NP-MRD: Showing NP-Card for Tomentin C (NP0086060)

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Record Information

Version

2.0

Created at

2022-04-29 06:26:27 UTC

Updated at

2022-04-29 06:26:28 UTC

NP-MRD ID

NP0086060

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Tomentin C

Description

Tomentin C belongs to the class of organic compounds known as 6-prenylated flavanones. These are flavanones that features a C5-isoprenoid substituent at the 6-position. Tomentin C is found in Paulownia tomentosa. Tomentin C was first documented in 2013 (PMID: 23623680). Based on a literature review very few articles have been published on Tomentin C.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292208262D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304292208262D          

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M  END
> <DATABASE_ID>
NP0086060

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(CC(=O)C2=C(O)C3=C(OC(C)(CCCC(C)(C)O)CC3)C=C2O1)C1=CC(O)=C(OC)C(OC)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C27H34O8/c1-26(2,31)8-6-9-27(3)10-7-16-20(35-27)14-21-23(24(16)30)17(28)13-19(34-21)15-11-18(29)25(33-5)22(12-15)32-4/h11-12,14,19,29-31H,6-10,13H2,1-5H3/t19-,27?/m0/s1

> <INCHI_KEY>
ZMYCAMWWCDPOSK-JDEXWRGDSA-N

> <FORMULA>
C27H34O8

> <MOLECULAR_WEIGHT>
486.561

> <EXACT_MASS>
486.225368055

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
53.411106342067434

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5S)-9-hydroxy-5-(3-hydroxy-4,5-dimethoxyphenyl)-13-(4-hydroxy-4-methylpentyl)-13-methyl-4,14-dioxatricyclo[8.4.0.0^{3,8}]tetradeca-1(10),2,8-trien-7-one

> <ALOGPS_LOGP>
3.92

> <JCHEM_LOGP>
4.519401240666667

> <ALOGPS_LOGS>
-4.79

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.882840559073083

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.921957645741088

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2540972234768386

> <JCHEM_POLAR_SURFACE_AREA>
114.68

> <JCHEM_REFRACTIVITY>
130.37779999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.81e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5S)-9-hydroxy-5-(3-hydroxy-4,5-dimethoxyphenyl)-13-(4-hydroxy-4-methylpentyl)-13-methyl-4,14-dioxatricyclo[8.4.0.0^{3,8}]tetradeca-1(10),2,8-trien-7-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   12  H   UNK     0       1.334  -3.850   0.000  0.00  0.00           H+0
HETATM   13  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.196  -1.633   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.186  -3.347   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.176  -2.168   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      14.693  -2.435   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      15.682  -1.255   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      16.672  -0.076   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      16.862  -2.245   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      14.503  -0.266   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   36                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6   10                                                       
CONECT   10    9   11   36                                                  
CONECT   11   10   12   13   34                                             
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   32                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   29                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20   27                                             
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25   26                                             
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   23                                                            
CONECT   27   18   28                                                       
CONECT   28   27   29                                                       
CONECT   29   16   28   30                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   14   33                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33   11                                                       
CONECT   35   33                                                            
CONECT   36   10    2                                                       
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₄O₈

Average Mass

486.5610 Da

Monoisotopic Mass

486.22537 Da

IUPAC Name

(5S)-9-hydroxy-5-(3-hydroxy-4,5-dimethoxyphenyl)-13-(4-hydroxy-4-methylpentyl)-13-methyl-4,14-dioxatricyclo[8.4.0.0^{3,8}]tetradeca-1(10),2,8-trien-7-one

Traditional Name

(5S)-9-hydroxy-5-(3-hydroxy-4,5-dimethoxyphenyl)-13-(4-hydroxy-4-methylpentyl)-13-methyl-4,14-dioxatricyclo[8.4.0.0^{3,8}]tetradeca-1(10),2,8-trien-7-one

CAS Registry Number

Not Available

SMILES

[H][C@]1(CC(=O)C2=C(O)C3=C(OC(C)(CCCC(C)(C)O)CC3)C=C2O1)C1=CC(O)=C(OC)C(OC)=C1

InChI Identifier

InChI=1S/C27H34O8/c1-26(2,31)8-6-9-27(3)10-7-16-20(35-27)14-21-23(24(16)30)17(28)13-19(34-21)15-11-18(29)25(33-5)22(12-15)32-4/h11-12,14,19,29-31H,6-10,13H2,1-5H3/t19-,27?/m0/s1

InChI Key

ZMYCAMWWCDPOSK-JDEXWRGDSA-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
Paulownia tomentosa	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 6-prenylated flavanones. These are flavanones that features a C5-isoprenoid substituent at the 6-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavans

Direct Parent

6-prenylated flavanones

Alternative Parents

Substituents

6-prenylated flavanone
Pyranoflavonoid
3p-methoxyflavonoid-skeleton
4p-methoxyflavonoid-skeleton
3'-hydroxyflavonoid
5-hydroxyflavonoid
Flavanone
Hydroxyflavonoid
Pyranochromene
Chromone
Chromane
Benzopyran
Methoxyphenol
1-benzopyran
O-dimethoxybenzene
Dimethoxybenzene
Aryl alkyl ketone
Aryl ketone
Anisole
Phenoxy compound
Phenol ether
Methoxybenzene
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Phenol
1-hydroxy-4-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Tertiary alcohol
Vinylogous acid
Ketone
Organoheterocyclic compound
Oxacycle
Ether
Organooxygen compound
Hydrocarbon derivative
Alcohol
Organic oxygen compound
Organic oxide
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	3.92	ALOGPS
logP	4.52	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	8.92	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	114.68 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	130.38 m³·mol⁻¹	ChemAxon
Polarizability	53.41 Å³	ChemAxon
Number of Rings	4	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

C00056177

Chemspider ID

30828026

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71659765

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Cho JK, Curtis-Long MJ, Lee KH, Kim DW, Ryu HW, Yuk HJ, Park KH: Geranylated flavonoids displaying SARS-CoV papain-like protease inhibition from the fruits of Paulownia tomentosa. Bioorg Med Chem. 2013 Jun 1;21(11):3051-7. doi: 10.1016/j.bmc.2013.03.027. Epub 2013 Mar 29. [PubMed:23623680 ]

Showing NP-Card for Tomentin C (NP0086060)

MOL for NP0086060 (Tomentin C)

3D MOL for NP0086060 (Tomentin C)

3D SDF for NP0086060 (Tomentin C)

3D-SDF for NP0086060 (Tomentin C)

PDB for NP0086060 (Tomentin C)

3D PDB for NP0086060 (Tomentin C)

SMILES for NP0086060 (Tomentin C)

INCHI for NP0086060 (Tomentin C)

Structure for NP0086060 (Tomentin C)

3D Structure for NP0086060 (Tomentin C)