NP-MRD: Showing NP-Card for (+)-Dexygoniopypyrone B (NP0332566)

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Record Information

Version

2.0

Created at

2024-02-24 08:04:54 UTC

Updated at

2024-09-03 04:19:38 UTC

NP-MRD ID

NP0332566

Natural Product DOI

https://doi.org/10.57994/1825

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Dexygoniopypyrone B

Description

(+)-Dexygoniopypyrone B 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. Based on a literature review very few articles have been published on (+)-Dexygoniopypyrone B.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02242408042D          

 23 25  0  0  1  0            999 V2000
    2.1339   -0.3825    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3882   -0.0297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6577    1.0482    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8955    0.7325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6577    1.8732    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1339    0.3231    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6577   -1.1076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8955   -0.7919    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5797   -0.0297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2453   -0.0297    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4199   -0.7919    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2589   -1.6010    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0032   -1.3753    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7356   -0.0297    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1939   -0.7157    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5606   -0.0297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9731    0.6848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7981    0.6848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2106   -0.0297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7981   -0.7442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9731   -0.7442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4199    0.7325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6577   -1.9326    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  1  0  0  0
  2  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  2  0  0  0  0
 11  7  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  1  0  0  0
 11 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  6  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 16 21  1  0  0  0  0
 14 22  1  0  0  0  0
  3 22  1  0  0  0  0
  7 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332566

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]C1([H])[C@]2([H])CC(=O)OC1([H])[C@]([H])(O)[C@]([H])(O2)C1=CC=CC=C1

> <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-/m1/s1

> <INCHI_KEY>
ZPVLUTBGTWEMGV-HHPMFDKESA-N

> <FORMULA>
C13H14O4

> <MOLECULAR_WEIGHT>
234.251

> <EXACT_MASS>
234.089208931

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
22.893400268027122

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5R,7R,8S)-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>
-3.638168293895544

> <JCHEM_POLAR_SURFACE_AREA>
55.760000000000005

> <JCHEM_REFRACTIVITY>
59.07870000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(5R,7R,8S)-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       3.983  -0.714   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       2.591  -0.055   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.094   1.957   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.672   1.367   0.000  0.00  0.00           C+0
HETATM    5  H   UNK     0       3.094   3.497   0.000  0.00  0.00           H+0
HETATM    6  H   UNK     0       3.983   0.603   0.000  0.00  0.00           H+0
HETATM    7  C   UNK     0       3.094  -2.068   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.672  -1.478   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.082  -0.055   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.458  -0.055   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.517  -1.478   0.000  0.00  0.00           C+0
HETATM   12  H   UNK     0       4.217  -2.989   0.000  0.00  0.00           H+0
HETATM   13  O   UNK     0       5.606  -2.567   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.106  -0.055   0.000  0.00  0.00           C+0
HETATM   15  H   UNK     0       5.962  -1.336   0.000  0.00  0.00           H+0
HETATM   16  C   UNK     0       6.646  -0.055   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.416   1.278   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.956   1.278   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.726  -0.055   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.956  -1.389   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.416  -1.389   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.517   1.367   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0       3.094  -3.608   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    6    7                                             
CONECT    3    2    4    5   22                                             
CONECT    4    3    9                                                       
CONECT    5    3                                                            
CONECT    6    2                                                            
CONECT    7    2    8   11   23                                             
CONECT    8    7    9                                                       
CONECT    9    8    4   10                                                  
CONECT   10    9                                                            
CONECT   11    7   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11   15   16   22                                             
CONECT   15   14                                                            
CONECT   16   14   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   16                                                       
CONECT   22   14    3                                                       
CONECT   23    7                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₄O₄

Average Mass

234.2510 Da

Monoisotopic Mass

234.08921 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

[H]C1([H])[C@]2([H])CC(=O)OC1([H])[C@]([H])(O)[C@]([H])(O2)C1=CC=CC=C1

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-/m1/s1

InChI Key

ZPVLUTBGTWEMGV-HHPMFDKESA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D_DEPT NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCl3, experimental)	Not Available	Atta-ur-Rahman Institute for Natural Products Universiti Teknologi Mara (UiTM)	Nor Nadirah Binti Abdullah	2024-05-02	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 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, 600 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
HMQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 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, 600 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, 151 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, 600 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, 600 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

Species Name	Source	Reference
lanceolatus		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
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Carbonyl group
Alcohol
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	22.89 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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for (+)-Dexygoniopypyrone B (NP0332566)

MOL for NP0332566 ((+)-Dexygoniopypyrone B)

3D MOL for NP0332566 ((+)-Dexygoniopypyrone B)

3D SDF for NP0332566 ((+)-Dexygoniopypyrone B)

3D-SDF for NP0332566 ((+)-Dexygoniopypyrone B)

PDB for NP0332566 ((+)-Dexygoniopypyrone B)

3D PDB for NP0332566 ((+)-Dexygoniopypyrone B)

SMILES for NP0332566 ((+)-Dexygoniopypyrone B)

INCHI for NP0332566 ((+)-Dexygoniopypyrone B)

Structure for NP0332566 ((+)-Dexygoniopypyrone B)

3D Structure for NP0332566 ((+)-Dexygoniopypyrone B)