NP-MRD: Showing NP-Card for Dihydrodioscorine (NP0085311)

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Record Information

Version

2.0

Created at

2022-04-29 05:52:52 UTC

Updated at

2022-04-29 05:52:52 UTC

NP-MRD ID

NP0085311

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dihydrodioscorine

Description

Dihydrodioscorine belongs to the class of organic compounds known as azaspirodecane derivatives. These are organic compounds containing a spirodecane moiety with at least one nitrogen atom. Dihydrodioscorine is a very strong basic compound (based on its pKa). Outside of the human body, Dihydrodioscorine has been detected, but not quantified in, root vegetables. Dihydrodioscorine is found in Dioscorea dumetorum . This could make dihydrodioscorine a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 39  0  0  0  0  0  0  0  0999 V2000
    3.4720    1.4418    0.5746 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4404    0.3857    0.9390 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0160   -0.9270    0.4934 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9859   -1.9822    0.3523 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1296   -3.1325    0.8639 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8799   -1.5843   -0.3798 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2604   -0.3670   -0.1125 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1091    0.7255    0.3882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8862   -0.6674    0.8667 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2079   -0.7232    0.1513 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1421   -1.5947   -1.0687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1957   -0.9844   -2.0565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4537    0.1437   -1.3754 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4382    1.1963   -0.9292 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6070    0.6145   -0.2998 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0342    1.3975    0.8567 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2848    2.3159    1.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4956    1.0472    0.6232 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2113    1.7567   -0.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4430    0.3576    2.0680 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7708   -1.2996    1.2097 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5348   -0.8432   -0.4982 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2507    1.5442   -0.3798 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5379    1.2591    1.2072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9390    0.1107    1.6477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7399   -1.6373    1.3718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9548   -1.1006    0.8688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8939   -2.6448   -0.8421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1900   -1.6246   -1.4901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4966   -1.7102   -2.5080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7737   -0.5315   -2.8823 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3021    0.6128   -2.0173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9806    1.8735   -0.1556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7494    1.8635   -1.7779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0973    1.6984    0.7533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3607    2.2496    1.0362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9832    0.7605    1.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  7  6  1  6
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
  8  2  1  0
 15 10  1  0
 13  7  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  1
  3 21  1  0
  3 22  1  0
  8 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  1
 11 28  1  0
 11 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  6
 14 33  1  0
 14 34  1  0
 16 35  1  0
 16 36  1  0
 16 37  1  0
M  END


  Mrv0541 05061304522D          

 16 18  0  0  0  0            999 V2000
   -1.9683   -2.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3244   -2.7536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9605   -0.1141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2052   -0.7200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3896   -0.6939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5475   -1.8483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2262   -2.1175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6614   -1.3425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3018   -1.5142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9228   -1.0102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0655   -1.7586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7231   -0.2077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1190   -1.3621    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8140   -2.1055    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8110    0.6126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0312   -0.5418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  9  1  1  0  0  0  0
  9  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  3  1  0  0  0  0
 10  8  1  0  0  0  0
 11  4  1  0  0  0  0
 11  7  1  0  0  0  0
 12  5  1  0  0  0  0
 13  6  1  0  0  0  0
 13  7  1  0  0  0  0
 13 10  1  0  0  0  0
 14  2  1  0  0  0  0
 14  8  1  0  0  0  0
 14 11  1  0  0  0  0
 15 12  2  0  0  0  0
 16 12  1  0  0  0  0
 16 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0085311

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1CC(=O)OC2(C1)CC1CCC2CN1C

> <INCHI_IDENTIFIER>
InChI=1S/C13H21NO2/c1-9-5-12(15)16-13(6-9)7-11-4-3-10(13)8-14(11)2/h9-11H,3-8H2,1-2H3

> <INCHI_KEY>
KUBGFNFNLFGTGA-UHFFFAOYSA-N

> <FORMULA>
C13H21NO2

> <MOLECULAR_WEIGHT>
223.3113

> <EXACT_MASS>
223.157228921

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
25.22877206945055

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4',5-dimethyl-5-azaspiro[bicyclo[2.2.2]octane-2,2'-oxane]-6'-one

> <ALOGPS_LOGP>
1.85

> <JCHEM_LOGP>
1.3418403189999992

> <ALOGPS_LOGS>
-1.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.296924103150458

> <JCHEM_POLAR_SURFACE_AREA>
29.540000000000003

> <JCHEM_REFRACTIVITY>
61.754400000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.16e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4',5-dimethyl-5-azaspiro[bicyclo[2.2.2]octane-2,2'-oxane]-6'-one

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -3.674  -3.734   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.339  -5.140   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.793  -0.213   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.250  -1.344   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.594  -1.295   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.022  -3.450   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.422  -3.953   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.101  -2.506   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.430  -2.827   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.723  -1.886   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.989  -3.283   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.350  -0.388   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.222  -2.543   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       3.386  -3.930   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0      -1.514   1.144   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.058  -1.011   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2   14                                                            
CONECT    3    4   10                                                       
CONECT    4    3   11                                                       
CONECT    5    9   12                                                       
CONECT    6    9   13                                                       
CONECT    7   11   13                                                       
CONECT    8   10   14                                                       
CONECT    9    1    5    6                                                  
CONECT   10    3    8   13                                                  
CONECT   11    4    7   14                                                  
CONECT   12    5   15   16                                                  
CONECT   13    6    7   10   16                                             
CONECT   14    2    8   11                                                  
CONECT   15   12                                                            
CONECT   16   12   13                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₂₁NO₂

Average Mass

223.3113 Da

Monoisotopic Mass

223.15723 Da

IUPAC Name

4',5-dimethyl-5-azaspiro[bicyclo[2.2.2]octane-2,2'-oxane]-6'-one

Traditional Name

4',5-dimethyl-5-azaspiro[bicyclo[2.2.2]octane-2,2'-oxane]-6'-one

CAS Registry Number

Not Available

SMILES

CC1CC(=O)OC2(C1)CC1CCC2CN1C

InChI Identifier

InChI=1S/C13H21NO2/c1-9-5-12(15)16-13(6-9)7-11-4-3-10(13)8-14(11)2/h9-11H,3-8H2,1-2H3

InChI Key

KUBGFNFNLFGTGA-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
Dioscorea dumetorum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as azaspirodecane derivatives. These are organic compounds containing a spirodecane moiety with at least one nitrogen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azaspirodecane derivatives

Sub Class

Not Available

Direct Parent

Azaspirodecane derivatives

Alternative Parents

Substituents

Azaspirodecane
Delta valerolactone
Delta_valerolactone
Oxane
Piperidine
Amino acid or derivatives
Carboxylic acid ester
Lactone
Tertiary aliphatic amine
Tertiary amine
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Azacycle
Amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	1.85	ALOGPS
logP	1.34	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Basic)	9.3	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	29.54 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	61.75 m³·mol⁻¹	ChemAxon
Polarizability	25.23 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0029828

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB001040

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

15931602

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Dihydrodioscorine (NP0085311)

MOL for NP0085311 (Dihydrodioscorine)

3D MOL for NP0085311 (Dihydrodioscorine)

3D SDF for NP0085311 (Dihydrodioscorine)

3D-SDF for NP0085311 (Dihydrodioscorine)

PDB for NP0085311 (Dihydrodioscorine)

3D PDB for NP0085311 (Dihydrodioscorine)

SMILES for NP0085311 (Dihydrodioscorine)

INCHI for NP0085311 (Dihydrodioscorine)

Structure for NP0085311 (Dihydrodioscorine)

3D Structure for NP0085311 (Dihydrodioscorine)