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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-08-28 20:13:26 UTC

Update Date

2021-09-26 22:48:54 UTC

HMDB ID

HMDB0242251

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(+)-Epibatidine

Description

Epibatidine belongs to the class of organic compounds known as epibatidine analogues. Epibatidine analogues are compounds containing an epibatidine moiety, with a structure characterized by a 2-chloropyridine moiety connected to an 7-azabicyclo[2.2.1]heptane in exo position. Based on a literature review a significant number of articles have been published on Epibatidine. This compound has been identified in human blood as reported by (PMID: 31557052 ). (+)-epibatidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (+)-Epibatidine 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 02241205382D          

 14 16  0  0  0  0            999 V2000
    5.0885   -0.4385    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.3004   -0.6826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1177   -1.4871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3297   -1.7312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7243   -1.1707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9069   -0.3662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6950   -0.1221    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9362   -1.4148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6411   -2.0402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9106   -1.6699    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1351   -2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5004   -1.3997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1407   -0.9495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9807   -0.1341    0.0000 N   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  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  8 13  1  0  0  0  0
 13 14  1  0  0  0  0
 10 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0242251

> <DATABASE_NAME>
hmdb

> <SMILES>
ClC1=CC=C(C=N1)C1CC2CCC1N2

> <INCHI_IDENTIFIER>
InChI=1S/C11H13ClN2/c12-11-4-1-7(6-13-11)9-5-8-2-3-10(9)14-8/h1,4,6,8-10,14H,2-3,5H2

> <INCHI_KEY>
NLPRAJRHRHZCQQ-UHFFFAOYSA-N

> <FORMULA>
C11H13ClN2

> <MOLECULAR_WEIGHT>
208.687

> <EXACT_MASS>
208.076726133

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
22.0612417407603

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(6-chloropyridin-3-yl)-7-azabicyclo[2.2.1]heptane

> <ALOGPS_LOGP>
1.98

> <JCHEM_LOGP>
1.8435768270000001

> <ALOGPS_LOGS>
-2.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.53983127735407

> <JCHEM_POLAR_SURFACE_AREA>
24.92

> <JCHEM_REFRACTIVITY>
57.391600000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.67e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
epibatidine

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1 Cl   UNK     0       9.499  -0.819   0.000  0.00  0.00          Cl+0
HETATM    2  C   UNK     0       8.027  -1.274   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.686  -2.776   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.215  -3.232   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.085  -2.185   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.426  -0.684   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       6.897  -0.228   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.614  -2.641   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.063  -3.808   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.700  -3.117   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.252  -3.846   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.934  -2.613   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.129  -1.772   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       1.831  -0.250   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
CONECT    8    5    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8   14                                                  
CONECT   14   13   10                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END

COMPND    HMDB0242582
HETATM    1 CL1  UNL     1       5.631   1.218   0.385  1.00  0.00          CL  
HETATM    2  C1  UNL     1       3.954   0.692   0.205  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.935   1.602   0.029  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.649   1.190  -0.108  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.317  -0.147  -0.077  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.021  -0.681  -0.215  1.00  0.00           C  
HETATM    7  C6  UNL     1      -0.773  -0.296  -1.443  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.991   0.401  -0.892  1.00  0.00           C  
HETATM    9  C8  UNL     1      -2.908  -0.564  -0.163  1.00  0.00           C  
HETATM   10  C9  UNL     1      -2.071  -0.978   1.056  1.00  0.00           C  
HETATM   11  C10 UNL     1      -0.871  -0.114   0.927  1.00  0.00           C  
HETATM   12  N1  UNL     1      -1.398   1.092   0.269  1.00  0.00           N  
HETATM   13  C11 UNL     1       2.366  -1.029   0.101  1.00  0.00           C  
HETATM   14  N2  UNL     1       3.639  -0.618   0.237  1.00  0.00           N  
HETATM   15  H1  UNL     1       3.188   2.670   0.003  1.00  0.00           H  
HETATM   16  H2  UNL     1       0.839   1.886  -0.246  1.00  0.00           H  
HETATM   17  H3  UNL     1      -0.011  -1.786  -0.154  1.00  0.00           H  
HETATM   18  H4  UNL     1      -1.050  -1.174  -2.076  1.00  0.00           H  
HETATM   19  H5  UNL     1      -0.252   0.416  -2.100  1.00  0.00           H  
HETATM   20  H6  UNL     1      -2.491   1.068  -1.573  1.00  0.00           H  
HETATM   21  H7  UNL     1      -3.190  -1.430  -0.766  1.00  0.00           H  
HETATM   22  H8  UNL     1      -3.746   0.027   0.230  1.00  0.00           H  
HETATM   23  H9  UNL     1      -1.788  -2.038   0.891  1.00  0.00           H  
HETATM   24  H10 UNL     1      -2.634  -0.857   1.989  1.00  0.00           H  
HETATM   25  H11 UNL     1      -0.312   0.092   1.820  1.00  0.00           H  
HETATM   26  H12 UNL     1      -2.228   1.465   0.799  1.00  0.00           H  
HETATM   27  H13 UNL     1       2.216  -2.105   0.140  1.00  0.00           H  
CONECT    1    2
CONECT    2    3    3   14
CONECT    3    4   15
CONECT    4    5    5   16
CONECT    5    6   13
CONECT    6    7   11   17
CONECT    7    8   18   19
CONECT    8    9   12   20
CONECT    9   10   21   22
CONECT   10   11   23   24
CONECT   11   12   25
CONECT   12   26
CONECT   13   14   14   27
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₁H₁₃ClN₂

