NP-MRD: Showing NP-Card for 3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan (NP0056798)

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Record Information

Version

2.0

Created at

2022-04-28 02:27:18 UTC

Updated at

2022-04-28 02:27:18 UTC

NP-MRD ID

NP0056798

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan

Description

Sophoracoumestan b belongs to the class of organic compounds known as coumestans. These are polycyclic aromatic compounds containing a coumestan moiety, which consists of a benzoxole fused to a chromen-2-one to form 1-Benzoxolo[3,2-c]chromen-6-one. They are oxidation products of pterocarpan. Thus, sophoracoumestan b is considered to be a flavonoid lipid molecule. 3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan is found in Cyclopia intermedia and Sophora franchetiana. Sophoracoumestan b is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 38  0  0  0  0  0  0  0  0999 V2000
   -5.0011    0.7475   -1.3751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4240   -0.4994   -1.0028 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5276   -0.5310    0.0517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0225   -0.7391    1.3206 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3760   -0.9173    1.5821 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1765   -0.7813    2.4167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8335   -0.6075    2.1817 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3103   -0.3979    0.9259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1741   -0.3594   -0.1559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6891   -0.1578   -1.3800 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4003    0.0093   -1.6086 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0180    0.1983   -2.7886 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5255   -0.0150   -0.5879 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8897    0.1189   -0.4773 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8813    0.3409   -1.4190 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1759    0.4258   -0.9673 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5434    0.3035    0.3616 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5439    0.0839    1.2774 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2217   -0.0097    0.8731 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0846   -0.2083    1.4939 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0586   -0.2217    0.6939 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9195    0.4357    0.4975 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4513    0.3451   -0.8078 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3501    0.6390   -1.6760 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0038    0.5538   -1.8168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4057    1.2569   -2.1442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0610    1.4047   -0.4867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9995   -0.8876    0.7857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5823   -0.9472    3.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1519   -0.6357    3.0177 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6106    0.4375   -2.4519 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8105   -0.0134    2.3125 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2811    1.0218   -1.0028 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7734   -0.6822   -1.0620 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 21  2  0
 21 20  1  0
 20 19  1  0
 19 18  2  0
 18 17  1  0
 17 16  2  0
 16 24  1  0
 24 23  1  0
 23 22  1  0
 16 15  1  0
 15 14  2  0
  9  3  1  0
 14 13  1  0
 21  8  1  0
 14 19  1  0
 22 17  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  5 28  1  0
  6 29  1  0
  7 30  1  0
 18 32  1  0
 23 33  1  0
 23 34  1  0
 15 31  1  0
M  END


  Mrv1533004261503392D          

 24 28  0  0  0  0            999 V2000
    6.5302    3.0632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7072    3.0058    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3454    2.2644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8066    1.5803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6296    1.6377    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4448    0.8389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6218    0.7815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1606    1.4656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5224    2.2070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0612    2.8911    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2382    2.8337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770    3.5178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8764    2.0923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3376    1.4082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8295    0.7582    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0543    1.0406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3258    0.6534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6263    1.0908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1668    0.8635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6280    1.5476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1199    2.1976    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6553    1.9152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3838    2.3024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0833    1.8651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
  8 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  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
 18 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 13 24  1  0  0  0  0
 16 24  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0056798

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C=CC2=C1OC(=O)C1=C2OC2=CC3=C(OCO3)C=C12

> <INCHI_IDENTIFIER>
InChI=1S/C17H10O7/c1-20-16-9(18)3-2-7-14-13(17(19)24-15(7)16)8-4-11-12(22-6-21-11)5-10(8)23-14/h2-5,18H,6H2,1H3

> <INCHI_KEY>
WFBFYJLFWIJBFD-UHFFFAOYSA-N

> <FORMULA>
C17H10O7

> <MOLECULAR_WEIGHT>
326.26

> <EXACT_MASS>
326.042652662

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
31.95966780914525

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
16-hydroxy-17-methoxy-5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-1(12),2,4(8),9,13(18),14,16-heptaen-20-one

> <ALOGPS_LOGP>
2.48

> <JCHEM_LOGP>
2.1664488459999998

> <ALOGPS_LOGS>
-2.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.690839395341939

> <JCHEM_PKA_STRONGEST_BASIC>
-3.046589442973609

> <JCHEM_POLAR_SURFACE_AREA>
87.36000000000001

> <JCHEM_REFRACTIVITY>
79.8687

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.81e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
sophoracoumestan B

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-15         0                                  
HETATM    1  C   UNK     0      12.190   5.718   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      10.654   5.611   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       9.978   4.227   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.839   2.950   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      12.375   3.057   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      10.164   1.566   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.627   1.459   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.766   2.736   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.442   4.120   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.581   5.397   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.045   5.290   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.184   6.566   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.369   3.906   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.230   2.629   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.282   1.415   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.835   1.942   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.475   1.220   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.169   2.036   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -0.311   1.612   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -1.172   2.889   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.224   4.102   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.223   3.575   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.583   4.298   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.889   3.481   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8    3   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   24                                                  
CONECT   14   13    8   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   24                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   22                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   18   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   13   16                                                  
MASTER        0    0    0    0    0    0    0    0   24    0   56    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₁₀O₇

Average Mass

326.2600 Da

Monoisotopic Mass

326.04265 Da

IUPAC Name

16-hydroxy-17-methoxy-5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-1(12),2,4(8),9,13(18),14,16-heptaen-20-one

Traditional Name

sophoracoumestan B

CAS Registry Number

Not Available

SMILES

COC1=C(O)C=CC2=C1OC(=O)C1=C2OC2=CC3=C(OCO3)C=C12

InChI Identifier

InChI=1S/C17H10O7/c1-20-16-9(18)3-2-7-14-13(17(19)24-15(7)16)8-4-11-12(22-6-21-11)5-10(8)23-14/h2-5,18H,6H2,1H3

InChI Key

WFBFYJLFWIJBFD-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
Cyclopia intermedia	LOTUS Database	35616633
Sophora franchetiana	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumestans. These are polycyclic aromatic compounds containing a coumestan moiety, which consists of a benzoxole fused to a chromen-2-one to form 1-Benzoxolo[3,2-c]chromen-6-one. They are oxidation products of pterocarpan.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isoflavonoids

Sub Class

Coumestans

Direct Parent

Coumestans

Alternative Parents

Substituents

Coumestan
Angular furanocoumarin
Furanocoumarin
Coumarin
Benzopyran
1-benzopyran
Benzodioxole
Benzofuran
Furopyran
Anisole
Pyranone
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Pyran
Benzenoid
Furan
Heteroaromatic compound
Lactone
Organoheterocyclic compound
Ether
Oxacycle
Acetal
Organooxygen compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Coumestan flavonoids (LMPK12090037 )

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	2.48	ALOGPS
logP	2.17	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	7.69	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	87.36 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	79.87 m³·mol⁻¹	ChemAxon
Polarizability	31.96 Å³	ChemAxon
Number of Rings	5	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

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

11131193

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan (NP0056798)

MOL for NP0056798 (3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan)

3D MOL for NP0056798 (3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan)

3D SDF for NP0056798 (3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan)

3D-SDF for NP0056798 (3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan)

PDB for NP0056798 (3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan)

3D PDB for NP0056798 (3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan)

SMILES for NP0056798 (3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan)

INCHI for NP0056798 (3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan)

Structure for NP0056798 (3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan)

3D Structure for NP0056798 (3-Hydroxy-4-methoxy-8,9-methylenedioxycoumestan)