NP-MRD: Showing NP-Card for (-)-Variabilin (NP0138460)

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Record Information

Version

1.0

Created at

2022-06-29 17:30:33 UTC

Updated at

2022-06-29 17:30:33 UTC

NP-MRD ID

NP0138460

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Variabilin

Description

(-)-Variabilin belongs to the class of organic compounds known as pterocarpans. These are benzo-pyrano-furano-benzene compounds, containing the 6H-[1]benzofuro[3,2-c]chromene skeleton. They are derivatives of isoflavonoids. (-)-Variabilin is found in Psammocinia bulbosa, Sophora flavescens and Trifolium pratense. Thus, (-)-variabilin is considered to be a flavonoid lipid molecule (-)-variabilin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 38 41  0  0  0  0  0  0  0  0999 V2000
   -6.7388    0.7270    0.7521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6610   -0.0219    1.2299 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3673    0.0794    0.7726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0499    0.9626   -0.2241 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7230    1.0286   -0.6541 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7322    0.2362   -0.1078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0657   -0.6451    0.8914 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3828   -0.7056    1.3130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0560   -1.4290    1.4237 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1453   -1.7397    0.7796 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4091   -0.9744   -0.4661 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2349   -1.6912   -1.6300 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8150   -0.4490   -0.3843 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0311   -1.0462   -0.5865 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2011   -0.3449   -0.4507 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2051    0.9889   -0.1056 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3895    1.7262    0.0389 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6246    1.0636   -0.1811 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9676    1.5621    0.0912 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7748    0.8778   -0.0393 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4300    1.2772    0.1168 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3515    0.3196   -0.5704 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.6885    1.7532    1.1974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7989    0.7722   -0.3549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6730    0.2628    1.1247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8100    1.6010   -0.6746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4802    1.7302   -1.4433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6074   -1.4102    2.1003 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0956   -2.8317    0.5039 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9646   -1.6756    1.5291 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1130   -1.0286   -2.3653 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1083   -2.0955   -0.8612 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1835   -0.8092   -0.6093 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4716    1.7468   -0.2270 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8118    0.2565    0.5543 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5748    0.5634   -1.1923 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9483    2.6161    0.3648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3136    0.6219   -1.6559 H   0  0  0  0  0  0  0  0  0  0  0  0
 22 21  1  0
 21 20  1  0
 20 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  2  0
 13 11  1  0
 11 12  1  6
 11 10  1  0
 10  9  1  0
  9  7  1  0
  7  6  2  0
  6  5  1  0
  5  4  2  0
  4  3  1  0
  3  2  1  0
  2  1  1  0
  3  8  2  0
 11 22  1  0
  8  7  1  0
  6 22  1  0
 19 20  1  0
 22 38  1  6
 14 32  1  0
 15 33  1  0
 18 34  1  0
 18 35  1  0
 18 36  1  0
 19 37  1  0
 12 31  1  0
 10 29  1  0
 10 30  1  0
  5 27  1  0
  4 26  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  8 28  1  0
M  END

(-)-Variabilin
  Mrv1652309271700132D          

 23 26  0  0  1  0            999 V2000
    5.1758   -0.8680    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1332    1.5054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4698    0.6375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6513   -2.3245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3252    1.6719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7598    0.2758    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0497   -0.0859    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3184   -0.2857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8014    1.0715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3815    0.3480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9581   -0.9912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4232    1.1439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1416   -0.2305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6480   -0.0401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3963   -1.6904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7343    1.6065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5957   -0.9194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2205   -1.6543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9483    0.4064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9917    1.2354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4473   -2.2865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6138    1.3129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4823   -0.4555    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1 11  1  0  0  0  0
  2  9  1  0  0  0  0
  2 12  1  0  0  0  0
  6  3  1  1  0  0  0
  4 18  1  0  0  0  0
  4 21  1  0  0  0  0
  5 20  1  0  0  0  0
  5 22  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
  7 23  1  1  0  0  0
  8 11  2  0  0  0  0
  8 13  1  0  0  0  0
 10 12  2  0  0  0  0
 10 14  1  0  0  0  0
 11 15  1  0  0  0  0
 12 16  1  0  0  0  0
 13 17  2  0  0  0  0
 14 19  2  0  0  0  0
 15 18  2  0  0  0  0
 16 20  2  0  0  0  0
 17 18  1  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0138460

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12OC3=C(C=CC(OC)=C3)[C@@]1(O)COC1=C2C=CC(OC)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C17H16O5/c1-19-10-3-5-12-14(7-10)21-9-17(18)13-6-4-11(20-2)8-15(13)22-16(12)17/h3-8,16,18H,9H2,1-2H3/t16-,17+/m1/s1

> <INCHI_KEY>
VVPGAJNPGZZNBM-SJORKVTESA-N

> <FORMULA>
C17H16O5

> <MOLECULAR_WEIGHT>
300.31

> <EXACT_MASS>
300.099773615

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
31.243117898899932

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,10R)-5,14-dimethoxy-8,17-dioxatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-2(7),3,5,11(16),12,14-hexaen-10-ol

