NP-MRD: Showing NP-Card for Phyllanthusiin E (NP0075658)

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Record Information

Version

2.0

Created at

2022-04-28 20:55:00 UTC

Updated at

2022-04-28 20:55:01 UTC

NP-MRD ID

NP0075658

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Phyllanthusiin E

Description

2-{11,12-Dihydroxy-3,8-dioxo-2,7-dioxatricyclo[7.3.1.0⁵,¹³]Trideca-1(13),4,9,11-tetraen-4-yl}acetic acid belongs to the class of organic compounds known as 7,8-dihydroxycoumarins. These are coumarins bearing two hydroxyl groups at the C7- and C8-positions of the coumarin skeleton, respectively. Phyllanthusiin E is found in Geranium thunbergii, Nymphaea alba , Pelargonium reniforme, Phyllanthus flexuosus and Punica granatum . 2-{11,12-Dihydroxy-3,8-dioxo-2,7-dioxatricyclo[7.3.1.0⁵,¹³]Trideca-1(13),4,9,11-tetraen-4-yl}acetic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 31  0  0  0  0  0  0  0  0999 V2000
    3.0817    0.4697   -1.4150 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6084    0.1033   -0.3242 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9691   -0.1728   -0.3847 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8392   -0.0274    0.9417 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4128    0.2837    0.6992 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5195   -0.6189    0.1322 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7790   -0.2113   -0.0658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7503   -1.0264   -0.6201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0610   -0.6225   -0.8219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4409    0.6509   -0.4596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7539    1.0616   -0.6602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4817    1.4656    0.0924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8519    2.7651    0.4665 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1603    1.0670    0.2989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2766    1.8571    0.8232 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9676    1.5249    1.0338 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7571    2.3974    1.5638 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3246   -2.3697   -0.9931 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1330   -3.1820   -1.5033 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0301   -2.7230   -0.7753 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9986   -1.9575   -0.2115 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5620   -0.0516    0.4095 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9895   -1.0776    1.2736 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2885    0.6927    1.6567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8094   -1.2898   -1.2634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0942    1.9712   -0.4207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2206    3.4180    0.8719 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3784   -2.5330    0.6592 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7950   -1.8649   -1.0038 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6 21  1  0
 21 20  1  0
 20 18  1  0
 18 19  2  0
 18  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 10 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 14  7  2  0
 16  5  1  0
  7  6  1  0
  7  8  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
 21 28  1  0
 21 29  1  0
  9 25  1  0
 11 26  1  0
 13 27  1  0
M  END


  Mrv1533004241511062D          

 21 23  0  0  0  0            999 V2000
   -0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
  5 19  1  0  0  0  0
 19 20  2  0  0  0  0
 17 21  2  0  0  0  0
  6 21  1  0  0  0  0
 11 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0075658

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CC1=C2COC(=O)C3=CC(O)=C(O)C(OC1=O)=C23

> <INCHI_IDENTIFIER>
InChI=1S/C13H8O8/c14-7-1-5-9-6(3-20-12(5)18)4(2-8(15)16)13(19)21-11(9)10(7)17/h1,14,17H,2-3H2,(H,15,16)

> <INCHI_KEY>
DBBOJUGDRHJPND-UHFFFAOYSA-N

> <FORMULA>
C13H8O8

> <MOLECULAR_WEIGHT>
292.199

> <EXACT_MASS>
292.021917218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
25.454501486833756

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{11,12-dihydroxy-3,8-dioxo-2,7-dioxatricyclo[7.3.1.0⁵,¹³]trideca-1(13),4,9,11-tetraen-4-yl}acetic acid

> <ALOGPS_LOGP>
1.26

> <JCHEM_LOGP>
0.6867838423333332

> <ALOGPS_LOGS>
-2.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.206187704865986

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9286648723273547

> <JCHEM_PKA_STRONGEST_BASIC>
-4.789831476791002

> <JCHEM_POLAR_SURFACE_AREA>
130.36

> <JCHEM_REFRACTIVITY>
65.95460000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.55e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{11,12-dihydroxy-3,8-dioxo-2,7-dioxatricyclo[7.3.1.0⁵,¹³]trideca-1(13),4,9,11-tetraen-4-yl}acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   19                                                  
CONECT    6    5    7   21                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   21                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   21                                                  
CONECT   18   17   19                                                       
CONECT   19   18    5   20                                                  
CONECT   20   19                                                            
CONECT   21   17    6   11                                                  
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Value	Source
2-{11,12-dihydroxy-3,8-dioxo-2,7-dioxatricyclo[7.3.1.0,]trideca-1(13),4,9,11-tetraen-4-yl}acetate	Generator

Chemical Formula

C₁₃H₈O₈

Average Mass

292.1990 Da

Monoisotopic Mass

292.02192 Da

IUPAC Name

2-{11,12-dihydroxy-3,8-dioxo-2,7-dioxatricyclo[7.3.1.0⁵,¹³]trideca-1(13),4,9,11-tetraen-4-yl}acetic acid

Traditional Name

{11,12-dihydroxy-3,8-dioxo-2,7-dioxatricyclo[7.3.1.0⁵,¹³]trideca-1(13),4,9,11-tetraen-4-yl}acetic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CC1=C2COC(=O)C3=CC(O)=C(O)C(OC1=O)=C23

InChI Identifier

InChI=1S/C13H8O8/c14-7-1-5-9-6(3-20-12(5)18)4(2-8(15)16)13(19)21-11(9)10(7)17/h1,14,17H,2-3H2,(H,15,16)

InChI Key

DBBOJUGDRHJPND-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
Geranium thunbergii	LOTUS Database	35616633
Nymphaea alba	Plant	KNApSAcK
Pelargonium reniforme	Plant	KNApSAcK
Phyllanthus flexuosus	LOTUS Database	35616633
Punica granatum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 7,8-dihydroxycoumarins. These are coumarins bearing two hydroxyl groups at the C7- and C8-positions of the coumarin skeleton, respectively.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Hydroxycoumarins

Direct Parent

7,8-dihydroxycoumarins

Alternative Parents

Substituents

7,8-dihydroxycoumarin
Gallic acid or derivatives
Dihydroxybenzoic acid
Benzopyran
2-benzopyran
1-benzopyran
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Dicarboxylic acid or derivatives
Benzenoid
Pyran
Heteroaromatic compound
Carboxylic acid ester
Lactone
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Carbonyl group
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	1.26	ALOGPS
logP	0.69	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	2.93	ChemAxon
pKa (Strongest Basic)	-4.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	130.36 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	65.95 m³·mol⁻¹	ChemAxon
Polarizability	25.45 Å³	ChemAxon
Number of Rings	3	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

15742123

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Phyllanthusiin E (NP0075658)

MOL for NP0075658 (Phyllanthusiin E)

3D MOL for NP0075658 (Phyllanthusiin E)

3D SDF for NP0075658 (Phyllanthusiin E)

3D-SDF for NP0075658 (Phyllanthusiin E)

PDB for NP0075658 (Phyllanthusiin E)

3D PDB for NP0075658 (Phyllanthusiin E)

SMILES for NP0075658 (Phyllanthusiin E)

INCHI for NP0075658 (Phyllanthusiin E)

Structure for NP0075658 (Phyllanthusiin E)

3D Structure for NP0075658 (Phyllanthusiin E)