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Showing NP-Card for 3-hydroxypicolinic acid (NP0304973)

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Record Information
Version2.0
Created at2022-09-10 20:26:13 UTC
Updated at2024-09-03 04:16:47 UTC
NP-MRD IDNP0304973
Natural Product DOIhttps://doi.org/10.57994/0805
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-hydroxypicolinic acid
Description3-Hydroxypicolinic acid, also known as HPA, belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group. 3-hydroxypicolinic acid is found in Aloe africana and Streptomyces virginiae. 3-hydroxypicolinic acid was first documented in 1966 (PMID: 5902481). 3-Hydroxypicolinic acid is a very strong basic compound (based on its pKa) (PMID: 8457722).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0304973 (3-hydroxypicolinic acid)


  Mrv1652303102016502D          

 10 10  0  0  0  0            999 V2000
   11.0928  -11.5010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2678  -11.5010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8553  -10.7866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2678  -10.0721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0928  -10.0721    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.5053  -10.7866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8553   -9.3576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2678   -8.6431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0303   -9.3576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0303  -10.7866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3 10  1  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
  5  6  2  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
Download

3D MOL for NP0304973 (3-hydroxypicolinic acid)

     RDKit          3D

 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.7968    0.7097    0.2048 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1329   -0.3399    0.1941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7010   -1.6069    0.3613 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6791   -0.2717   -0.0018 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0904   -1.3591   -0.0236 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4158   -1.3390   -0.1992 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0568   -0.1342   -0.3714 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2965    1.0159   -0.3554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0647    0.9591   -0.1724 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8256    2.1283   -0.1577 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2501   -2.4387    0.0612 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0318   -2.2337   -0.2149 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1315   -0.0826   -0.5164 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7939    1.9881   -0.4917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3662    3.0046   -0.2821 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  0
  2  4  1  0
  4  9  2  0
  9 10  1  0
  9  8  1  0
  8  7  2  0
  7  6  1  0
  6  5  2  0
  5  4  1  0
  3 11  1  0
 10 15  1  0
  8 14  1  0
  7 13  1  0
  6 12  1  0
M  END
Download

3D SDF for NP0304973 (3-hydroxypicolinic acid)


  Mrv1652303102016502D          

 10 10  0  0  0  0            999 V2000
   11.0928  -11.5010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2678  -11.5010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8553  -10.7866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2678  -10.0721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0928  -10.0721    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.5053  -10.7866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8553   -9.3576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2678   -8.6431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0303   -9.3576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0303  -10.7866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3 10  1  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
  5  6  2  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0304973

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)C1=C(O)C=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H5NO3/c8-4-2-1-3-7-5(4)6(9)10/h1-3,8H,(H,9,10)

> <INCHI_KEY>
BRARRAHGNDUELT-UHFFFAOYSA-N

> <FORMULA>
C6H5NO3

> <MOLECULAR_WEIGHT>
139.1088

> <EXACT_MASS>
139.026943031

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
12.21695586881242

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxypyridine-2-carboxylic acid

> <ALOGPS_LOGP>
0.79

> <JCHEM_LOGP>
-0.5213333799091218

> <ALOGPS_LOGS>
-0.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.90657626436559

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.41070724176744067

> <JCHEM_PKA_STRONGEST_BASIC>
6.124763450634564

> <JCHEM_POLAR_SURFACE_AREA>
70.42

> <JCHEM_REFRACTIVITY>
32.7662

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.37e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxypicolinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0304973 (3-hydroxypicolinic acid)

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PDB for NP0304973 (3-hydroxypicolinic acid)
HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0      20.707 -21.469   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      19.167 -21.469   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.397 -20.135   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      19.167 -18.801   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      20.707 -18.801   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      21.477 -20.135   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.397 -17.468   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      19.167 -16.134   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      16.857 -17.468   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      16.857 -20.135   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    1    5                                                       
CONECT    7    4    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    3                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0304973 (3-hydroxypicolinic acid)
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SMILES for NP0304973 (3-hydroxypicolinic acid)
OC(=O)C1=C(O)C=CC=N1
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INCHI for NP0304973 (3-hydroxypicolinic acid)
InChI=1S/C6H5NO3/c8-4-2-1-3-7-5(4)6(9)10/h1-3,8H,(H,9,10)
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View in JSmol
Synonyms
ValueSource
3-Hydroxy-2-pyridinecarboxylic acidChEBI
HPAChEBI
3-Hydroxy-2-pyridinecarboxylateGenerator
3-HydroxypicolinateGenerator
3-Hydroxypyridine-2-carboxylateHMDB
3-Hydroxypyridine-2-carboxylic acidHMDB
Chemical FormulaC6H5NO3
Average Mass139.1088 Da
Monoisotopic Mass139.02694 Da
IUPAC Name3-hydroxypyridine-2-carboxylic acid
Traditional Name3-hydroxypicolinic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1=C(O)C=CC=N1
InChI Identifier
InChI=1S/C6H5NO3/c8-4-2-1-3-7-5(4)6(9)10/h1-3,8H,(H,9,10)
InChI KeyBRARRAHGNDUELT-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)[email protected]Not AvailableNot Available2023-08-11View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)[email protected]Not AvailableNot Available2023-08-11View Spectrum
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
Aloe africanaLOTUS Database
Streptomyces virginiaeLOTUS 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
    • 

  • Vinylogous acid
    • 

  • Heteroaromatic compound
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Azacycle
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • 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
logP0.79ALOGPS
logP-0.52ChemAxon
logS-0.77ALOGPS
pKa (Strongest Acidic)0.41ChemAxon
pKa (Strongest Basic)6.12ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area70.42 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.77 m³·mol⁻¹ChemAxon
Polarizability12.22 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0013188  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029323  
KNApSAcK IDNot Available
Chemspider ID12827  
KEGG Compound IDC18620  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Hydroxypicolinic_acid  
METLIN IDNot Available
PubChem Compound13401  
PDB IDMHW  
ChEBI ID64342  
Good Scents IDNot Available
References
General References
  1. Sheehan JT: 3-hydroxypicolinic acid and some of its derivatives. J Org Chem. 1966 Feb;31(2):636-7. doi: 10.1021/jo01340a533. [PubMed:5902481  ] 
  2. Wu KJ, Steding A, Becker CH: Matrix-assisted laser desorption time-of-flight mass spectrometry of oligonucleotides using 3-hydroxypicolinic acid as an ultraviolet-sensitive matrix. Rapid Commun Mass Spectrom. 1993 Feb;7(2):142-6. doi: 10.1002/rcm.1290070206. [PubMed:8457722  ] 
  3. LOTUS database [Link]