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Showing NP-Card for (+)-Amphorogynine D (NP0082988)

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Record Information
Version2.0
Created at2022-04-29 04:03:00 UTC
Updated at2022-04-29 04:03:01 UTC
NP-MRD IDNP0082988
Secondary Accession NumbersNone
Natural Product Identification
Common Name(+)-Amphorogynine D
DescriptionAmphorogynine D belongs to the class of organic compounds known as pyrrolizidines. Pyrrolizidines are compounds containing a pyrrolizidine, which is a bicyclic ring system made up of two fused pyrrolidine ring sharing a nitrogen atom. (+)-Amphorogynine D is found in Amphorogyne spicata. (+)-Amphorogynine D was first documented in 2005 (PMID: 16209578). Based on a literature review very few articles have been published on Amphorogynine D.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0082988 ((+)-Amphorogynine D)


  Mrv1652304292206032D          

 12 13  0  0  1  0            999 V2000
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.3349    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7846   -1.0799    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5692   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8792   -0.6674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549   -2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2971   -2.7326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0619   -2.2910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  6  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  7  9  1  6  0  0  0
  3 10  1  6  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
Download

3D MOL for NP0082988 ((+)-Amphorogynine D)

     RDKit          3D

 25 26  0  0  0  0  0  0  0  0999 V2000
   -2.2091    0.2298    2.1603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9035    0.6901    1.0227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9141    2.0717    0.9022 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5547   -0.1522   -0.1198 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4770   -1.6008    0.4068 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0150   -1.9198    0.4278 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5838   -0.6196    0.4345 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9117   -0.4853   -0.0311 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9264    0.8672   -0.7279 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7185    1.7873   -0.0834 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4492    1.3142   -0.7430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1954   -0.0027   -0.6579 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5053    2.5643    0.2462 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3454   -0.1170   -0.9027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0166   -2.2629   -0.2975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8499   -1.6807    1.4291 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2467   -2.3850   -0.5731 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2946   -2.5721    1.2599 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2646   -1.2945   -0.6904 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5897   -0.3931    0.8540 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2787    0.6882   -1.7663 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2444    2.0910    0.7286 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2408    1.9999    0.0694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2936    1.7649   -1.7579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0869   -0.5829   -1.5903 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9 11  1  0
 11 12  1  0
 12  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  8  9  1  0
  7 12  1  0
 10 22  1  0
  9 21  1  6
 11 23  1  0
 11 24  1  0
 12 25  1  6
  4 14  1  6
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  8 19  1  0
  8 20  1  0
  3 13  1  0
M  END
Download

3D SDF for NP0082988 ((+)-Amphorogynine D)


  Mrv1652304292206032D          

 12 13  0  0  1  0            999 V2000
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.3349    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7846   -1.0799    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5692   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8792   -0.6674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549   -2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2971   -2.7326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0619   -2.2910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  6  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  7  9  1  6  0  0  0
  3 10  1  6  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0082988

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1C[C@@H]2[C@@H](CCN2C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H13NO3/c10-5-3-7-6(8(11)12)1-2-9(7)4-5/h5-7,10H,1-4H2,(H,11,12)/t5-,6-,7-/m1/s1

> <INCHI_KEY>
TUHKEMPPAFZCIP-FSDSQADBSA-N

> <FORMULA>
C8H13NO3

> <MOLECULAR_WEIGHT>
171.196

> <EXACT_MASS>
171.089543283

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.818678914750556

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,6R,7aR)-6-hydroxy-hexahydro-1H-pyrrolizine-1-carboxylic acid

> <ALOGPS_LOGP>
-1.54

> <JCHEM_LOGP>
-3.438523791772348

> <ALOGPS_LOGS>
0.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.838057625957017

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3855108659166384

> <JCHEM_PKA_STRONGEST_BASIC>
10.157387852510775

> <JCHEM_POLAR_SURFACE_AREA>
60.769999999999996

> <JCHEM_REFRACTIVITY>
42.1441

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.60e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,6R,7aR)-6-hydroxy-hexahydro-1H-pyrrolizine-1-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0082988 ((+)-Amphorogynine D)

Download
PDB for NP0082988 ((+)-Amphorogynine D)
HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0      -0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.905  -1.246   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000  -2.492   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.465  -2.016   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.465  -0.476   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       2.929   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.929  -2.492   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.374  -1.246   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -0.476  -3.956   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.555  -5.101   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -1.982  -4.277   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7    4                                                       
CONECT    9    7                                                            
CONECT   10    3   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END

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3D PDB for NP0082988 ((+)-Amphorogynine D)
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SMILES for NP0082988 ((+)-Amphorogynine D)
O[C@@H]1C[C@@H]2[C@@H](CCN2C1)C(O)=O
Download
INCHI for NP0082988 ((+)-Amphorogynine D)
InChI=1S/C8H13NO3/c10-5-3-7-6(8(11)12)1-2-9(7)4-5/h5-7,10H,1-4H2,(H,11,12)/t5-,6-,7-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC8H13NO3
Average Mass171.1960 Da
Monoisotopic Mass171.08954 Da
IUPAC Name(1R,6R,7aR)-6-hydroxy-hexahydro-1H-pyrrolizine-1-carboxylic acid
Traditional Name(1R,6R,7aR)-6-hydroxy-hexahydro-1H-pyrrolizine-1-carboxylic acid
CAS Registry NumberNot Available
SMILES
O[C@@H]1C[C@@H]2[C@@H](CCN2C1)C(O)=O
InChI Identifier
InChI=1S/C8H13NO3/c10-5-3-7-6(8(11)12)1-2-9(7)4-5/h5-7,10H,1-4H2,(H,11,12)/t5-,6-,7-/m1/s1
InChI KeyTUHKEMPPAFZCIP-FSDSQADBSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Amphorogyne spicata-
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolizidines. Pyrrolizidines are compounds containing a pyrrolizidine, which is a bicyclic ring system made up of two fused pyrrolidine ring sharing a nitrogen atom.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyrrolizidines  
Sub ClassNot Available
Direct ParentPyrrolizidines  
Alternative Parents
Substituents
  • Pyrrolidine carboxylic acid
    • 

  • Pyrrolidine carboxylic acid or derivatives
    • 

  • Pyrrolizidine
    • 

  • N-alkylpyrrolidine
    • 

  • Pyrrolidine
    • 

  • Amino acid
    • 

  • 1,2-aminoalcohol
    • 

  • Tertiary aliphatic amine
    • 

  • Tertiary amine
    • 

  • Secondary alcohol
    • 

  • Amino acid or derivatives
    • 

  • Azacycle
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Hydrocarbon derivative
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Amine
    • 

  • Alcohol
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.5ALOGPS
logP-3.4ChemAxon
logS0.75ALOGPS
pKa (Strongest Acidic)3.39ChemAxon
pKa (Strongest Basic)10.16ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area60.77 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity42.14 m³·mol⁻¹ChemAxon
Polarizability16.82 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00049982  
Chemspider ID4482015  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5324491  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Roche C, Kadlecikova K, Veyron A, Delair P, Philouze C, Greene AE, Flot D, Burghammer M: New asymmetric approach to natural pyrrolizidines: synthesis of (+)-amphorogynine A, (+)-amphorogynine D, and (+)-retronecine. J Org Chem. 2005 Oct 14;70(21):8352-63. doi: 10.1021/jo050983o. [PubMed:16209578  ]