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Showing NP-Card for Ginkgotoxin hydrochloride (NP0139152)

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Record Information
Version2.0
Created at2022-06-29 19:41:32 UTC
Updated at2022-06-29 19:41:32 UTC
NP-MRD IDNP0139152
Secondary Accession NumbersNone
Natural Product Identification
Common NameGinkgotoxin hydrochloride
Description3131-27-9 Belongs to the class of organic compounds known as pyridoxines. These are pyridoxal derivatives in which the carbaldehyde group at position 2 of the pyridoxal moiety is replaced by a hydroxymethyl group. Based on a literature review very few articles have been published on 3131-27-9.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0139152 (Ginkgotoxin hydrochloride)


  Mrv1652306292221412D          

 14 13  0  0  0  0            999 V2000
    0.6595    1.9038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6595    1.0788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3740    0.6663    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3740   -0.1587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6595   -0.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0550   -0.1587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0550    0.6663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7694    1.0788    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7694   -0.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4839   -0.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1984   -0.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6595   -1.3962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0550   -1.8087    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3776    0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
Download

3D MOL for NP0139152 (Ginkgotoxin hydrochloride)

     RDKit          3D

 28 27  0  0  0  0  0  0  0  0999 V2000
    3.1557   -1.7002   -0.1768 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8210   -1.3189   -0.5017 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4196   -0.3770    0.4571 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0171    0.0754    0.2717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3037    1.3872    0.1348 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7338    2.4353    0.0891 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1356    3.7174    0.0154 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6296    1.7667    0.0423 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6103    0.8253    0.0862 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3392   -0.4546    0.2199 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4313   -1.4728    0.2583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9889   -0.8578    0.3155 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7688   -2.2057    0.4410 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6863    0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.1993   -2.0754    0.8690 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9112   -0.9317   -0.3709 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3249   -2.6249   -0.8281 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6111   -0.6037    1.4983 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0484    0.5524    0.0910 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3969    2.2814   -0.7995 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3379    2.4043    1.0106 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8231    4.3626    0.3856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8934    2.7930   -0.0626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3135   -1.1418   -0.2957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0868   -2.4472   -0.2054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6754   -1.7321    1.3026 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1053   -2.6573    0.5455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6863    0.0000    0.0000 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 12  2  0
 12 13  1  0
 12 10  1  0
 10 11  1  0
 10  9  2  0
  9  8  1  0
  8  5  2  0
  5  6  1  0
  6  7  1  0
  5  4  1  0
 14 28  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  3 19  1  0
 13 27  1  0
 11 24  1  0
 11 25  1  0
 11 26  1  0
  8 23  1  0
  6 20  1  0
  6 21  1  0
  7 22  1  0
M  END
Download

3D SDF for NP0139152 (Ginkgotoxin hydrochloride)


  Mrv1652306292221412D          

 14 13  0  0  0  0            999 V2000
    0.6595    1.9038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6595    1.0788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3740    0.6663    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3740   -0.1587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6595   -0.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0550   -0.1587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0550    0.6663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7694    1.0788    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7694   -0.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4839   -0.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1984   -0.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6595   -1.3962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0550   -1.8087    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3776    0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0139152

> <DATABASE_NAME>
NP-MRD

> <SMILES>
Cl.COCC1=C(O)C(C)=NC=C1CO

> <INCHI_IDENTIFIER>
InChI=1S/C9H13NO3.ClH/c1-6-9(12)8(5-13-2)7(4-11)3-10-6;/h3,11-12H,4-5H2,1-2H3;1H

> <INCHI_KEY>
WIQVPGFUYBUXNC-UHFFFAOYSA-N

> <FORMULA>
C9H14ClNO3

> <MOLECULAR_WEIGHT>
219.67

> <EXACT_MASS>
219.066221

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
19.19360382661684

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol hydrochloride

> <ALOGPS_LOGP>
-0.08

> <JCHEM_LOGP>
-0.3081947946666664

> <ALOGPS_LOGS>
-1.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.82780786123508

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.594956692546308

> <JCHEM_PKA_STRONGEST_BASIC>
5.584579744880171

> <JCHEM_POLAR_SURFACE_AREA>
62.58000000000001

> <JCHEM_REFRACTIVITY>
48.856500000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.35e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ginkgotoxin hydrochloride

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0139152 (Ginkgotoxin hydrochloride)

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PDB for NP0139152 (Ginkgotoxin hydrochloride)
HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0       1.231   3.554   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.231   2.014   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.565   1.244   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       2.565  -0.296   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.231  -1.066   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.103  -0.296   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.103   1.244   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.436   2.014   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.436  -1.066   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.770  -0.296   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -4.104  -1.066   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.231  -2.606   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.103  -3.376   0.000  0.00  0.00           O+0
HETATM   14 Cl   UNK     0       6.305   0.000   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
CONECT    9    6   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    5   13                                                       
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

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3D PDB for NP0139152 (Ginkgotoxin hydrochloride)
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SMILES for NP0139152 (Ginkgotoxin hydrochloride)
Cl.COCC1=C(O)C(C)=NC=C1CO
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INCHI for NP0139152 (Ginkgotoxin hydrochloride)
InChI=1S/C9H13NO3.ClH/c1-6-9(12)8(5-13-2)7(4-11)3-10-6;/h3,11-12H,4-5H2,1-2H3;1H
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View in JSmol
Synonyms
ValueSource
4-O-MethoxypyridoxineMeSH
4-O-MethylpyridoxineMeSH
4-MethoxymethylpyridoxineMeSH
4-Methoxymethylpyridoxine hydrochlorideMeSH
4-MethoxypyridoxineMeSH
Chemical FormulaC9H14ClNO3
Average Mass219.6700 Da
Monoisotopic Mass219.06622 Da
IUPAC Name5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol hydrochloride
Traditional Nameginkgotoxin hydrochloride
CAS Registry NumberNot Available
SMILES
Cl.COCC1=C(O)C(C)=NC=C1CO
InChI Identifier
InChI=1S/C9H13NO3.ClH/c1-6-9(12)8(5-13-2)7(4-11)3-10-6;/h3,11-12H,4-5H2,1-2H3;1H
InChI KeyWIQVPGFUYBUXNC-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridoxines. These are pyridoxal derivatives in which the carbaldehyde group at position 2 of the pyridoxal moiety is replaced by a hydroxymethyl group.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyridines and derivatives  
Sub ClassPyridoxines  
Direct ParentPyridoxines  
Alternative Parents
Substituents
  • Pyridoxine
    • 

  • Methylpyridine
    • 

  • Hydroxypyridine
    • 

  • Heteroaromatic compound
    • 

  • Dialkyl ether
    • 

  • Ether
    • 

  • Azacycle
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Hydrochloride
    • 

  • Aromatic alcohol
    • 

  • Organopnictogen compound
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic 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-0.08ALOGPS
logP-0.31ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)8.59ChemAxon
pKa (Strongest Basic)5.58ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area62.58 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity48.86 m³·mol⁻¹ChemAxon
Polarizability19.19 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID69045  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound76580  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available