NP-MRD: Showing NP-Card for Leucadenone D (NP0060517)

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Record Information

Version

2.0

Created at

2022-04-28 05:33:11 UTC

Updated at

2022-04-28 05:33:11 UTC

NP-MRD ID

NP0060517

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Leucadenone D

Description

Leucadenone d belongs to the class of organic compounds known as prenylated neoflavonoids. These are neoflavonoids that features a C5-isoprenoid substituent at any position of the A, B, or C ring. Neoflavonoids are compounds with a structure based on the 4-phenylchromene backbone. Thus, leucadenone D is considered to be a flavonoid. Leucadenone D is found in Melaleuca leucadendra and Melaleuca leucadendron . Based on a literature review very few articles have been published on Leucadenone d.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282207332D          

 40 45  0  0  1  0            999 V2000
    5.0352   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3052    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1154    0.7243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7651    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9550    1.0361    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6850    0.2566    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2251   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9550   -1.1466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8748    0.1007    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3347    0.7243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.4149    1.6598    0.0000 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


  Mrv1652304282207332D          

 40 45  0  0  1  0            999 V2000
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  2  3  2  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  6  0  0  0
  1  7  1  0  0  0  0
  7  8  2  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
  5 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 10 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 20 21  2  0  0  0  0
 18 22  1  6  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 22 27  1  0  0  0  0
 14 28  1  0  0  0  0
 13 29  1  0  0  0  0
  9 30  1  6  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 30 35  1  0  0  0  0
  5 36  1  6  0  0  0
  4 37  1  0  0  0  0
  4 38  1  0  0  0  0
  1 39  1  0  0  0  0
  1 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0060517

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C(O)C2=C(O[C@@H](CC2=O)C2=CC=CC=C2)C2=C1O[C@]1(O)[C@@H]([C@@H]2C2=CC=CC=C2)C(=O)C(C)(C)C(=O)C1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C33H32O7/c1-17-26(35)23-20(34)16-21(18-12-8-6-9-13-18)39-28(23)24-22(19-14-10-7-11-15-19)25-29(36)31(2,3)30(37)32(4,5)33(25,38)40-27(17)24/h6-15,21-22,25,35,38H,16H2,1-5H3/t21-,22+,25-,33+/m0/s1

> <INCHI_KEY>
VAJKIKOYPOZJCO-PTMAZNHLSA-N

> <FORMULA>
C33H32O7

> <MOLECULAR_WEIGHT>
540.612

> <EXACT_MASS>
540.21480337

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
56.64463990817257

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,7aR,11aS,12R)-5,7a-dihydroxy-6,8,8,10,10-pentamethyl-2,12-diphenyl-2,3,4,7a,8,9,10,11,11a,12-decahydro-1,7-dioxatetraphene-4,9,11-trione

> <ALOGPS_LOGP>
4.64

> <JCHEM_LOGP>
7.639826470333333

> <ALOGPS_LOGS>
-5.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.959284566120566

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.98864124832626

> <JCHEM_PKA_STRONGEST_BASIC>
-4.574421678613835

> <JCHEM_POLAR_SURFACE_AREA>
110.13000000000002

> <JCHEM_REFRACTIVITY>
148.34760000000009

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.72e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
leucadenone D

