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Showing NP-Card for 4-deoxypyridoxine (NP0281783)

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Record Information
Version2.0
Created at2022-09-09 08:20:54 UTC
Updated at2022-09-09 08:20:54 UTC
NP-MRD IDNP0281783
Secondary Accession NumbersNone
Natural Product Identification
Common Name4-deoxypyridoxine
Description4-Deoxypyridoxine belongs to the class of organic compounds known as methylpyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group. 4-Deoxypyridoxine is a very strong basic compound (based on its pKa). 4-Deoxypyridoxine may be a unique S. 4-deoxypyridoxine is found in Ginkgo biloba. Cerevisiae (yeast) metabolite.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0281783 (4-deoxypyridoxine)


  Mrv0541 06081214512D          

 11 11  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   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
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 11  1  0  0  0  0
M  END
Download

3D MOL for NP0281783 (4-deoxypyridoxine)

     RDKit          3D

 22 22  0  0  0  0  0  0  0  0999 V2000
    3.3412    0.1582   -0.4249 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9076   -0.2428   -0.3996 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4592   -1.4587   -0.6291 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1774   -1.8288   -0.5413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8081   -0.8937   -0.1783 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1546   -1.3599    0.0463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1882   -0.6375   -0.5505 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3720    0.3804    0.0630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3746    1.4290    0.4167 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9815    0.7513   -0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4440    2.0255    0.2042 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7315    0.0010    0.6190 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8744   -0.4432   -1.1639 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3899    1.2094   -0.6712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1479   -2.8433   -0.7493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2414   -2.3969   -0.5202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3744   -1.6389    1.1060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7642   -0.2522    0.1740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8980    2.4183    0.2671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1939    1.4204   -0.3759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7591    1.3673    1.4334 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9697    2.8350    0.4483 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 10  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  4 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  9 19  1  0
  9 20  1  0
  9 21  1  0
 11 22  1  0
M  END
Download

3D SDF for NP0281783 (4-deoxypyridoxine)


  Mrv0541 06081214512D          

 11 11  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   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
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0281783

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=NC=C(CO)C(C)=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C8H11NO2/c1-5-7(4-10)3-9-6(2)8(5)11/h3,10-11H,4H2,1-2H3

> <INCHI_KEY>
KKOWAYISKWGDBG-UHFFFAOYSA-N

> <FORMULA>
C8H11NO2

> <MOLECULAR_WEIGHT>
153.1784

> <EXACT_MASS>
153.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
16.240002204893177

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-(hydroxymethyl)-2,4-dimethylpyridin-3-ol

> <ALOGPS_LOGP>
0.38

> <JCHEM_LOGP>
0.32944985833333346

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.936173266273713

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.408001830564865

> <JCHEM_PKA_STRONGEST_BASIC>
6.673690219362241

> <JCHEM_POLAR_SURFACE_AREA>
53.35000000000001

> <JCHEM_REFRACTIVITY>
42.3306

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.63e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-deoxypyridoxine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0281783 (4-deoxypyridoxine)

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PDB for NP0281783 (4-deoxypyridoxine)
HEADER    PROTEIN                                 08-JUN-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-JUN-12         0                                  
HETATM    1  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
CONECT    9    4   10                                                       
CONECT   10    9                                                            
CONECT   11    3                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0281783 (4-deoxypyridoxine)
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SMILES for NP0281783 (4-deoxypyridoxine)
CC1=NC=C(CO)C(C)=C1O
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INCHI for NP0281783 (4-deoxypyridoxine)
InChI=1S/C8H11NO2/c1-5-7(4-10)3-9-6(2)8(5)11/h3,10-11H,4H2,1-2H3
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View in JSmol
Synonyms
ValueSource
4-DeoxypyridoxalChEBI
4-DeoxypyridoxolChEBI
4-Deoxypyridoxine hydrochlorideMeSH
4'-DeoxypyridoxineMeSH
Chemical FormulaC8H11NO2
Average Mass153.1784 Da
Monoisotopic Mass153.07898 Da
IUPAC Name5-(hydroxymethyl)-2,4-dimethylpyridin-3-ol
Traditional Name4-deoxypyridoxine
CAS Registry NumberNot Available
SMILES
CC1=NC=C(CO)C(C)=C1O
InChI Identifier
InChI=1S/C8H11NO2/c1-5-7(4-10)3-9-6(2)8(5)11/h3,10-11H,4H2,1-2H3
InChI KeyKKOWAYISKWGDBG-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 Origin
Species NameSourceReference
Ginkgo bilobaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as methylpyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyridines and derivatives  
Sub ClassMethylpyridines  
Direct ParentMethylpyridines  
Alternative Parents
Substituents
  • Methylpyridine
    • 

  • Hydroxypyridine
    • 

  • Heteroaromatic compound
    • 

  • Azacycle
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Aromatic alcohol
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Alcohol
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
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
logP0.38ALOGPS
logP0.33ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)9.41ChemAxon
pKa (Strongest Basic)6.67ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area53.35 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity42.33 m³·mol⁻¹ChemAxon
Polarizability16.24 ųChemAxon
Number of Rings1ChemAxon
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 IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDCPD0-1605  
BiGG IDNot Available
Wikipedia Link4-Deoxypyridoxine  
METLIN IDNot Available
PubChem Compound6094  
PDB IDNot Available
ChEBI ID65083  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]