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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 03:33:35 UTC

Update Date

2021-09-26 22:59:41 UTC

HMDB ID

HMDB0249074

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Benzyl nicotinate

Description

benzyl nicotinate, also known as pycaril or pykaryl, belongs to the class of organic compounds known as benzyloxycarbonyls. These are organic compounds containing a carbonyl group substituted with a benzyloxyl group. Based on a literature review a significant number of articles have been published on benzyl nicotinate. This compound has been identified in human blood as reported by (PMID: 31557052 ). Benzyl nicotinate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Benzyl nicotinate is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 05031419002D          

 16 17  0  0  0  0            999 V2000
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  2  0  0  0  0
  7  4  2  0  0  0  0
  8  4  1  0  0  0  0
 11  5  2  0  0  0  0
 11  6  1  0  0  0  0
 11 10  1  0  0  0  0
 12  7  1  0  0  0  0
 12  9  2  0  0  0  0
 13 12  1  0  0  0  0
 14  8  2  0  0  0  0
 14  9  1  0  0  0  0
 15 13  2  0  0  0  0
 16 10  1  0  0  0  0
 16 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0249074

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C(OCC1=CC=CC=C1)C1=CN=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C13H11NO2/c15-13(12-7-4-8-14-9-12)16-10-11-5-2-1-3-6-11/h1-9H,10H2

> <INCHI_KEY>
KVYGGMBOZFWZBQ-UHFFFAOYSA-N

> <FORMULA>
C13H11NO2

> <MOLECULAR_WEIGHT>
213.2319

> <EXACT_MASS>
213.078978601

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
22.390105431669106

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
benzyl pyridine-3-carboxylate

> <ALOGPS_LOGP>
2.40

> <JCHEM_LOGP>
2.4835234703333335

> <ALOGPS_LOGS>
-2.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
3.240598242853329

> <JCHEM_POLAR_SURFACE_AREA>
39.19

> <JCHEM_REFRACTIVITY>
60.53900000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.04e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
benzyl nicotinate

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    7    8                                                       
CONECT    5    2   11                                                       
CONECT    6    3   11                                                       
CONECT    7    4   12                                                       
CONECT    8    4   14                                                       
CONECT    9   12   14                                                       
CONECT   10   11   16                                                       
CONECT   11    5    6   10                                                  
CONECT   12    7    9   13                                                  
CONECT   13   12   15   16                                                  
CONECT   14    8    9                                                       
CONECT   15   13                                                            
CONECT   16   10   13                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

COMPND    HMDB0249074
HETATM    1  O1  UNL     1       1.420  -1.918   1.683  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.408  -0.941   0.892  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.171  -0.480   0.495  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.047  -1.052   0.934  1.00  0.00           C  
HETATM    5  C3  UNL     1      -2.221  -0.386   0.373  1.00  0.00           C  
HETATM    6  C4  UNL     1      -3.498  -0.794   0.678  1.00  0.00           C  
HETATM    7  C5  UNL     1      -4.615  -0.180   0.159  1.00  0.00           C  
HETATM    8  C6  UNL     1      -4.451   0.885  -0.699  1.00  0.00           C  
HETATM    9  C7  UNL     1      -3.164   1.322  -1.028  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.072   0.676  -0.485  1.00  0.00           C  
HETATM   11  C9  UNL     1       2.662  -0.353   0.441  1.00  0.00           C  
HETATM   12  C10 UNL     1       2.699   0.723  -0.429  1.00  0.00           C  
HETATM   13  C11 UNL     1       3.910   1.248  -0.830  1.00  0.00           C  
HETATM   14  C12 UNL     1       5.080   0.672  -0.341  1.00  0.00           C  
HETATM   15  N1  UNL     1       5.044  -0.386   0.514  1.00  0.00           N  
HETATM   16  C13 UNL     1       3.852  -0.882   0.892  1.00  0.00           C  
HETATM   17  H1  UNL     1      -1.112  -2.140   0.639  1.00  0.00           H  
HETATM   18  H2  UNL     1      -1.080  -0.978   2.056  1.00  0.00           H  
HETATM   19  H3  UNL     1      -3.684  -1.639   1.359  1.00  0.00           H  
HETATM   20  H4  UNL     1      -5.612  -0.530   0.424  1.00  0.00           H  
HETATM   21  H5  UNL     1      -5.303   1.412  -1.143  1.00  0.00           H  
HETATM   22  H6  UNL     1      -2.996   2.154  -1.699  1.00  0.00           H  
HETATM   23  H7  UNL     1      -1.084   1.012  -0.737  1.00  0.00           H  
HETATM   24  H8  UNL     1       1.779   1.154  -0.796  1.00  0.00           H  
HETATM   25  H9  UNL     1       3.991   2.087  -1.508  1.00  0.00           H  
HETATM   26  H10 UNL     1       6.054   1.037  -0.618  1.00  0.00           H  
HETATM   27  H11 UNL     1       3.868  -1.723   1.573  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   11
CONECT    3    4
CONECT    4    5   17   18
CONECT    5    6    6   10
CONECT    6    7   19
CONECT    7    8    8   20
CONECT    8    9   21
CONECT    9   10   10   22
CONECT   10   23
CONECT   11   12   12   16
CONECT   12   13   24
CONECT   13   14   14   25
CONECT   14   15   26
CONECT   15   16   16
CONECT   16   27
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-Pyridinecarboxylic acid phenylmethyl ester	ChEBI
Benzyl pyridine-3-carboxylate	ChEBI
Nicotinic acid benzyl ester	ChEBI
Phenylmethyl 3-pyridinecarboxylate	ChEBI
Pycaril	ChEBI
Pykaryl	ChEBI
Rubriment	ChEBI
3-Pyridinecarboxylate phenylmethyl ester	Generator
Benzyl pyridine-3-carboxylic acid	Generator
Nicotinate benzyl ester	Generator
Phenylmethyl 3-pyridinecarboxylic acid	Generator
Benzyl nicotinic acid	Generator
Nicotinic acid benzyl ester, hexafluorosilicate (2-) (2:1)	MeSH
Pyridine-3-carboxylic acid benzyl ester	MeSH