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       9.399  -0.394   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.903   1.061   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      11.415   1.352   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       8.895   2.225   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.383   1.934   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.879   0.479   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.887  -0.685   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.383  -2.140   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       5.366   0.188   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.358   1.352   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.862   2.807   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.375   3.098   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       3.854   3.971   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.342   3.680   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.838   2.225   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.846   1.061   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.342  -0.394   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       0.830  -0.685   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.179   0.479   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.326   1.934   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.683   3.098   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       0.326  -2.140   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.334  -3.304   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.830  -4.760   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.683  -5.051   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.691  -3.887   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.187  -2.431   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       1.334   4.844   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       4.358   5.427   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.862  -1.267   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.870  -2.431   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.366  -3.887   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.854  -4.178   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.846  -3.013   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.350  -1.558   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       7.887   3.389   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      10.023   3.273   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       8.657   3.747   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      10.836  -0.949   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       9.743  -1.895   0.000  0.00  0.00           C+0
CONECT    1    2    7   39   40                                             
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   37   38                                             
CONECT    5    4    6   12   36                                             
CONECT    6    5    7    9                                                  
CONECT    7    6    1    8                                                  
CONECT    8    7                                                            
CONECT    9    6   10   30                                                  
CONECT   10    9   11   16                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11    5                                                       
CONECT   13   11   14   29                                                  
CONECT   14   13   15   28                                                  
CONECT   15   14   16   20                                                  
CONECT   16   15   10   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   22                                                  
CONECT   19   18   20                                                       
CONECT   20   19   15   21                                                  
CONECT   21   20                                                            
CONECT   22   18   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   22                                                       
CONECT   28   14                                                            
CONECT   29   13                                                            
CONECT   30    9   31   35                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   30                                                       
CONECT   36    5                                                            
CONECT   37    4                                                            
CONECT   38    4                                                            
CONECT   39    1                                                            
CONECT   40    1                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₃H₃₂O₇

Average Mass

540.6120 Da

Monoisotopic Mass

540.21480 Da

IUPAC Name

(2S,7aR,11aS,12R)-5,7a-dihydroxy-6,8,8,10,10-pentamethyl-2,12-diphenyl-2,3,4,7a,8,9,10,11,11a,12-decahydro-1,7-dioxatetraphene-4,9,11-trione

Traditional Name

leucadenone D

CAS Registry Number

Not Available

SMILES

CC1=C(O)C2=C(O[C@@H](CC2=O)C2=CC=CC=C2)C2=C1O[C@]1(O)[C@@H]([C@@H]2C2=CC=CC=C2)C(=O)C(C)(C)C(=O)C1(C)C

InChI Identifier

InChI=1S/C33H32O7/c1-17-26(35)23-20(34)16-21(18-12-8-6-9-13-18)39-28(23)24-22(19-14-10-7-11-15-19)25-29(36)31(2,3)30(37)32(4,5)33(25,38)40-27(17)24/h6-15,21-22,25,35,38H,16H2,1-5H3/t21-,22+,25-,33+/m0/s1

InChI Key

VAJKIKOYPOZJCO-PTMAZNHLSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Melaleuca leucadendra	LOTUS Database	35616633
Melaleuca leucadendron	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as prenylated neoflavonoids. These are neoflavonoids that features a C5-isoprenoid substituent at any position of the A, B, or C ring. Neoflavonoids are compounds with a structure based on the 4-phenylchromene backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Neoflavonoids

Sub Class

Prenylated neoflavonoids

Direct Parent

Prenylated neoflavonoids

Alternative Parents

Substituents

Pyranoflavonoid
Prenylated neoflavonoid
Linear 1,7-diphenylheptane skeleton
5-hydroxyflavonoid
Hydroxyflavonoid
Flavanone
Neoflavan
Flavan
Xanthene
Dibenzopyran
Pyranochromene
Chromone
1-benzopyran
Benzopyran
Chromane
Aryl alkyl ketone
Aryl ketone
Alkyl aryl ether
Monocyclic benzene moiety
Benzenoid
Vinylogous acid
Cyclic alcohol
Hemiacetal
Cyclic ketone
Ketone
Ether
Organoheterocyclic compound
Oxacycle
Organic oxide
Carbonyl group
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Flavanones (LMPK12140155 )

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	4.64	ALOGPS
logP	7.64	ChemAxon
logS	-5.5	ALOGPS
pKa (Strongest Acidic)	8.99	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	110.13 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	148.35 m³·mol⁻¹	ChemAxon
Polarizability	56.64 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

C00014277

Chemspider ID

24846305

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15409093

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Leucadenone D (NP0060517)

MOL for NP0060517 (Leucadenone D)

3D MOL for NP0060517 (Leucadenone D)

3D SDF for NP0060517 (Leucadenone D)

3D-SDF for NP0060517 (Leucadenone D)

PDB for NP0060517 (Leucadenone D)

3D PDB for NP0060517 (Leucadenone D)

SMILES for NP0060517 (Leucadenone D)

INCHI for NP0060517 (Leucadenone D)

Structure for NP0060517 (Leucadenone D)

3D Structure for NP0060517 (Leucadenone D)