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Showing NP-Card for 5-pyridoxic acid (NP0245026)

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Record Information
Version2.0
Created at2022-09-07 05:57:23 UTC
Updated at2022-09-07 05:57:23 UTC
NP-MRD IDNP0245026
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-pyridoxic acid
Description5-Pyridoxic acid, also known as 5-pyridoxate, belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group. 5-pyridoxic acid is found in Trypanosoma brucei. 5-pyridoxic acid was first documented in 1958 (PMID: 13610871). 5-Pyridoxic acid is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0245026 (5-pyridoxic acid)


  Mrv0541 05031422382D          

 13 13  0  0  0  0            999 V2000
    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
   -0.7145    1.2375    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
    0.7145    1.2375    0.0000 C   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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  2  0  0  0  0
  7  4  2  0  0  0  0
  7  6  1  0  0  0  0
  8  5  1  0  0  0  0
  9  2  2  0  0  0  0
  9  4  1  0  0  0  0
 10  3  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  2  0  0  0  0
 13  8  1  0  0  0  0
M  END
Download

3D MOL for NP0245026 (5-pyridoxic acid)

     RDKit          3D

 22 22  0  0  0  0  0  0  0  0999 V2000
   -3.1727   -0.2517   -0.1394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6965   -0.4692   -0.1732 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2256   -1.7014   -0.3720 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0885   -1.9170   -0.3926 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9856   -0.9090   -0.2075 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3831   -1.3135   -0.1805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8840   -1.8778   -1.1734 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1450   -1.0843    0.9359 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5253    0.3702    0.0094 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4833    1.5059    0.0891 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1723    2.2420    1.2603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8266    0.5625    0.0195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3251    1.8737    0.2313 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5164    0.5062   -0.8319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4902   -0.0692    0.9408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6992   -1.1979   -0.4446 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3927   -2.9585   -0.5561 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2084   -1.7782    1.7144 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5225    1.0968    0.3495 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5310    2.1613   -0.7763 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9289    3.1760    0.9767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2981    2.0330    0.2624 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2 12  2  0
 12 13  1  0
 12  9  1  0
  9 10  1  0
 10 11  1  0
  9  5  2  0
  5  4  1  0
  4  3  2  0
  5  6  1  0
  6  8  1  0
  6  7  2  0
  3  2  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
 13 22  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
  4 17  1  0
  8 18  1  0
M  END
Download

3D SDF for NP0245026 (5-pyridoxic acid)


  Mrv0541 05031422382D          

 13 13  0  0  0  0            999 V2000
    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
   -0.7145    1.2375    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
    0.7145    1.2375    0.0000 C   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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  2  0  0  0  0
  7  4  2  0  0  0  0
  7  6  1  0  0  0  0
  8  5  1  0  0  0  0
  9  2  2  0  0  0  0
  9  4  1  0  0  0  0
 10  3  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  2  0  0  0  0
 13  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0245026

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C(O)C(CO)=C(C=N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H9NO4/c1-4-7(11)6(3-10)5(2-9-4)8(12)13/h2,10-11H,3H2,1H3,(H,12,13)

> <INCHI_KEY>
VJZTVPVXKYQRJZ-UHFFFAOYSA-N

> <FORMULA>
C8H9NO4

> <MOLECULAR_WEIGHT>
183.1614

> <EXACT_MASS>
183.053157781

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
17.219014051682073

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-hydroxy-4-(hydroxymethyl)-6-methylpyridine-3-carboxylic acid

> <ALOGPS_LOGP>
-0.05

> <JCHEM_LOGP>
-2.125541304981875

> <ALOGPS_LOGS>
-1.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.603476994894356

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8416150448528414

> <JCHEM_PKA_STRONGEST_BASIC>
6.014686738716824

> <JCHEM_POLAR_SURFACE_AREA>
90.65000000000002

> <JCHEM_REFRACTIVITY>
44.5456

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-pyridoxic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0245026 (5-pyridoxic acid)

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PDB for NP0245026 (5-pyridoxic acid)
HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    4                                                            
CONECT    2    5    9                                                       
CONECT    3    6   10                                                       
CONECT    4    1    7    9                                                  
CONECT    5    2    6    8                                                  
CONECT    6    3    5    7                                                  
CONECT    7    4    6   11                                                  
CONECT    8    5   12   13                                                  
CONECT    9    2    4                                                       
CONECT   10    3                                                            
CONECT   11    7                                                            
CONECT   12    8                                                            
CONECT   13    8                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

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3D PDB for NP0245026 (5-pyridoxic acid)
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SMILES for NP0245026 (5-pyridoxic acid)
CC1=C(O)C(CO)=C(C=N1)C(O)=O
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INCHI for NP0245026 (5-pyridoxic acid)
InChI=1S/C8H9NO4/c1-4-7(11)6(3-10)5(2-9-4)8(12)13/h2,10-11H,3H2,1H3,(H,12,13)
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View in JSmol
Synonyms
ValueSource
5-Hydroxy-4-(hydroxymethyl)-6-methyl-3-pyridinecarboxylic acidChEBI
5-Hydroxy-4-(hydroxymethyl)-6-methylnicotinic acidChEBI
5-PyridoxateKegg
5-Hydroxy-4-(hydroxymethyl)-6-methyl-3-pyridinecarboxylateGenerator
5-Hydroxy-4-(hydroxymethyl)-6-methylnicotinateGenerator
Chemical FormulaC8H9NO4
Average Mass183.1614 Da
Monoisotopic Mass183.05316 Da
IUPAC Name5-hydroxy-4-(hydroxymethyl)-6-methylpyridine-3-carboxylic acid
Traditional Name5-pyridoxic acid
CAS Registry NumberNot Available
SMILES
CC1=C(O)C(CO)=C(C=N1)C(O)=O
InChI Identifier
InChI=1S/C8H9NO4/c1-4-7(11)6(3-10)5(2-9-4)8(12)13/h2,10-11H,3H2,1H3,(H,12,13)
InChI KeyVJZTVPVXKYQRJZ-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
Trypanosoma bruceiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyridines and derivatives  
Sub ClassPyridinecarboxylic acids and derivatives  
Direct ParentPyridinecarboxylic acids  
Alternative Parents
Substituents
  • Pyridine carboxylic acid
    • 

  • Hydroxypyridine
    • 

  • Methylpyridine
    • 

  • Heteroaromatic compound
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Azacycle
    • 

  • Aromatic alcohol
    • 

  • Organic nitrogen compound
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • 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
logP-0.05ALOGPS
logP-2.1ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)1.84ChemAxon
pKa (Strongest Basic)6.01ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area90.65 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity44.55 m³·mol⁻¹ChemAxon
Polarizability17.22 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 IDC04773  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440474  
PDB IDNot Available
ChEBI ID16409  
Good Scents IDNot Available
References
General References
  1. RODWELL VW, VOLCANI BE, IKAWA M, SNELL EE: Bacterial oxidation of vitamin B6. I. Isopyridoxal and 5-pyridoxic acid. J Biol Chem. 1958 Dec;233(6):1548-54. [PubMed:13610871  ] 
  2. LOTUS database [Link]