NP-MRD: Showing NP-Card for Phyllanthusmin B (NP0071626)

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Record Information

Version

2.0

Created at

2022-04-28 16:58:42 UTC

Updated at

2022-04-28 16:58:43 UTC

NP-MRD ID

NP0071626

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Phyllanthusmin B

Description

(3R,4S,5S,6R)-6-{[9-(2H-1,3-benzodioxol-5-yl)-6,7-dimethoxy-1-oxo-1H,3H-naphtho[2,3-c]furan-4-yl]oxy}-4,5-dihydroxyoxan-3-yl acetate belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones. Phyllanthusmin B is found in Phyllanthus oligospermus. Based on a literature review very few articles have been published on (3R,4S,5S,6R)-6-{[9-(2H-1,3-benzodioxol-5-yl)-6,7-dimethoxy-1-oxo-1H,3H-naphtho[2,3-c]furan-4-yl]oxy}-4,5-dihydroxyoxan-3-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282218582D          

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M  END

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M  END


  Mrv1652304282218582D          

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 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  8 13  1  0  0  0  0
 11 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 10 18  1  6  0  0  0
  9 19  1  1  0  0  0
  5 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  4 22  1  0  0  0  0
 22 23  2  0  0  0  0
  3 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
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 24 29  1  0  0  0  0
 27 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 26 32  1  0  0  0  0
  2 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
  1 36  1  0  0  0  0
 35 37  1  0  0  0  0
 37 38  1  0  0  0  0
 34 39  1  0  0  0  0
 39 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0071626

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC2=C(O[C@H]3OC[C@@H](OC(C)=O)[C@@H](O)[C@@H]3O)C3=C(C(=O)OC3)C(C3=CC4=C(OCO4)C=C3)=C2C=C1OC

> <INCHI_IDENTIFIER>
InChI=1S/C28H26O12/c1-12(29)39-21-10-36-28(25(31)24(21)30)40-26-15-8-19(34-3)18(33-2)7-14(15)22(23-16(26)9-35-27(23)32)13-4-5-17-20(6-13)38-11-37-17/h4-8,21,24-25,28,30-31H,9-11H2,1-3H3/t21-,24-,25+,28-/m1/s1

> <INCHI_KEY>
PDCZTHZYQGOSBV-DAHKTCFSSA-N

> <FORMULA>
C28H26O12

> <MOLECULAR_WEIGHT>
554.504

> <EXACT_MASS>
554.142426277

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
55.65826710334585

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5S,6R)-6-{[9-(2H-1,3-benzodioxol-5-yl)-6,7-dimethoxy-1-oxo-1H,3H-naphtho[2,3-c]furan-4-yl]oxy}-4,5-dihydroxyoxan-3-yl acetate

> <ALOGPS_LOGP>
2.18

> <JCHEM_LOGP>
1.972370073666665

> <ALOGPS_LOGS>
-3.39

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.350925238833593

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.236212104269914

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6877834781413705

> <JCHEM_POLAR_SURFACE_AREA>
148.44

> <JCHEM_REFRACTIVITY>
134.2319

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.24e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4S,5S,6R)-6-{[9-(2H-1,3-benzodioxol-5-yl)-6,7-dimethoxy-1-oxo-3H-naphtho[2,3-c]furan-4-yl]oxy}-4,5-dihydroxyoxan-3-yl acetate

> <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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.000  -0.000   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  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -0.320  -4.586   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -1.852  -4.747   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -2.478  -3.340   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -3.984  -3.020   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -6.799   2.016   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -7.705   0.770   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -6.799  -0.476   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
CONECT    1    2    6   36                                                  
CONECT    2    1    3   33                                                  
CONECT    3    2    4   24                                                  
CONECT    4    3    5   22                                                  
CONECT    5    4    6   20                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10   19                                                  
CONECT   10    9   11   18                                                  
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14   11   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   10                                                            
CONECT   19    9                                                            
CONECT   20    5   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21    4   23                                                  
CONECT   23   22                                                            
CONECT   24    3   25   29                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   32                                                  
CONECT   27   26   28   30                                                  
CONECT   28   27   29                                                       
CONECT   29   28   24                                                       
CONECT   30   27   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   26                                                       
CONECT   33    2   34                                                       
CONECT   34   33   35   39                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35    1                                                       
CONECT   37   35   38                                                       
CONECT   38   37                                                            
CONECT   39   34   40                                                       
CONECT   40   39                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   90    0
END

