NP-MRD: Showing NP-Card for Phrymarolin I (NP0051515)

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Record Information

Version

2.0

Created at

2022-04-27 22:51:12 UTC

Updated at

2022-04-27 22:51:12 UTC

NP-MRD ID

NP0051515

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Phrymarolin I

Description

Phrymarolin I belongs to the class of organic compounds known as benzodioxoles. These are organic compounds containing a benzene ring fused to either isomers of dioxole. Dioxole is a five-membered unsaturated ring of two oxygen atoms and three carbon atoms. Phrymarolin I is an extremely weak basic (essentially neutral) compound (based on its pKa). Phrymarolin I is found in Phryma leptostachya and Sparanskia tuberculata. Phrymarolin I is a potentially toxic compound.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 08291401202D          

 38 43  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv0541 08291401202D          

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M  END
> <DATABASE_ID>
NP0051515

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(OC2=C(OC)C=C3OCOC3=C2)OC[C@]2([H])[C@]([H])(OC[C@]12OC(C)=O)C1=CC2=C(OCO2)C=C1OC

> <INCHI_IDENTIFIER>
InChI=1S/C24H24O11/c1-12(25)35-24-9-29-22(13-4-17-18(31-10-30-17)5-15(13)26-2)14(24)8-28-23(24)34-21-7-20-19(32-11-33-20)6-16(21)27-3/h4-7,14,22-23H,8-11H2,1-3H3/t14-,22-,23+,24-/m1/s1

> <INCHI_KEY>
ZGBQEJGNORPNKC-PDLWQGAHSA-N

> <FORMULA>
C24H24O11

> <MOLECULAR_WEIGHT>
488.4408

> <EXACT_MASS>
488.13186161

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
48.44350518225935

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,3aS,4S,6aR)-1-(6-methoxy-2H-1,3-benzodioxol-5-yl)-4-[(6-methoxy-2H-1,3-benzodioxol-5-yl)oxy]-hexahydrofuro[3,4-c]furan-3a-yl acetate

> <ALOGPS_LOGP>
2.26

> <JCHEM_LOGP>
2.2081613353333323

> <ALOGPS_LOGS>
-3.38

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.765849496644876

> <JCHEM_POLAR_SURFACE_AREA>
109.37000000000003

> <JCHEM_REFRACTIVITY>
113.71179999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.04e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
phrymarolin I

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-AUG-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-AUG-14         0                                  
HETATM    1  C   UNK     0       7.728  -1.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.434  -8.299   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.029  -4.343   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.508  -6.651   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.447  -8.940   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.923  -1.414   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.138   0.875   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.596  -4.866   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.525  -2.374   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.229 -10.273   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.645   2.209   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.395  -0.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.001  -6.331   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.061  -4.390   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.971  -7.475   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.584  -1.734   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.984  -8.115   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.953  -9.260   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.399   0.051   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.368   1.196   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.614  -0.589   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.525  -4.866   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.596  -2.374   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.061  -2.850   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       6.395   1.000   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       4.465  -7.155   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       1.059  -3.198   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       2.691  -3.620   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       7.431  -3.620   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      10.390  -8.742   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       8.723 -10.593   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -2.806   0.677   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -1.138   2.529   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       3.120  -0.909   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       5.061  -1.310   0.000  0.00  0.00           O+0
HETATM   36  H   UNK     0       5.061  -5.930   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       8.047  -5.107   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0       2.075  -2.133   0.000  0.00  0.00           H+0
CONECT    1   12                                                            
CONECT    2   26                                                            
CONECT    3   27                                                            
CONECT    4   13   17                                                       
CONECT    5   15   18                                                       
CONECT    6   16   19                                                       
CONECT    7   20   21                                                       
CONECT    8   14   28                                                       
CONECT    9   24   29                                                       
CONECT   10   30   31                                                       
CONECT   11   32   33                                                       
CONECT   12    1   25   35                                                  
CONECT   13    4   15   22                                                  
CONECT   14    8   22   24   36                                             
CONECT   15    5   13   26                                                  
CONECT   16    6   21   27                                                  
CONECT   17    4   18   30                                                  
CONECT   18    5   17   31                                                  
CONECT   19    6   20   32                                                  
CONECT   20    7   19   33                                                  
CONECT   21    7   16   34                                                  
CONECT   22   13   14   29   37                                             
CONECT   23   24   28   34   38                                             
CONECT   24    9   14   23   35                                             
CONECT   25   12                                                            
CONECT   26    2   15                                                       
CONECT   27    3   16                                                       
CONECT   28    8   23                                                       
CONECT   29    9   22                                                       
CONECT   30   10   17                                                       
CONECT   31   10   18                                                       
CONECT   32   11   19                                                       
CONECT   33   11   20                                                       
CONECT   34   21   23                                                       
CONECT   35   12   24                                                       
CONECT   36   14                                                            
CONECT   37   22                                                            
CONECT   38   23                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   86    0
END