Chemical Formula

C₁₃H₁₁NO₂

Average Molecular Weight

213.2319

Monoisotopic Molecular Weight

213.078978601

IUPAC Name

benzyl pyridine-3-carboxylate

Traditional Name

benzyl nicotinate

CAS Registry Number

Not Available

SMILES

O=C(OCC1=CC=CC=C1)C1=CN=CC=C1

InChI Identifier

InChI=1S/C13H11NO2/c15-13(12-7-4-8-14-9-12)16-10-11-5-2-1-3-6-11/h1-9H,10H2

InChI Key

KVYGGMBOZFWZBQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzyloxycarbonyls. These are organic compounds containing a carbonyl group substituted with a benzyloxyl group.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzyloxycarbonyls

Direct Parent

Benzyloxycarbonyls

Alternative Parents

Substituents

Benzyloxycarbonyl
Pyridine carboxylic acid
Pyridine carboxylic acid or derivatives
Pyridine
Heteroaromatic compound
Carboxylic acid ester
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Azacycle
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

carboxylic ester (CHEBI:31268 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	2.4	ALOGPS
logP	2.48	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Basic)	3.24	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	39.19 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	60.54 m³·mol⁻¹	ChemAxon
Polarizability	22.39 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	146.214	30932474
DeepCCS	[M-H]-	143.818	30932474
DeepCCS	[M-2H]-	177.56	30932474
DeepCCS	[M+Na]+	152.292	30932474
AllCCS	[M+H]+	148.1	32859911
AllCCS	[M+H-H2O]+	143.9	32859911
AllCCS	[M+NH4]+	152.0	32859911
AllCCS	[M+Na]+	153.1	32859911
AllCCS	[M-H]-	150.8	32859911
AllCCS	[M+Na-2H]-	150.7	32859911
AllCCS	[M+HCOO]-	150.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Benzyl nicotinate	O=C(OCC1=CC=CC=C1)C1=CN=CC=C1	2665.4	Standard polar	33892256
Benzyl nicotinate	O=C(OCC1=CC=CC=C1)C1=CN=CC=C1	1851.0	Standard non polar	33892256
Benzyl nicotinate	O=C(OCC1=CC=CC=C1)C1=CN=CC=C1	1792.8	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Benzyl nicotinate GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9200000000-7fd349a3c0bf94c71efd	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Benzyl nicotinate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 10V, Positive-QTOF	splash10-03dl-5090000000-04c72541b15d19b6abc1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 20V, Positive-QTOF	splash10-0006-9010000000-71c9e8a3e73f0e901718	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 40V, Positive-QTOF	splash10-0006-9000000000-3aaa81e9d8f6765d27f4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 10V, Negative-QTOF	splash10-03di-1090000000-b050d4e026d0cea4a3ce	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 20V, Negative-QTOF	splash10-03mi-9770000000-3f721ea815e97ba58506	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 40V, Negative-QTOF	splash10-004i-9100000000-dca1e0b725258575209a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 10V, Positive-QTOF	splash10-03di-3190000000-19600f308a2d5b113acd	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 20V, Positive-QTOF	splash10-0006-9100000000-32fb161c5efede741a88	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 40V, Positive-QTOF	splash10-052f-9300000000-2df6b590d039172cb152	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 10V, Negative-QTOF	splash10-03di-0090000000-1bc63a3967eb8ad02d83	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 20V, Negative-QTOF	splash10-03di-4390000000-b9c1457355d581ed58e7	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Benzyl nicotinate 40V, Negative-QTOF	splash10-004i-9600000000-071e79c67979d58147fa	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

6923

KEGG Compound ID

C12865

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

7191

PDB ID

Not Available

ChEBI ID

31268

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1222581

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Benzyl nicotinate (HMDB0249074)

MOL for HMDB0249074 (Benzyl nicotinate)

3D MOL for HMDB0249074 (Benzyl nicotinate)

3D SDF for HMDB0249074 (Benzyl nicotinate)

3D-SDF for HMDB0249074 (Benzyl nicotinate)

PDB for HMDB0249074 (Benzyl nicotinate)

3D PDB for HMDB0249074 (Benzyl nicotinate)

SMILES for HMDB0249074 (Benzyl nicotinate)

INCHI for HMDB0249074 (Benzyl nicotinate)

Structure for HMDB0249074 (Benzyl nicotinate)

3D Structure for HMDB0249074 (Benzyl nicotinate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra