NP-MRD: Showing NP-Card for 1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone (NP0332570)

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Record Information

Version

2.0

Created at

2024-02-24 08:15:56 UTC

Updated at

2024-09-03 04:19:39 UTC

NP-MRD ID

NP0332570

Natural Product DOI

https://doi.org/10.57994/1829

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone

Description

Parvistone D belongs to the class of organic compounds known as c-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a C-glycosidic bond. 1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone was first documented in 2016 (PMID: 27518479). Based on a literature review very few articles have been published on Parvistone D (PMID: 32045683).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02242408152D          

 25 27  0  0  1  0            999 V2000
   -0.5040    0.9153    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0456    0.2293    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8706    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2831   -0.4851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1081   -0.4851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5206    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1081    0.9438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2831    0.9438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2701   -0.5329    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5391   -0.3719    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3133   -1.1162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323   -0.8486    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0323   -1.6736    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7945   -0.5329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1102    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9352    0.2293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7628    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5086   -0.1235    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5086    0.5822    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323    1.3072    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0323    2.1322    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7945    0.9915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5697    1.2737    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0767    1.7668    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2701    0.9915    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  1  0  0  0
  3  4  2  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  2  0  0  0  0
  3  8  1  0  0  0  0
  9  2  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  1  0  0  0
  9 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 12 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 20 17  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 15 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 20 25  1  0  0  0  0
  2 25  1  0  0  0  0
M  END


  Mrv2104 02242408152D          

 25 27  0  0  1  0            999 V2000
   -0.5040    0.9153    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0456    0.2293    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8706    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2831   -0.4851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1081   -0.4851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5206    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1081    0.9438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2831    0.9438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2701   -0.5329    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5391   -0.3719    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3133   -1.1162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323   -0.8486    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0323   -1.6736    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7945   -0.5329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1102    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9352    0.2293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7628    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5086   -0.1235    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5086    0.5822    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323    1.3072    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0323    2.1322    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7945    0.9915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5697    1.2737    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0767    1.7668    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2701    0.9915    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  1  0  0  0
  3  4  2  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  2  0  0  0  0
  3  8  1  0  0  0  0
  9  2  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  1  0  0  0
  9 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 12 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 20 17  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 15 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 20 25  1  0  0  0  0
  2 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332570

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]C1([H])C(=O)O[C@@]2([H])C([H])([H])[C@]1([H])O[C@]([H])(C1=CC=CC=C1)[C@]2([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C13H14O4/c14-11-7-9-6-10(17-11)12(15)13(16-9)8-4-2-1-3-5-8/h1-5,9-10,12-13,15H,6-7H2/t9-,10-,12+,13+/m0/s1

> <INCHI_KEY>
ZPVLUTBGTWEMGV-YRRQLQLVSA-N

> <FORMULA>
C13H14O4

> <MOLECULAR_WEIGHT>
234.251

> <EXACT_MASS>
234.089208931

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
23.53156279386728

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,5S,7R,8R)-8-hydroxy-7-phenyl-2,6-dioxabicyclo[3.3.1]nonan-3-one

> <JCHEM_LOGP>
0.9757887733333328

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.081005272300999

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6381682938955433

> <JCHEM_POLAR_SURFACE_AREA>
55.760000000000005

> <JCHEM_REFRACTIVITY>
59.078700000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,5S,7R,8R)-8-hydroxy-7-phenyl-2,6-dioxabicyclo[3.3.1]nonan-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-24   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-24         0                                  
HETATM    1  H   UNK     0      -0.941   1.709   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      -0.085   0.428   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.625   0.428   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.395  -0.906   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.935  -0.906   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.705   0.428   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.935   1.762   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.395   1.762   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.504  -0.995   0.000  0.00  0.00           C+0
HETATM   10  H   UNK     0      -1.006  -0.694   0.000  0.00  0.00           H+0
HETATM   11  O   UNK     0      -0.585  -2.084   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.927  -1.584   0.000  0.00  0.00           C+0
HETATM   13  H   UNK     0       1.927  -3.124   0.000  0.00  0.00           H+0
HETATM   14  O   UNK     0       3.350  -0.995   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.939   0.428   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.479   0.428   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.424   0.428   0.000  0.00  0.00           C+0
HETATM   18  H   UNK     0       2.816  -0.231   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       2.816   1.087   0.000  0.00  0.00           H+0
HETATM   20  C   UNK     0       1.927   2.440   0.000  0.00  0.00           C+0
HETATM   21  H   UNK     0       1.927   3.980   0.000  0.00  0.00           H+0
HETATM   22  C   UNK     0       3.350   1.851   0.000  0.00  0.00           C+0
HETATM   23  H   UNK     0       4.797   2.378   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       3.876   3.298   0.000  0.00  0.00           H+0
HETATM   25  O   UNK     0       0.504   1.851   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9   25                                             
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
CONECT    9    2   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9   13   14   17                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15                                                            
CONECT   17   12   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17   21   22   25                                             
CONECT   21   20                                                            
CONECT   22   20   15   23   24                                             
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   20    2                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

View in JSmol

Synonyms

Value	Source
Parvistone e	MeSH

Chemical Formula

C₁₃H₁₄O₄

Average Mass

234.2510 Da

Monoisotopic Mass

234.08921 Da

IUPAC Name

(1S,5S,7R,8R)-8-hydroxy-7-phenyl-2,6-dioxabicyclo[3.3.1]nonan-3-one

Traditional Name

(1S,5S,7R,8R)-8-hydroxy-7-phenyl-2,6-dioxabicyclo[3.3.1]nonan-3-one

CAS Registry Number

Not Available

SMILES

[H]C1([H])C(=O)O[C@@]2([H])C([H])([H])[C@]1([H])O[C@]([H])(C1=CC=CC=C1)[C@]2([H])O

InChI Identifier

InChI=1S/C13H14O4/c14-11-7-9-6-10(17-11)12(15)13(16-9)8-4-2-1-3-5-8/h1-5,9-10,12-13,15H,6-7H2/t9-,10-,12+,13+/m0/s1

InChI Key

ZPVLUTBGTWEMGV-YRRQLQLVSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCl3, experimental)	Not Available	Atta-ur-Rahman Institute for Natural Products Universiti Teknologi Mara (UiTM)	Nor Nadirah Binti Abdullah	2024-02-24	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	Not Available	Atta-ur-Rahman Institute for Natural Products Universiti Teknologi Mara (UiTM)	Nor Nadirah Binti Abdullah	2024-02-24	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	Not Available	Atta-ur-Rahman Institute for Natural Products Universiti Teknologi Mara (UiTM)	Nor Nadirah Binti Abdullah	2024-02-24	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	Not Available	Atta-ur-Rahman Institute for Natural Products Universiti Teknologi Mara (UiTM)	Nor Nadirah Binti Abdullah	2024-02-24	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	Not Available	Atta-ur-Rahman Institute for Natural Products Universiti Teknologi Mara (UiTM)	Nor Nadirah Binti Abdullah	2024-02-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CDCl3, experimental)	Not Available	Atta-ur-Rahman Institute for Natural Products Universiti Teknologi Mara (UiTM)	Nor Nadirah Binti Abdullah	2024-02-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCl3, experimental)	Not Available	Atta-ur-Rahman Institute for Natural Products Universiti Teknologi Mara (UiTM)	Nor Nadirah Binti Abdullah	2024-02-24	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as c-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a C-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

C-glycosyl compounds

Alternative Parents

Substituents

C-glycosyl compound
Delta valerolactone
Delta_valerolactone
Monocyclic benzene moiety
Benzenoid
Monosaccharide
Oxane
Carboxylic acid ester
Lactone
Secondary alcohol
Organoheterocyclic compound
Ether
Dialkyl ether
Oxacycle
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
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	0.98	ChemAxon
pKa (Strongest Acidic)	13.08	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	55.76 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	59.08 m³·mol⁻¹	ChemAxon
Polarizability	23.53 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

28284065

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

51013994

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ramesh P, Rao TP: Biosynthesis-Inspired Total Synthesis of Bioactive Styryllactones (+)-Goniodiol, (6S,7S,8S)-Goniodiol, (-)-Parvistone D, and (+)-Parvistone E. J Nat Prod. 2016 Aug 26;79(8):2060-5. doi: 10.1021/acs.jnatprod.6b00386. Epub 2016 Aug 12. [PubMed:27518479 ]
Kaharudin FA, Zohdi RM, Mukhtar SM, Sidek HM, Bihud NV, Rasol NE, Ahmad FB, Ismail NH: In vitro antiplasmodial and cytotoxicity activities of crude extracts and major compounds from Goniothalamus lanceolatus. J Ethnopharmacol. 2020 May 23;254:112657. doi: 10.1016/j.jep.2020.112657. Epub 2020 Feb 8. [PubMed:32045683 ]

Showing NP-Card for 1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone (NP0332570)

MOL for NP0332570 (1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone)

3D MOL for NP0332570 (1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone)

3D SDF for NP0332570 (1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone)

3D-SDF for NP0332570 (1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone)

PDB for NP0332570 (1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone)

3D PDB for NP0332570 (1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone)

SMILES for NP0332570 (1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone)

INCHI for NP0332570 (1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone)

Structure for NP0332570 (1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone)

3D Structure for NP0332570 (1S,5S,7R,8R,3-exo,7-endo-(+)-9-deoxygoniopypyrone)