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Showing NP-Card for (5r)-5,6-dihydropyridine-2,5-diol (NP0245728)

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Record Information
Version2.0
Created at2022-09-07 06:55:06 UTC
Updated at2022-09-07 06:55:07 UTC
NP-MRD IDNP0245728
Secondary Accession NumbersNone
Natural Product Identification
Common Name(5r)-5,6-dihydropyridine-2,5-diol
DescriptionAKOS006356455 belongs to the class of organic compounds known as hydropyridines. Hydropyridines are compounds containing a hydrogenated pyridine ring (i.E. Containing less than the maximum number of double bonds.). (5r)-5,6-dihydropyridine-2,5-diol is found in Piper sintenense. Based on a literature review very few articles have been published on AKOS006356455.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0245728 ((5r)-5,6-dihydropyridine-2,5-diol)


  Mrv1652309072208552D          

  8  8  0  0  1  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 N   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  2  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   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
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
M  END
Download

3D MOL for NP0245728 ((5r)-5,6-dihydropyridine-2,5-diol)

     RDKit          3D

 15 15  0  0  0  0  0  0  0  0999 V2000
    2.8844   -0.2171    0.3624 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5034   -0.2284    0.1328 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9683   -0.5860   -0.9534 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4128   -0.6099   -1.2170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2956   -0.1727   -0.1191 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0281    0.9707   -0.6027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6297    0.2246    1.1016 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6590    0.2160    1.2650 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4669    0.2885   -0.2804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6697   -0.0835   -2.1962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6948   -1.7092   -1.4112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1159   -0.9396    0.0866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5003    1.7669   -0.3171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2593    0.5580    1.9526 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1243    0.5217    2.1962 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2  8  1  0
  8  7  2  0
  7  5  1  0
  6 13  1  0
  5 12  1  1
  4 10  1  0
  4 11  1  0
  1  9  1  0
  8 15  1  0
  7 14  1  0
M  END
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3D SDF for NP0245728 ((5r)-5,6-dihydropyridine-2,5-diol)


  Mrv1652309072208552D          

  8  8  0  0  1  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 N   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  2  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   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
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0245728

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1CN=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NO2/c7-4-1-2-5(8)6-3-4/h1-2,4,7H,3H2,(H,6,8)/t4-/m1/s1

> <INCHI_KEY>
OJUNZJSEHXGBLM-SCSAIBSYSA-N

> <FORMULA>
C5H7NO2

> <MOLECULAR_WEIGHT>
113.116

> <EXACT_MASS>
113.047678469

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.638539483633547

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5R)-5,6-dihydropyridine-2,5-diol

> <JCHEM_LOGP>
-0.23660916366666684

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.535236271998176

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.300939845963368

> <JCHEM_PKA_STRONGEST_BASIC>
4.235422268031333

> <JCHEM_POLAR_SURFACE_AREA>
52.82000000000001

> <JCHEM_REFRACTIVITY>
29.6814

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(5R)-5,6-dihydropyridine-2,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0245728 ((5r)-5,6-dihydropyridine-2,5-diol)

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PDB for NP0245728 ((5r)-5,6-dihydropyridine-2,5-diol)
HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         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  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+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  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+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   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    2                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END

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3D PDB for NP0245728 ((5r)-5,6-dihydropyridine-2,5-diol)
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SMILES for NP0245728 ((5r)-5,6-dihydropyridine-2,5-diol)
O[C@H]1CN=C(O)C=C1
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INCHI for NP0245728 ((5r)-5,6-dihydropyridine-2,5-diol)
InChI=1S/C5H7NO2/c7-4-1-2-5(8)6-3-4/h1-2,4,7H,3H2,(H,6,8)/t4-/m1/s1
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SynonymsNot Available
Chemical FormulaC5H7NO2
Average Mass113.1160 Da
Monoisotopic Mass113.04768 Da
IUPAC Name(5R)-5,6-dihydropyridine-2,5-diol
Traditional Name(5R)-5,6-dihydropyridine-2,5-diol
CAS Registry NumberNot Available
SMILES
O[C@H]1CN=C(O)C=C1
InChI Identifier
InChI=1S/C5H7NO2/c7-4-1-2-5(8)6-3-4/h1-2,4,7H,3H2,(H,6,8)/t4-/m1/s1
InChI KeyOJUNZJSEHXGBLM-SCSAIBSYSA-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
Piper sintenenseLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydropyridines. Hydropyridines are compounds containing a hydrogenated pyridine ring (i.E. Containing less than the maximum number of double bonds.).
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyridines and derivatives  
Sub ClassHydropyridines  
Direct ParentHydropyridines  
Alternative Parents
Substituents
  • Hydropyridine
    • 

  • Carboxamide group
    • 

  • Lactam
    • 

  • Secondary carboxylic acid amide
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid derivative
    • 

  • Azacycle
    • 

  • Alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic 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-0.24ChemAxon
pKa (Strongest Acidic)6.3ChemAxon
pKa (Strongest Basic)4.24ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area52.82 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.68 m³·mol⁻¹ChemAxon
Polarizability10.64 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 ID32976884  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12019563  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]