> <ALOGPS_LOGP>
2.82

> <JCHEM_LOGP>
1.9999370703333335

> <ALOGPS_LOGS>
-3.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.036948329184675

> <JCHEM_PKA_STRONGEST_BASIC>
-4.094838800814622

> <JCHEM_POLAR_SURFACE_AREA>
57.150000000000006

> <JCHEM_REFRACTIVITY>
78.63130000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.48e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,10R)-5,14-dimethoxy-8,17-dioxatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-2(7),3,5,11(16),12,14-hexaen-10-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: (-)-Variabilin                                    
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-17         0                                  
HETATM    1  O   UNK     0       9.661  -1.620   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       9.582   2.810   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      12.077   1.190   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      14.282  -4.339   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       4.340   3.121   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      10.752   0.515   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.426  -0.160   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.794  -0.533   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.829   2.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.179   0.650   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.122  -1.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.257   2.135   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.331  -0.430   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.810  -0.075   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.940  -3.155   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.971   2.999   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      14.179  -1.716   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.478  -3.088   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.503   0.759   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.585   2.306   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      15.768  -4.268   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.012   2.451   0.000  0.00  0.00           C+0
HETATM   23  H   UNK     0       8.367  -0.850   0.000  0.00  0.00           H+0
CONECT    1    7   11                                                       
CONECT    2    9   12                                                       
CONECT    3    6                                                            
CONECT    4   18   21                                                       
CONECT    5   20   22                                                       
CONECT    6    3    7    8    9                                             
CONECT    7    1    6   10   23                                             
CONECT    8    6   11   13                                                  
CONECT    9    2    6                                                       
CONECT   10    7   12   14                                                  
CONECT   11    1    8   15                                                  
CONECT   12    2   10   16                                                  
CONECT   13    8   17                                                       
CONECT   14   10   19                                                       
CONECT   15   11   18                                                       
CONECT   16   12   20                                                       
CONECT   17   13   18                                                       
CONECT   18    4   15   17                                                  
CONECT   19   14   20                                                       
CONECT   20    5   16   19                                                  
CONECT   21    4                                                            
CONECT   22    5                                                            
CONECT   23    7                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₁₆O₅

Average Mass

300.3100 Da

Monoisotopic Mass

300.09977 Da

IUPAC Name

(1R,10R)-5,14-dimethoxy-8,17-dioxatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-2(7),3,5,11(16),12,14-hexaen-10-ol

Traditional Name

(1R,10R)-5,14-dimethoxy-8,17-dioxatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-2(7),3,5,11(16),12,14-hexaen-10-ol

CAS Registry Number

370102-93-5

SMILES

[H][C@]12OC3=C(C=CC(OC)=C3)[C@@]1(O)COC1=C2C=CC(OC)=C1

InChI Identifier

InChI=1S/C17H16O5/c1-19-10-3-5-12-14(7-10)21-9-17(18)13-6-4-11(20-2)8-15(13)22-16(12)17/h3-8,16,18H,9H2,1-2H3/t16-,17+/m1/s1

InChI Key

VVPGAJNPGZZNBM-SJORKVTESA-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
Psammocinia bulbosa	LOTUS Database	35616633
Sophora flavescens	LOTUS Database	35616633
Trifolium pratense	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pterocarpans. These are benzo-pyrano-furano-benzene compounds, containing the 6H-[1]benzofuro[3,2-c]chromene skeleton. They are derivatives of isoflavonoids.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isoflavonoids

Sub Class

Furanoisoflavonoids

Direct Parent

Pterocarpans

Alternative Parents

Substituents

Pterocarpan
Isoflavanol
Isoflavan
Chromane
1-benzopyran
Benzopyran
Coumaran
Benzofuran
Anisole
Alkyl aryl ether
Benzenoid
Tertiary alcohol
Oxacycle
Organoheterocyclic compound
Ether
Alcohol
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

pterocarpans (CHEBI:123 )
pterocarpans (C10539 )
Pterocarpanes (C10539 )
Pterocarpans (LMPK12070130 )

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	2.82	ALOGPS
logP	2	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	12.04	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	57.15 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	78.63 m³·mol⁻¹	ChemAxon
Polarizability	31.24 Å³	ChemAxon
Number of Rings	4	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

C00002582

Chemspider ID

Not Available

KEGG Compound ID

C10539

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442828

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Variabilin (NP0138460)

MOL for NP0138460 ((-)-Variabilin)

3D MOL for NP0138460 ((-)-Variabilin)

3D SDF for NP0138460 ((-)-Variabilin)

3D-SDF for NP0138460 ((-)-Variabilin)

PDB for NP0138460 ((-)-Variabilin)

3D PDB for NP0138460 ((-)-Variabilin)

SMILES for NP0138460 ((-)-Variabilin)

INCHI for NP0138460 ((-)-Variabilin)

Structure for NP0138460 ((-)-Variabilin)

3D Structure for NP0138460 ((-)-Variabilin)