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       5.196  -2.714   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.830  -0.761   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.610  -1.701   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.127  -3.151   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.257  -4.422   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.666  -3.108   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       4.606  -4.328   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       2.718   0.775   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.141   0.582   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -0.826   2.736   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.366   2.708   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.160   4.027   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -2.415   5.375   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -0.875   5.403   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.081   4.084   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.120  -1.447   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -0.415  -1.573   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       1.562  -2.922   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   26                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    9   34                                             
CONECT    6    5    7                                                       
CONECT    7    6    8   27   28                                             
CONECT    8    7    9                                                       
CONECT    9    8    5   10                                                  
CONECT   10    9   11   26                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11   13                                                       
CONECT   13   12   11   14   16                                             
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20   24                                             
CONECT   19   18                                                            
CONECT   20   18   21   26                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   18   25                                                  
CONECT   25   24                                                            
CONECT   26   20    2   10   27                                             
CONECT   27   26    7                                                       
CONECT   28    7   29   33                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   28                                                       
CONECT   34    5   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₀O₉

Average Mass

498.5280 Da

Monoisotopic Mass

498.18898 Da

IUPAC Name

6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one

Traditional Name

6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one

CAS Registry Number

Not Available

SMILES

CC1C(O)C2(OC3(OC2C2C4OC4(CO)C(O)C4(O)C(C=C(C)C4=O)C12O3)C1=CC=CC=C1)C(C)=C

InChI Identifier

InChI=1S/C27H30O9/c1-12(2)25-19(30)14(4)26-16-10-13(3)18(29)24(16,32)22(31)23(11-28)20(33-23)17(26)21(25)34-27(35-25,36-26)15-8-6-5-7-9-15/h5-10,14,16-17,19-22,28,30-32H,1,11H2,2-4H3

InChI Key

ATCCMDINGQUBOE-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
Daphne acutiloba	LOTUS Database	35616633
Daphne mezereum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as rhamnofolane and daphnane diterpenoids. These are diterpenoids with a structure based on one the rhamnofolane or daphnane skeleton. The rhamnofolane and daphnane skeletons are closely related, being formally derived from casbane by two cyclizations (6,10 and 5,14) followed by cleavage of the 1,15 (daphnane) or 2,15 (rhamnofolane) cyclopropane bonds.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Rhamnofolane and daphnane diterpenoids

Alternative Parents

Substituents

Daphnane diterpenoid
1,3-dioxepane
Carboxylic acid orthoester
Dioxepane
Ortho ester
Meta-dioxane
Monocyclic benzene moiety
Benzenoid
Meta-dioxolane
Cyclic alcohol
Tertiary alcohol
Secondary alcohol
Ketone
Orthocarboxylic acid derivative
Polyol
Ether
Oxirane
Organoheterocyclic compound
Dialkyl ether
Oxacycle
Primary alcohol
Organic oxide
Carbonyl group
Hydrocarbon derivative
Alcohol
Organic oxygen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	1.2	ALOGPS
logP	1.3	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	11.64	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	138.21 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	123.82 m³·mol⁻¹	ChemAxon
Polarizability	50.43 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

99841

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one (NP0159550)

MOL for NP0159550 (6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one)

3D MOL for NP0159550 (6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one)

3D SDF for NP0159550 (6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one)

3D-SDF for NP0159550 (6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one)

PDB for NP0159550 (6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one)

3D PDB for NP0159550 (6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one)

SMILES for NP0159550 (6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one)

INCHI for NP0159550 (6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one)

Structure for NP0159550 (6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one)

3D Structure for NP0159550 (6,7,17-trihydroxy-8-(hydroxymethyl)-4,18-dimethyl-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-5-one)