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Showing NP-Card for Benzonitrile (NP0002680)

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Record Information
Version1.0
Created at2020-11-23 18:26:44 UTC
Updated at2021-08-12 19:51:50 UTC
NP-MRD IDNP0002680
Secondary Accession NumbersNone
Natural Product Identification
Common NameBenzonitrile
Provided ByBMRBBMRB logo
DescriptionBenzonitrile, also known as cyanobenzene or phenyl cyanide, belongs to the class of organic compounds known as benzonitriles. These are organic compounds containing a benzene bearing a nitrile substituent. Benzonitrile exists in all living organisms, ranging from bacteria to humans. Benzonitrile is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. It was first documented in 2008 (PMID: 17984079). Based on a literature review very few articles have been published on Benzonitrile (PMID: 24129580) (PMID: 34403555) (PMID: 34381897) (PMID: 34378946) (PMID: 34355893) (PMID: 34354107).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002680 (Benzonitrile)


     RDKit          2D

 13 13  0  0  0  0  0  0  0  0999 V2000
    4.1538    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6538    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1538   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4038   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0962   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8462    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0962    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4038    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1538   -2.5981    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8462   -2.5981    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3462    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8462    2.5981    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1538    2.5981    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
  7 12  1  0
  8 13  1  0
M  END
Download

3D MOL for NP0002680 (Benzonitrile)

NP0002680
     RDKit          3D

 13 13  0  0  0  0  0  0  0  0999 V2000
    3.6424    0.0617   -0.1284 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4728    0.0446   -0.0875 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0554    0.0232   -0.0373 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3681   -1.1824   -0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0077   -1.2402    0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7034   -0.0505    0.0598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0248    1.1681    0.0611 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3515    1.2092    0.0128 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9004   -2.1236   -0.0768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5741   -2.1592    0.0109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7835    0.0023    0.0995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5711    2.0939    0.1000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8739    2.1528    0.0139 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
  7 12  1  0
  8 13  1  0
M  END
Download

3D SDF for NP0002680 (Benzonitrile)


     RDKit          2D

 13 13  0  0  0  0  0  0  0  0999 V2000
    4.1538    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6538    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1538   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4038   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0962   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8462    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0962    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4038    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1538   -2.5981    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8462   -2.5981    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3462    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8462    2.5981    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1538    2.5981    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
  7 12  1  0
  8 13  1  0
M  END
> <DATABASE_ID>
NP0002680

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H5N/c8-6-7-4-2-1-3-5-7/h1-5H

> <INCHI_KEY>
JFDZBHWFFUWGJE-UHFFFAOYSA-N

> <FORMULA>
C7H5N

> <MOLECULAR_WEIGHT>
103.1213

> <EXACT_MASS>
103.042199165

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
10.833603981411567

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
benzonitrile

> <ALOGPS_LOGP>
1.55

> <JCHEM_LOGP>
1.8293420043333333

> <ALOGPS_LOGS>
-1.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
23.79

> <JCHEM_REFRACTIVITY>
31.7796

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.25e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
benzonitrile

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0002680 (Benzonitrile)

NP0002680
     RDKit          3D

 13 13  0  0  0  0  0  0  0  0999 V2000
    3.6424    0.0617   -0.1284 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4728    0.0446   -0.0875 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0554    0.0232   -0.0373 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3681   -1.1824   -0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0077   -1.2402    0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7034   -0.0505    0.0598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0248    1.1681    0.0611 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3515    1.2092    0.0128 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9004   -2.1236   -0.0768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5741   -2.1592    0.0109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7835    0.0023    0.0995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5711    2.0939    0.1000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8739    2.1528    0.0139 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
  7 12  1  0
  8 13  1  0
M  END
Download

PDB for NP0002680 (Benzonitrile)

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0       1.083   3.602   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.250   2.832   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.250   1.291   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.083   0.521   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.417   1.291   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.417   2.832   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.750   3.602   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       5.084   2.832   0.000  0.00  0.00           N+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for NP0002680 (Benzonitrile)

COMPND    NP0002680
HETATM    1  N1  UNL     1       3.642   0.062  -0.128  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.473   0.045  -0.088  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.055   0.023  -0.037  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.368  -1.182  -0.038  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.008  -1.240   0.010  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.703  -0.051   0.060  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.025   1.168   0.061  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.352   1.209   0.013  1.00  0.00           C  
HETATM    9  H1  UNL     1       0.900  -2.124  -0.077  1.00  0.00           H  
HETATM   10  H2  UNL     1      -1.574  -2.159   0.011  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.784   0.002   0.100  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.571   2.094   0.100  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.874   2.153   0.014  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   12
CONECT    8   13
END
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SMILES for NP0002680 (Benzonitrile)

N#CC1=CC=CC=C1
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INCHI for NP0002680 (Benzonitrile)

InChI=1S/C7H5N/c8-6-7-4-2-1-3-5-7/h1-5H
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View in JSmol
Synonyms
ValueSource
BenzenenitrileChEBI
Benzoic acid nitrileChEBI
C6H5-CNChEBI
CyanobenzeneChEBI
Phenyl cyanideChEBI
Benzoate nitrileGenerator
Chemical FormulaC7H5N
Average Mass103.1213 Da
Monoisotopic Mass103.04220 Da
IUPAC Namebenzonitrile
Traditional Namebenzonitrile
CAS Registry NumberNot Available
SMILES
N#CC1=CC=CC=C1
InChI Identifier
InChI=1S/C7H5N/c8-6-7-4-2-1-3-5-7/h1-5H
InChI KeyJFDZBHWFFUWGJE-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Cannabis sativaCannabisDB
      Not Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzonitriles. These are organic compounds containing a benzene bearing a nitrile substituent.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassBenzonitriles
Direct ParentBenzonitriles
Alternative Parents
Substituents
  • Benzonitrile
  • Nitrile
  • Carbonitrile
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic 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
logP1.55ALOGPS
logP1.83ChemAxon
logS-1ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area23.79 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity31.78 m³·mol⁻¹ChemAxon
Polarizability10.83 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0062085
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029710
KNApSAcK IDNot Available
Chemspider ID7224
KEGG Compound IDC09814
BioCyc IDCPD-15582
BiGG IDNot Available
Wikipedia LinkBenzonitrile
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID27991
Good Scents IDrw1703641
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. Imamura K, Yoshikawa T, Nakanishi K, Hashimoto K, Kominami H: Photocatalytic reduction of benzonitrile to benzylamine in aqueous suspensions of palladium-loaded titanium(IV) oxide. Chem Commun (Camb). 2013 Dec 4;49(93):10911-3. doi: 10.1039/c3cc46439c. [PubMed:24129580 ]
  3. Rong MK, Bobylev EO, Holtrop F, Nieger M, Ehlers AW, Slootweg JC, Lammertsma K: Atypical And Asymmetric 1,3-P,N-Ligands: The Synthesis, Coordination and Catalytic Performance of Cycloiminophosphanes. Chemistry. 2021 Aug 17. doi: 10.1002/chem.202101921. [PubMed:34403555 ]
  4. Shanmugapriya N, Balachandran V, Revathi B, Narayana B, Salian VV, Vanasundari K, Sivakumar C: Quantum chemical calculation, performance of selective antimicrobial activity using molecular docking analysis, RDG and experimental (FT-IR, FT-Raman) investigation of 4-[{2-[3-(4-chlorophenyl)-5-(4-propan-2-yl) phenyl)-4, 5-dihydro- 1H- pyrazol-1-yl]-4-oxo-1, 3- thiazol-5(4H)-ylidene} methyl] benzonitrile. Heliyon. 2021 Jul 22;7(7):e07634. doi: 10.1016/j.heliyon.2021.e07634. eCollection 2021 Jul. [PubMed:34381897 ]
  5. Maitra A, Sarkar S, Leitner DM, Dawlaty JM: Electric Fields Influence Intramolecular Vibrational Energy Relaxation and Line Widths. J Phys Chem Lett. 2021 Aug 19;12(32):7818-7825. doi: 10.1021/acs.jpclett.1c02238. Epub 2021 Aug 11. [PubMed:34378946 ]
  6. Khatri J, Roy TK, Chatterjee K, Schwaab G, Havenith M: Vibrational Spectroscopy of Benzonitrile-(Water)1-2 Clusters in Helium Droplets. J Phys Chem A. 2021 Aug 19;125(32):6954-6963. doi: 10.1021/acs.jpca.1c04553. Epub 2021 Aug 6. [PubMed:34355893 ]
  7. Mody M, Petibon Y, Han P, Kuruppu D, Ma C, Yokell D, Neelamegam R, Normandin MD, Fakhri GE, Brownell AL: In vivo imaging of mGlu5 receptor expression in humans with Fragile X Syndrome towards development of a potential biomarker. Sci Rep. 2021 Aug 5;11(1):15897. doi: 10.1038/s41598-021-94967-y. [PubMed:34354107 ]
  8. Suhasini R, Karpagam R, Thirumoorthy K, Thiagarajan V: "Turn-on" unsymmetrical azine based fluorophore for the selective detection of diethylchlorophosphate via photoinduced electron transfer to intramolecular charge transfer pathway. Spectrochim Acta A Mol Biomol Spectrosc. 2021 Jul 21;263:120206. doi: 10.1016/j.saa.2021.120206. [PubMed:34325173 ]
  9. Takele WM, Piatkowski L, Wackenhut F, Gawinkowski S, Meixner AJ, Waluk J: Scouting for strong light-matter coupling signatures in Raman spectra. Phys Chem Chem Phys. 2021 Aug 12;23(31):16837-16846. doi: 10.1039/d1cp01863a. [PubMed:34323915 ]
  10. de Souza APM, Costa MCA, de Aguiar AR, Bressan GC, de Almeida Lima GD, Lima WP, Borsodi MPG, Bergmann BR, Ferreira MMC, Teixeira RR: Leishmanicidal and cytotoxic activities and 4D-QSAR of 2-arylidene indan-1,3-diones. Arch Pharm (Weinheim). 2021 Jul 29:e2100081. doi: 10.1002/ardp.202100081. [PubMed:34323311 ]
  11. Choi S, Park J, Kwak K, Cho M: Substituent Effects on the Vibrational Properties of the CN Stretch Mode of Aromatic Nitriles: IR Probes Useful for Time-resolved IR Spectroscopy. Chem Asian J. 2021 Sep 20;16(18):2626-2632. doi: 10.1002/asia.202100657. Epub 2021 Aug 3. [PubMed:34288497 ]