NP-MRD: Showing NP-Card for (3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid (NP0312479)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-11 09:17:47 UTC

Updated at

2022-09-11 09:17:47 UTC

NP-MRD ID

NP0312479

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid

Description

Dioscoretine belongs to the class of organic compounds known as heterocyclic fatty acids. These are fatty acids containing a heterocyclic attached to the acyl chain. (3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid is found in Dioscorea dumetorum. (3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid was first documented in 1990 (PMID: 2392490). Based on a literature review very few articles have been published on Dioscoretine (PMID: 2356236).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 41  0  0  0  0  0  0  0  0999 V2000
    2.8987   -2.1323    0.0659 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0515   -0.8888   -0.2669 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9962    0.2659   -0.2548 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0700    0.0247   -1.2806 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0311   -1.0082   -1.9541 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0907    0.9457   -1.4708 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9246   -0.8187    0.7218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0158    0.3108    0.5704 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6491    1.5177    0.7131 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1345    0.3000    1.5891 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4856    0.4954    0.9230 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5193    1.7529    0.0904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3659    1.7038   -0.8942 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6868    0.3548   -0.7896 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6987   -0.7623   -0.8994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7258   -0.6368    0.0861 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0561   -0.7735   -0.3941 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0443   -2.7719   -0.8123 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3328   -2.7479    0.8107 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8075   -1.8089    0.5695 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6763   -1.0580   -1.3151 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5044    0.3918    0.7193 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4685    1.2190   -0.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1866    1.7403   -0.8503 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4372   -1.8198    0.7088 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4133   -0.7454    1.7409 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2130    2.1379    1.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0161    1.0986    2.3509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2047   -0.6945    2.1146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2314    0.5944    1.7348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4474    1.7224   -0.5149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5082    2.6778    0.7027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6179    2.4539   -0.5243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6733    1.9426   -1.9203 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0682    0.2511   -1.5915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1350   -1.7103   -0.6636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0680   -0.8783   -1.9194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5398   -1.6113    0.1836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6886    0.1154   -0.3182 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0449   -1.1500   -1.4544 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  6  1  0
  4  5  2  0
  2  7  1  0
  7  8  1  0
  8  9  1  1
  8 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
 16 17  1  0
 14  8  1  0
 16 11  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  6
  3 22  1  0
  3 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  1
 12 31  1  0
 12 32  1  0
 13 33  1  0
 13 34  1  0
 14 35  1  6
 15 36  1  0
 15 37  1  0
 17 38  1  0
 17 39  1  0
 17 40  1  0
M  END


  Mrv1652309112211172D          

 17 18  0  0  1  0            999 V2000
   -1.1926    2.2993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1926    1.4743    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9071    1.0618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6216    1.4743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3360    1.0618    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6216    2.2993    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4782    1.0618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2363    1.4743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5185    0.6990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2940    2.1063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0118    2.8815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4470    2.5486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8006    2.1272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0488    1.6175    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3309    2.3928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8006    3.0248    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0828    3.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  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
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  1  0  0  0
  8 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 11 16  1  6  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0312479

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CC(O)=O)CC1(O)C[C@H]2CC[C@@H]1CN2C

> <INCHI_IDENTIFIER>
InChI=1S/C13H23NO3/c1-9(5-12(15)16)6-13(17)7-11-4-3-10(13)8-14(11)2/h9-11,17H,3-8H2,1-2H3,(H,15,16)/t9-,10-,11-,13?/m1/s1

> <INCHI_KEY>
YWVYEZNFPRWGMM-RUPPFBPSSA-N

> <FORMULA>
C13H23NO3

> <MOLECULAR_WEIGHT>
241.331

> <EXACT_MASS>
241.167793605

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
26.4941040759793

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-4-[(1R,4R)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid

> <JCHEM_LOGP>
-2.050772308074806

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.454748913652402

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.482864001764739

> <JCHEM_PKA_STRONGEST_BASIC>
8.949438803015438

> <JCHEM_POLAR_SURFACE_AREA>
60.77

> <JCHEM_REFRACTIVITY>
65.2466

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-4-[(1R,4R)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.226   4.292   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.226   2.752   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.560   1.982   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.894   2.752   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -6.227   1.982   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -4.894   4.292   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -0.893   1.982   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.441   2.752   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.968   1.305   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -0.549   3.932   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.022   5.379   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.834   4.757   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.494   3.971   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.958   3.019   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.484   4.467   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       1.495   5.646   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       2.021   7.093   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2    8                                                       
CONECT    8    7    9   10   14                                             
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    8   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   11   17                                                  
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₂₃NO₃

Average Mass

241.3310 Da

Monoisotopic Mass

241.16779 Da

IUPAC Name

(3S)-4-[(1R,4R)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid

Traditional Name

(3S)-4-[(1R,4R)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid

CAS Registry Number

Not Available

SMILES

C[C@H](CC(O)=O)CC1(O)C[C@H]2CC[C@@H]1CN2C

InChI Identifier

InChI=1S/C13H23NO3/c1-9(5-12(15)16)6-13(17)7-11-4-3-10(13)8-14(11)2/h9-11,17H,3-8H2,1-2H3,(H,15,16)/t9-,10-,11-,13?/m1/s1

InChI Key

YWVYEZNFPRWGMM-RUPPFBPSSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as heterocyclic fatty acids. These are fatty acids containing a heterocyclic attached to the acyl chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Heterocyclic fatty acids

Alternative Parents

Substituents

Methyl-branched fatty acid
Hydroxy fatty acid
Heterocyclic fatty acid
Branched fatty acid
Piperidine
Tertiary alcohol
Cyclic alcohol
Amino acid
Tertiary aliphatic amine
Tertiary amine
Amino acid or derivatives
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Alcohol
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	-2.1	ChemAxon
pKa (Strongest Acidic)	4.48	ChemAxon
pKa (Strongest Basic)	8.95	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	60.77 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	65.25 m³·mol⁻¹	ChemAxon
Polarizability	26.49 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

21244479

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

124966

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Iwu MM, Okunji CO, Ohiaeri GO, Akah P, Corley D, Tempesta MS: Hypoglycaemic activity of dioscoretine from tubers of Dioscorea dumetorum in normal and alloxan diabetic rabbits. Planta Med. 1990 Jun;56(3):264-7. doi: 10.1055/s-2006-960952. [PubMed:2392490 ]
Iwu MM, Okunji CO, Akah P, Tempesta MS, Corley D: Dioscoretine: the hypoglycemic principle of Dioscorea dumetorum. Planta Med. 1990 Feb;56(1):119-20. doi: 10.1055/s-2006-960901. [PubMed:2356236 ]
LOTUS database [Link]

Showing NP-Card for (3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid (NP0312479)

MOL for NP0312479 ((3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid)

3D MOL for NP0312479 ((3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid)

3D SDF for NP0312479 ((3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid)

3D-SDF for NP0312479 ((3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid)

PDB for NP0312479 ((3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid)

3D PDB for NP0312479 ((3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid)

SMILES for NP0312479 ((3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid)

INCHI for NP0312479 ((3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid)

Structure for NP0312479 ((3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid)

3D Structure for NP0312479 ((3s)-4-[(1r,4r)-5-hydroxy-2-methyl-2-azabicyclo[2.2.2]octan-5-yl]-3-methylbutanoic acid)