Np mrd loader

Showing NP-Card for dipicolinic acid (NP0189085)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2022-09-04 05:31:00 UTC
Updated at2022-09-04 05:31:00 UTC
NP-MRD IDNP0189085
Secondary Accession NumbersNone
Natural Product Identification
Common Namedipicolinic acid
Description2,6-Pyridinedicarboxylic acid, also known as 2,6-dipicolinic acid or 2,6-dicarboxypyridine, belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group. 2,6-Pyridinedicarboxylic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). dipicolinic acid is found in Penicillium bilaiae. dipicolinic acid was first documented in 2013 (PMID: 23396907). A pyridinedicarboxylic acid carrying two carboxy groups at positions 2 and 6 (PMID: 24123749).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0189085 (dipicolinic acid)


  Mrv0541 02231217342D          

 12 12  0  0  0  0            999 V2000
    2.1434   -1.2375    0.0000 O   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
    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 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
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   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
    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
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  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
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
M  END
Download

3D MOL for NP0189085 (dipicolinic acid)

     RDKit          3D

 17 17  0  0  0  0  0  0  0  0999 V2000
    1.8311   -2.5450    0.3392 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0102   -1.3062    0.4519 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2872   -0.8705    0.7617 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9385   -0.3555    0.2694 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2128    0.9947    0.4098 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2031    1.8971    0.2383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0623    1.4322   -0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3352    0.0908   -0.2100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6563   -0.4117   -0.5332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6484    0.3415   -0.7095 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8788   -1.7747   -0.6628 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3255   -0.7659   -0.0358 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8987   -0.6378   -0.0050 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2326    1.2785    0.6532 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3890    2.9486    0.3414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9029    2.1088   -0.2176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1937   -2.4248   -1.0205 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  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8 12  2  0
  8  9  1  0
  9 11  1  0
  9 10  2  0
 12  4  1  0
  3 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
 11 17  1  0
M  END
Download

3D SDF for NP0189085 (dipicolinic acid)


  Mrv0541 02231217342D          

 12 12  0  0  0  0            999 V2000
    2.1434   -1.2375    0.0000 O   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
    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 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
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   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
    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
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  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
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0189085

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H5NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-3H,(H,9,10)(H,11,12)

> <INCHI_KEY>
WJJMNDUMQPNECX-UHFFFAOYSA-N

> <FORMULA>
C7H5NO4

> <MOLECULAR_WEIGHT>
167.1189

> <EXACT_MASS>
167.021857653

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
14.571938589663489

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyridine-2,6-dicarboxylic acid

> <ALOGPS_LOGP>
0.54

> <JCHEM_LOGP>
0.8424398563333333

> <ALOGPS_LOGS>
-1.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.991217267638345

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.240665380380044

> <JCHEM_PKA_STRONGEST_BASIC>
-2.4986114606290792

> <JCHEM_POLAR_SURFACE_AREA>
87.49000000000001

> <JCHEM_REFRACTIVITY>
37.6695

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.46e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dipicolinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0189085 (dipicolinic acid)

Download
PDB for NP0189085 (dipicolinic acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+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  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8    4                                                       
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Download
3D PDB for NP0189085 (dipicolinic acid)
Download
SMILES for NP0189085 (dipicolinic acid)
OC(=O)C1=CC=CC(=N1)C(O)=O
Download
INCHI for NP0189085 (dipicolinic acid)
InChI=1S/C7H5NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-3H,(H,9,10)(H,11,12)
Download
View in JSmol
Synonyms
ValueSource
2,6-DicarboxypyridineChEBI
2,6-Dipicolinic acidChEBI
PYRIDINE-2,6-dicarboxylIC ACIDChEBI
2,6-DipicolinateGenerator
PYRIDINE-2,6-dicarboxylateGenerator
2,6-PyridinedicarboxylateGenerator
DipicolinateHMDB
Dipicolinic acidHMDB
3,4-PyridinedicarboxylateHMDB
Dipicolinic acid, disodium saltHMDB
Dipicolinic acid, monosodium saltHMDB
Zinc dipicolinateHMDB
Dipicolinic acid, calcium saltHMDB
2,6-Pyridine dicarboxylateHMDB
Dipicolinic acid, zinc saltHMDB
Dipicolinic acid, dipotassium saltHMDB
2,6-Pyridinedicarboxylic acidChEBI
Chemical FormulaC7H5NO4
Average Mass167.1189 Da
Monoisotopic Mass167.02186 Da
IUPAC Namepyridine-2,6-dicarboxylic acid
Traditional Namedipicolinic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1=CC=CC(=N1)C(O)=O
InChI Identifier
InChI=1S/C7H5NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-3H,(H,9,10)(H,11,12)
InChI KeyWJJMNDUMQPNECX-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
Penicillium bilaiaeLOTUS 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
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Heteroaromatic compound
    • 

  • Azacycle
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen 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
logP0.54ALOGPS
logP0.84ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)3.24ChemAxon
pKa (Strongest Basic)-2.5ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area87.49 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity37.67 m³·mol⁻¹ChemAxon
Polarizability14.57 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0033161  
DrugBank IDDB04267  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB011167  
KNApSAcK IDNot Available
Chemspider ID9940  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDipicolinic_acid  
METLIN IDNot Available
PubChem Compound10367  
PDB IDPDC  
ChEBI ID46837  
Good Scents IDNot Available
References
General References
  1. Zhang JQ, Griffiths KK, Cowan A, Setlow P, Yu J: Expression level of Bacillus subtilis germinant receptors determines the average rate but not the heterogeneity of spore germination. J Bacteriol. 2013 Apr;195(8):1735-40. doi: 10.1128/JB.02212-12. Epub 2013 Feb 8. [PubMed:23396907  ] 
  2. Moeller R, Raguse M, Reitz G, Okayasu R, Li Z, Klein S, Setlow P, Nicholson WL: Resistance of Bacillus subtilis spore DNA to lethal ionizing radiation damage relies primarily on spore core components and DNA repair, with minor effects of oxygen radical detoxification. Appl Environ Microbiol. 2014 Jan;80(1):104-9. doi: 10.1128/AEM.03136-13. Epub  2013 Oct 11. [PubMed:24123749  ] 
  3. LOTUS database [Link]