View in JSmol

Synonyms

Value	Source
(3R,4S,5S,6R)-6-{[9-(2H-1,3-benzodioxol-5-yl)-6,7-dimethoxy-1-oxo-1H,3H-naphtho[2,3-c]furan-4-yl]oxy}-4,5-dihydroxyoxan-3-yl acetic acid	Generator

Chemical Formula

C₂₈H₂₆O₁₂

Average Mass

554.5040 Da

Monoisotopic Mass

554.14243 Da

IUPAC Name

(3R,4S,5S,6R)-6-{[9-(2H-1,3-benzodioxol-5-yl)-6,7-dimethoxy-1-oxo-1H,3H-naphtho[2,3-c]furan-4-yl]oxy}-4,5-dihydroxyoxan-3-yl acetate

Traditional Name

(3R,4S,5S,6R)-6-{[9-(2H-1,3-benzodioxol-5-yl)-6,7-dimethoxy-1-oxo-3H-naphtho[2,3-c]furan-4-yl]oxy}-4,5-dihydroxyoxan-3-yl acetate

CAS Registry Number

Not Available

SMILES

COC1=CC2=C(O[C@H]3OC[C@@H](OC(C)=O)[C@@H](O)[C@@H]3O)C3=C(C(=O)OC3)C(C3=CC4=C(OCO4)C=C3)=C2C=C1OC

InChI Identifier

InChI=1S/C28H26O12/c1-12(29)39-21-10-36-28(25(31)24(21)30)40-26-15-8-19(34-3)18(33-2)7-14(15)22(23-16(26)9-35-27(23)32)13-4-5-17-20(6-13)38-11-37-17/h4-8,21,24-25,28,30-31H,9-11H2,1-3H3/t21-,24-,25+,28-/m1/s1

InChI Key

PDCZTHZYQGOSBV-DAHKTCFSSA-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
Phyllanthus oligospermus	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Lignan glycosides

Sub Class

Not Available

Direct Parent

Lignan glycosides

Alternative Parents

Substituents

Lignan glycoside
Arylnaphthalene lignan skeleton
Lignan lactone
Phenolic glycoside
Naphthofuran
Glycosyl compound
O-glycosyl compound
Isobenzofuranone
Phthalide
Naphthalene
Isocoumaran
Benzodioxole
Anisole
Alkyl aryl ether
Dicarboxylic acid or derivatives
Benzenoid
Monosaccharide
Oxane
Lactone
1,2-diol
Carboxylic acid ester
Secondary alcohol
Acetal
Organoheterocyclic compound
Ether
Carboxylic acid derivative
Oxacycle
Carbonyl group
Hydrocarbon derivative
Organic oxide
Alcohol
Organic oxygen compound
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	2.18	ALOGPS
logP	1.97	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	12.24	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	148.44 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	134.23 m³·mol⁻¹	ChemAxon
Polarizability	55.66 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

Not Available

Chemspider ID

17240776

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

16082067

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Phyllanthusmin B (NP0071626)

MOL for NP0071626 (Phyllanthusmin B)

3D MOL for NP0071626 (Phyllanthusmin B)

3D SDF for NP0071626 (Phyllanthusmin B)

3D-SDF for NP0071626 (Phyllanthusmin B)

PDB for NP0071626 (Phyllanthusmin B)

3D PDB for NP0071626 (Phyllanthusmin B)

SMILES for NP0071626 (Phyllanthusmin B)

INCHI for NP0071626 (Phyllanthusmin B)

Structure for NP0071626 (Phyllanthusmin B)

3D Structure for NP0071626 (Phyllanthusmin B)