View in JSmol

Synonyms

Value	Source
(1S,3AS,4S,6ar)-1-(6-methoxy-2H-1,3-benzodioxol-5-yl)-4-[(6-methoxy-2H-1,3-benzodioxol-5-yl)oxy]-hexahydrofuro[3,4-c]furan-3a-yl acetic acid	Generator

Chemical Formula

C₂₄H₂₄O₁₁

Average Mass

488.4408 Da

Monoisotopic Mass

488.13186 Da

IUPAC Name

(1S,3aS,4S,6aR)-1-(6-methoxy-2H-1,3-benzodioxol-5-yl)-4-[(6-methoxy-2H-1,3-benzodioxol-5-yl)oxy]-hexahydrofuro[3,4-c]furan-3a-yl acetate

Traditional Name

phrymarolin I

CAS Registry Number

Not Available

SMILES

[H][C@@]1(OC2=C(OC)C=C3OCOC3=C2)OC[C@]2([H])[C@]([H])(OC[C@]12OC(C)=O)C1=CC2=C(OCO2)C=C1OC

InChI Identifier

InChI=1S/C24H24O11/c1-12(25)35-24-9-29-22(13-4-17-18(31-10-30-17)5-15(13)26-2)14(24)8-28-23(24)34-21-7-20-19(32-11-33-20)6-16(21)27-3/h4-7,14,22-23H,8-11H2,1-3H3/t14-,22-,23+,24-/m1/s1

InChI Key

ZGBQEJGNORPNKC-PDLWQGAHSA-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
Phryma leptostachya	Plant	KNApSAcK
Sparanskia tuberculata	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzodioxoles. These are organic compounds containing a benzene ring fused to either isomers of dioxole. Dioxole is a five-membered unsaturated ring of two oxygen atoms and three carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzodioxoles

Sub Class

Not Available

Direct Parent

Benzodioxoles

Alternative Parents

Substituents

Benzodioxole
Anisole
Furofuran
Alkyl aryl ether
Benzenoid
Tetrahydrofuran
Carboxylic acid ester
Monocarboxylic acid or derivatives
Oxacycle
Ether
Dialkyl ether
Carboxylic acid derivative
Acetal
Organooxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

benzodioxoles (CHEBI:8173 )
Lignans (C10737 )
Phytotoxins (C10737 )

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	2.26	ALOGPS
logP	2.21	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	109.37 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	113.71 m³·mol⁻¹	ChemAxon
Polarizability	48.44 Å³	ChemAxon
Number of Rings	6	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

C00002617

Chemspider ID

Not Available

KEGG Compound ID

C10737

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442932

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Phrymarolin I (NP0051515)

MOL for NP0051515 (Phrymarolin I)

3D MOL for NP0051515 (Phrymarolin I)

3D SDF for NP0051515 (Phrymarolin I)

3D-SDF for NP0051515 (Phrymarolin I)

PDB for NP0051515 (Phrymarolin I)

3D PDB for NP0051515 (Phrymarolin I)

SMILES for NP0051515 (Phrymarolin I)

INCHI for NP0051515 (Phrymarolin I)

Structure for NP0051515 (Phrymarolin I)

3D Structure for NP0051515 (Phrymarolin I)