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Showing NP-Card for 3-Pyridinecarbonitrile (NP0002819)

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Record Information
Version1.0
Created at2020-11-23 19:41:14 UTC
Updated at2021-08-12 19:52:14 UTC
NP-MRD IDNP0002819
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Pyridinecarbonitrile
Provided ByBMRBBMRB logo
Description3-Pyridinecarbonitrile is also known as 3-azabenzonitrile or 3-cyanopyridine. It was first documented in 2008 (PMID: 17984079). Based on a literature review a significant number of articles have been published on 3-pyridinecarbonitrile (PMID: 25679457) (PMID: 33527006) (PMID: 31759207) (PMID: 31236864).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002819 (3-Pyridinecarbonitrile)


     RDKit          2D

 12 12  0  0  0  0  0  0  0  0999 V2000
    3.9522   -0.6535    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4877   -0.3292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0232   -0.0048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0100   -1.1110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4545   -0.7866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9059    0.6438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8927    1.7500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5718    1.4256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4614   -2.5415    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4676   -1.8928    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3704    0.9682    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5849    2.5318    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  3  1  0
  4  9  1  0
  5 10  1  0
  6 11  1  0
  8 12  1  0
M  END
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3D MOL for NP0002819 (3-Pyridinecarbonitrile)

NP0002819
     RDKit          3D

 12 12  0  0  0  0  0  0  0  0999 V2000
    3.5134    0.3429   -0.2447 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3686    0.1935   -0.1590 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9330   -0.0177   -0.0574 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0615    1.0586   -0.0586 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2856    0.7894    0.0404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7938   -0.4830    0.1388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9311   -1.5154    0.1382 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4027   -1.2871    0.0422 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4580    2.0773   -0.1367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9936    1.6094    0.0423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8607   -0.6569    0.2151 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1278   -2.1111    0.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  3  1  0
  4  9  1  0
  5 10  1  0
  6 11  1  0
  8 12  1  0
M  END
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3D SDF for NP0002819 (3-Pyridinecarbonitrile)


     RDKit          2D

 12 12  0  0  0  0  0  0  0  0999 V2000
    3.9522   -0.6535    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4877   -0.3292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0232   -0.0048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0100   -1.1110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4545   -0.7866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9059    0.6438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8927    1.7500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5718    1.4256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4614   -2.5415    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4676   -1.8928    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3704    0.9682    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5849    2.5318    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  3  1  0
  4  9  1  0
  5 10  1  0
  6 11  1  0
  8 12  1  0
M  END
> <DATABASE_ID>
NP0002819

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N#CC1=CN=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C6H4N2/c7-4-6-2-1-3-8-5-6/h1-3,5H

> <INCHI_KEY>
GZPHSAQLYPIAIN-UHFFFAOYSA-N

> <FORMULA>
C6H4N2

> <MOLECULAR_WEIGHT>
104.1094

> <EXACT_MASS>
104.037448138

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
10.165297019837116

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyridine-3-carbonitrile

> <ALOGPS_LOGP>
0.36

> <JCHEM_LOGP>
0.6116695773333334

> <ALOGPS_LOGS>
-0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
1.3959222301602507

> <JCHEM_POLAR_SURFACE_AREA>
36.68

> <JCHEM_REFRACTIVITY>
29.6227

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.48e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-cyanopyridine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0002819 (3-Pyridinecarbonitrile)

NP0002819
     RDKit          3D

 12 12  0  0  0  0  0  0  0  0999 V2000
    3.5134    0.3429   -0.2447 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3686    0.1935   -0.1590 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9330   -0.0177   -0.0574 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0615    1.0586   -0.0586 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2856    0.7894    0.0404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7938   -0.4830    0.1388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9311   -1.5154    0.1382 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4027   -1.2871    0.0422 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4580    2.0773   -0.1367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9936    1.6094    0.0423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8607   -0.6569    0.2151 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1278   -2.1111    0.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  3  1  0
  4  9  1  0
  5 10  1  0
  6 11  1  0
  8 12  1  0
M  END
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PDB for NP0002819 (3-Pyridinecarbonitrile)

HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         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  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1    8                                                       
CONECT    4    6    7                                                       
CONECT    5    6    8                                                       
CONECT    6    2    4    5                                                  
CONECT    7    4                                                            
CONECT    8    3    5                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for NP0002819 (3-Pyridinecarbonitrile)

