NP-MRD: Showing NP-Card for Kermadecin D (NP0073588)

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Record Information

Version

2.0

Created at

2022-04-28 18:48:34 UTC

Updated at

2022-04-28 18:48:34 UTC

NP-MRD ID

NP0073588

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Kermadecin D

Description

8,8-Dimethyl-2,9-dioxatetracyclo[25.3.1.0³,¹².0⁵,¹⁰]Hentriaconta-1(31),3,5(10),6,11,27,29-heptaene-4,29-diol belongs to the class of organic compounds known as 2,2-dimethyl-1-benzopyrans. These are organic compounds containing a 1-benzopyran moiety that carries two methyl groups at the 2-position. Kermadecin D is found in Kermadecia elliptica. 8,8-Dimethyl-2,9-dioxatetracyclo[25.3.1.0³,¹².0⁵,¹⁰]Hentriaconta-1(31),3,5(10),6,11,27,29-heptaene-4,29-diol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171513582D          

 35 38  0  0  0  0            999 V2000
    8.3767   -1.0453    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


  Mrv1533004171513582D          

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 14 15  1  0  0  0  0
 15 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
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
  7 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  2  0  0  0  0
  5 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
  2 34  1  0  0  0  0
 27 35  2  0  0  0  0
 22 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0073588

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)OC2=CC3=C(OC4=CC(CCCCCCCCCCCCCC3)=CC(O)=C4)C(O)=C2C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C31H42O4/c1-31(2)18-17-27-28(35-31)21-24-16-14-12-10-8-6-4-3-5-7-9-11-13-15-23-19-25(32)22-26(20-23)34-30(24)29(27)33/h17-22,32-33H,3-16H2,1-2H3

> <INCHI_KEY>
XUQKTJCXAXIZDH-UHFFFAOYSA-N

> <FORMULA>
C31H42O4

> <MOLECULAR_WEIGHT>
478.673

> <EXACT_MASS>
478.308309832

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
56.97165103886423

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
8,8-dimethyl-2,9-dioxatetracyclo[25.3.1.0³,¹².0⁵,¹⁰]hentriaconta-1(31),3(12),4,6,10,27,29-heptaene-4,29-diol

> <ALOGPS_LOGP>
8.45

> <JCHEM_LOGP>
9.664966613666667

> <ALOGPS_LOGS>
-6.73

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.267800600398221

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.376861961949121

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6993671707014557

> <JCHEM_POLAR_SURFACE_AREA>
58.92

> <JCHEM_REFRACTIVITY>
144.14619999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.93e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8,8-dimethyl-2,9-dioxatetracyclo[25.3.1.0³,¹².0⁵,¹⁰]hentriaconta-1(31),3(12),4,6,10,27,29-heptaene-4,29-diol

> <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      15.636  -1.951   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.829  -0.640   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.261  -0.073   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      13.678  -1.662   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      12.216  -1.177   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.065  -2.199   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.604  -1.714   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.452  -2.736   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.762  -4.245   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.611  -5.267   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.150  -4.782   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.840  -3.273   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.378  -2.787   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.068  -1.279   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.607  -0.793   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.297   0.715   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.835   1.201   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.525   2.710   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.677   3.732   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.138   3.246   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.290   4.269   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.751   3.783   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.902   4.806   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.364   4.320   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       9.515   5.343   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       8.674   2.812   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.522   1.789   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       7.832   0.281   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       9.294  -0.205   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.445   0.818   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      10.135   2.326   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      11.906   0.332   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      13.058   1.354   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      14.519   0.869   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.061   2.275   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4   34                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   32                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   29                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   35                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28   35                                                  
CONECT   28   27   29                                                       
CONECT   29   28    7   30                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30    5   33                                                  
CONECT   33   32   34                                                       
CONECT   34   33    2                                                       
CONECT   35   27   22                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₁H₄₂O₄

Average Mass

478.6730 Da

Monoisotopic Mass

478.30831 Da

IUPAC Name

8,8-dimethyl-2,9-dioxatetracyclo[25.3.1.0³,¹².0⁵,¹⁰]hentriaconta-1(31),3(12),4,6,10,27,29-heptaene-4,29-diol

Traditional Name

8,8-dimethyl-2,9-dioxatetracyclo[25.3.1.0³,¹².0⁵,¹⁰]hentriaconta-1(31),3(12),4,6,10,27,29-heptaene-4,29-diol

CAS Registry Number

Not Available

SMILES

CC1(C)OC2=CC3=C(OC4=CC(CCCCCCCCCCCCCC3)=CC(O)=C4)C(O)=C2C=C1

InChI Identifier

InChI=1S/C31H42O4/c1-31(2)18-17-27-28(35-31)21-24-16-14-12-10-8-6-4-3-5-7-9-11-13-15-23-19-25(32)22-26(20-23)34-30(24)29(27)33/h17-22,32-33H,3-16H2,1-2H3

InChI Key

XUQKTJCXAXIZDH-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, 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
Kermadecia elliptica	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2,2-dimethyl-1-benzopyrans. These are organic compounds containing a 1-benzopyran moiety that carries two methyl groups at the 2-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

2,2-dimethyl-1-benzopyrans

Alternative Parents

Substituents

2,2-dimethyl-1-benzopyran
Diaryl ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Benzenoid
Oxacycle
Ether
Organic oxygen compound
Hydrocarbon derivative
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	8.45	ALOGPS
logP	9.66	ChemAxon
logS	-6.7	ALOGPS
pKa (Strongest Acidic)	8.38	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.92 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	144.15 m³·mol⁻¹	ChemAxon
Polarizability	56.97 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	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

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

24761008

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Kermadecin D (NP0073588)

MOL for NP0073588 (Kermadecin D)

3D MOL for NP0073588 (Kermadecin D)

3D SDF for NP0073588 (Kermadecin D)

3D-SDF for NP0073588 (Kermadecin D)

PDB for NP0073588 (Kermadecin D)

3D PDB for NP0073588 (Kermadecin D)

SMILES for NP0073588 (Kermadecin D)

INCHI for NP0073588 (Kermadecin D)

Structure for NP0073588 (Kermadecin D)

3D Structure for NP0073588 (Kermadecin D)