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Showing NP-Card for 3-Hydroxystachydrine (NP0051131)

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Record Information
Version2.0
Created at2022-04-27 22:33:04 UTC
Updated at2022-04-27 22:33:04 UTC
NP-MRD IDNP0051131
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Hydroxystachydrine
Description(2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 3-Hydroxystachydrine is found in Boscia senegalensis , Capparis biloba, Dolichandra unguis-cati and Steriphoma paradoxum. Based on a literature review very few articles have been published on (2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0051131 (3-Hydroxystachydrine)


  Mrv1652304282200332D          

 11 11  0  0  1  0            999 V2000
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1913    1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6329    0.3323    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.1628    1.8330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9728    1.8330    0.0000 C   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  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  1  0  0  0
  4  7  1  1  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  3 10  1  0  0  0  0
  3 11  1  0  0  0  0
M  CHG  2   3   1   9  -1
M  END
Download

3D MOL for NP0051131 (3-Hydroxystachydrine)

     RDKit          3D

 24 24  0  0  0  0  0  0  0  0999 V2000
    1.7478   -0.0887    1.0023 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6097   -0.1664    0.0786 N   0  0  1  0  0  4  0  0  0  0  0  0
    1.1510   -0.0341   -1.2404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0434   -1.4189    0.3239 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5121   -1.1521    0.4719 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6564    0.2695   -0.0256 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8323    0.3356   -1.3974 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3402    0.8598    0.4223 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0783    2.1610   -0.1565 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8057    2.9070    0.3075 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8123    2.5945   -1.2401 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.4302    0.7332    0.6609 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3077   -1.0330    0.9110 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4117    0.0703    2.0440 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0112   -0.7516   -1.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6055    0.9734   -1.3193 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4714   -0.2806   -2.0534 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1728   -2.1797   -0.4513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2939   -1.8837    1.2963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8332   -1.1441    1.5408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1379   -1.8356   -0.1379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5049    0.7829    0.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8859   -0.6103   -1.7442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3815    0.8915    1.5434 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 11  1  0
  9 10  2  0
  8  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  1
  7 23  1  0
  8 24  1  1
M  CHG  2   2   1  11  -1
M  END
Download

3D SDF for NP0051131 (3-Hydroxystachydrine)


  Mrv1652304282200332D          

 11 11  0  0  1  0            999 V2000
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1913    1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6329    0.3323    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.1628    1.8330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9728    1.8330    0.0000 C   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  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  1  0  0  0
  4  7  1  1  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  3 10  1  0  0  0  0
  3 11  1  0  0  0  0
M  CHG  2   3   1   9  -1
M  END
> <DATABASE_ID>
NP0051131

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[N+]1(C)CC[C@H](O)[C@@H]1C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO3/c1-8(2)4-3-5(9)6(8)7(10)11/h5-6,9H,3-4H2,1-2H3/t5-,6+/m0/s1

> <INCHI_KEY>
DJMIFDZBCUUQJN-NTSWFWBYSA-N

> <FORMULA>
C7H13NO3

> <MOLECULAR_WEIGHT>
159.185

> <EXACT_MASS>
159.089543283

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
15.813182088885853

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S)-3-hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate

> <ALOGPS_LOGP>
-1.43

> <JCHEM_LOGP>
-5.024127701138411

> <ALOGPS_LOGS>
-1.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.130689957672523

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.021729377611736

> <JCHEM_PKA_STRONGEST_BASIC>
-3.744738202784416

> <JCHEM_POLAR_SURFACE_AREA>
60.36

> <JCHEM_REFRACTIVITY>
61.4276

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxystachydrine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0051131 (3-Hydroxystachydrine)

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PDB for NP0051131 (3-Hydroxystachydrine)
HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.060   2.080   0.000  0.00  0.00           N+1
HETATM    4  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.735  -1.536   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.770   1.651   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.091   3.157   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.915   0.620   0.000  0.00  0.00           O-1
HETATM   10  C   UNK     0       0.304   3.422   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.816   3.422   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   10   11                                             
CONECT    4    3    5    7                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5                                                            
CONECT    7    4    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    3                                                            
CONECT   11    3                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0051131 (3-Hydroxystachydrine)
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SMILES for NP0051131 (3-Hydroxystachydrine)
C[N+]1(C)CC[C@H](O)[C@@H]1C([O-])=O
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INCHI for NP0051131 (3-Hydroxystachydrine)
InChI=1S/C7H13NO3/c1-8(2)4-3-5(9)6(8)7(10)11/h5-6,9H,3-4H2,1-2H3/t5-,6+/m0/s1
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View in JSmol
Synonyms
ValueSource
(2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylic acidGenerator
Chemical FormulaC7H13NO3
Average Mass159.1850 Da
Monoisotopic Mass159.08954 Da
IUPAC Name(2R,3S)-3-hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate
Traditional Name3-hydroxystachydrine
CAS Registry NumberNot Available
SMILES
C[N+]1(C)CC[C@H](O)[C@@H]1C([O-])=O
InChI Identifier
InChI=1S/C7H13NO3/c1-8(2)4-3-5(9)6(8)7(10)11/h5-6,9H,3-4H2,1-2H3/t5-,6+/m0/s1
InChI KeyDJMIFDZBCUUQJN-NTSWFWBYSA-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
Boscia senegalensisPlant
Capparis bilobaPlant
Macfadyena unguis-catiLOTUS Database
Steriphoma paradoxumPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentProline and derivatives  
Alternative Parents
Substituents
  • Proline or derivatives
    • 

  • Alpha-amino acid
    • 

  • D-alpha-amino acid
    • 

  • Pyrrolidine carboxylic acid
    • 

  • Pyrrolidine carboxylic acid or derivatives
    • 

  • Beta-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • N-alkylpyrrolidine
    • 

  • Tetraalkylammonium salt
    • 

  • Pyrrolidine
    • 

  • Quaternary ammonium salt
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid salt
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Organic salt
    • 

  • Organic nitrogen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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-1.4ALOGPS
logP-5ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)2.02ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area60.36 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity61.43 m³·mol⁻¹ChemAxon
Polarizability15.81 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0242121  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID391002  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound442640  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References