COMPND    NP0002819
HETATM    1  N1  UNL     1       3.513   0.343  -0.245  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.369   0.193  -0.159  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.933  -0.018  -0.057  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.061   1.059  -0.059  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.286   0.789   0.040  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.794  -0.483   0.139  1.00  0.00           C  
HETATM    7  N2  UNL     1      -0.931  -1.515   0.138  1.00  0.00           N  
HETATM    8  C6  UNL     1       0.403  -1.287   0.042  1.00  0.00           C  
HETATM    9  H1  UNL     1       0.458   2.077  -0.137  1.00  0.00           H  
HETATM   10  H2  UNL     1      -1.994   1.609   0.042  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.861  -0.657   0.215  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.128  -2.111   0.039  1.00  0.00           H  
CONECT    1    2    2    2
CONECT    2    3
CONECT    3    4    4    8
CONECT    4    5    9
CONECT    5    6    6   10
CONECT    6    7   11
CONECT    7    8    8
CONECT    8   12
END
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SMILES for NP0002819 (3-Pyridinecarbonitrile)

N#CC1=CN=CC=C1
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INCHI for NP0002819 (3-Pyridinecarbonitrile)

InChI=1S/C6H4N2/c7-4-6-2-1-3-8-5-6/h1-3,5H
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View in JSmol
Synonyms
ValueSource
3-AzabenzonitrileChEBI
3-CyanopyridineChEBI
NicotinonitrileChEBI
Nicotinic acid nitrileMeSH
Chemical FormulaC6H4N2
Average Mass104.1094 Da
Monoisotopic Mass104.03745 Da
IUPAC Namepyridine-3-carbonitrile
Traditional Name3-cyanopyridine
CAS Registry NumberNot Available
SMILES
N#CC1=CN=CC=C1
InChI Identifier
InChI=1S/C6H4N2/c7-4-6-2-1-3-8-5-6/h1-3,5H
InChI KeyGZPHSAQLYPIAIN-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as 3-pyridinecarbonitriles. These are organic compounds containing a pyridine ring substituted at the 3-position by a carbonitrile group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub Class3-pyridinecarbonitriles
Direct Parent3-pyridinecarbonitriles
Alternative Parents
Substituents
  • 3-pyridinecarbonitrile
  • Heteroaromatic compound
  • Azacycle
  • Nitrile
  • Carbonitrile
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • 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
logP0.36ALOGPS
logP0.61ChemAxon
logS-0.85ALOGPS
pKa (Strongest Basic)1.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area36.68 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.62 m³·mol⁻¹ChemAxon
Polarizability10.17 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0062027
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID86556
Good Scents IDNot Available
References
General References
  1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
  2. Mohan DC, Ravi C, Rao SN, Adimurthy S: Copper-mediated synthesis of pyrazolo[1,5-a]pyridines through oxidative linkage of C-C/N-N bonds. Org Biomol Chem. 2015 Mar 28;13(12):3556-60. doi: 10.1039/c5ob00018a. [PubMed:25679457 ]
  3. Shen L, Xiao Y, Xie H, Zhao H, Luo T, Liu L, Pan X: A naturally derived small molecule NDSM253 inhibits IKK1 to suppress inflammation response and promote bone healing after fracture. Am J Transl Res. 2021 Jan 15;13(1):24-37. eCollection 2021. [PubMed:33527006 ]
  4. Tu X, Meng X, Pan Y, Crittenden JC, Wang Y: Degradation kinetics of target compounds and correlations with spectral indices during UV/H2O2 post-treatment of biologically treated acrylonitrile wastewater. Chemosphere. 2020 Mar;243:125384. doi: 10.1016/j.chemosphere.2019.125384. Epub 2019 Nov 15. [PubMed:31759207 ]
  5. Tu X, Pan Y, Gao H, Li B, Song Y: Post-treatment of bio-treated acrylonitrile wastewater using UV/Fenton process: degradation kinetics of target compounds. Environ Sci Pollut Res Int. 2019 Aug;26(24):24570-24580. doi: 10.1007/s11356-019-05663-4. Epub 2019 Jun 24. [PubMed:31236864 ]