Average Molecular Weight

208.687

Monoisotopic Molecular Weight

208.076726133

IUPAC Name

2-(6-chloropyridin-3-yl)-7-azabicyclo[2.2.1]heptane

Traditional Name

epibatidine

CAS Registry Number

Not Available

SMILES

ClC1=CC=C(C=N1)C1CC2CCC1N2

InChI Identifier

InChI=1S/C11H13ClN2/c12-11-4-1-7(6-13-11)9-5-8-2-3-10(9)14-8/h1,4,6,8-10,14H,2-3,5H2

InChI Key

NLPRAJRHRHZCQQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as epibatidine analogues. Epibatidine analogues are compounds containing an epibatidine moiety, with a structure characterized by a 2-chloropyridine moiety connected to an 7-azabicyclo[2.2.1]Heptane in exo position.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Epibatidine analogues

Sub Class

Not Available

Direct Parent

Epibatidine analogues

Alternative Parents

Substituents

Epibatidine-skeleton
Pyrrolidinylpyridine
2-halopyridine
Aralkylamine
Aryl chloride
Aryl halide
Pyridine
Heteroaromatic compound
Pyrrolidine
Azacycle
Secondary aliphatic amine
Secondary amine
Organoheterocyclic compound
Amine
Organonitrogen compound
Organochloride
Organohalogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Cellular substructure

Cytoplasm (HMDB: HMDB0242251)
Extracellular (HMDB: HMDB0242251)

Source

Exogenous

Exogenous (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	1.98	ALOGPS
logP	1.84	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Basic)	10.54	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	24.92 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	57.39 m³·mol⁻¹	ChemAxon
Polarizability	22.06 Å³	ChemAxon
Number of Rings	3	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]+	149.21	30932474
DeepCCS	[M-H]-	146.852	30932474
DeepCCS	[M-2H]-	181.513	30932474
DeepCCS	[M+Na]+	156.53	30932474
AllCCS	[M+H]+	148.5	32859911
AllCCS	[M+H-H2O]+	144.5	32859911
AllCCS	[M+NH4]+	152.2	32859911
AllCCS	[M+Na]+	153.2	32859911
AllCCS	[M-H]-	148.0	32859911
AllCCS	[M+Na-2H]-	148.3	32859911
AllCCS	[M+HCOO]-	148.6	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.7598 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.0 minutes	32390414

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(+)-Epibatidine,1TMS,isomer #1	C[Si](C)(C)N1C2CCC1C(C1=CC=C(Cl)N=C1)C2	1847.1	Semi standard non polar	33892256
(+)-Epibatidine,1TMS,isomer #1	C[Si](C)(C)N1C2CCC1C(C1=CC=C(Cl)N=C1)C2	2012.6	Standard non polar	33892256
(+)-Epibatidine,1TMS,isomer #1	C[Si](C)(C)N1C2CCC1C(C1=CC=C(Cl)N=C1)C2	2436.9	Standard polar	33892256
(+)-Epibatidine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2CCC1C(C1=CC=C(Cl)N=C1)C2	2116.2	Semi standard non polar	33892256
(+)-Epibatidine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2CCC1C(C1=CC=C(Cl)N=C1)C2	2279.9	Standard non polar	33892256
(+)-Epibatidine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2CCC1C(C1=CC=C(Cl)N=C1)C2	2589.2	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (+)-Epibatidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-017l-9800000000-f9be6efcb287e3c5e76d	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (+)-Epibatidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (+)-Epibatidine 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 - (+)-Epibatidine 10V, Positive-QTOF	splash10-0a4i-0190000000-046959b515e82db7e6fb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 20V, Positive-QTOF	splash10-0a4i-3390000000-8f766845caae11ffc884	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 40V, Positive-QTOF	splash10-0fsi-8900000000-8bd101dee7036183998d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 10V, Negative-QTOF	splash10-0a4i-0190000000-8d4deb0cede3f9c09d4f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 20V, Negative-QTOF	splash10-0a4i-0590000000-9918548508966d5ecabf	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 40V, Negative-QTOF	splash10-05fu-2900000000-26082d9becf367cbadfd	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 10V, Positive-QTOF	splash10-0a4i-0090000000-535cc7ec7e9fa7416616	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 20V, Positive-QTOF	splash10-0a4i-0090000000-535cc7ec7e9fa7416616	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 40V, Positive-QTOF	splash10-057l-0920000000-669298ad58e120ed70c3	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 10V, Negative-QTOF	splash10-0a4i-0090000000-31fc562f3420cf79d8c8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 20V, Negative-QTOF	splash10-0a4i-1190000000-4c8b54092b4670dea254	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (+)-Epibatidine 40V, Negative-QTOF	splash10-001i-9200000000-bb84d221e09ef401c376	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

C00028244

Chemspider ID

1167

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Epibatidine

METLIN ID

Not Available

PubChem Compound

1204

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

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 (+)-Epibatidine (HMDB0242251)

MOL for HMDB0242251 ((+)-Epibatidine)

3D MOL for HMDB0242251 ((+)-Epibatidine)

3D SDF for HMDB0242251 ((+)-Epibatidine)

3D-SDF for HMDB0242251 ((+)-Epibatidine)

PDB for HMDB0242251 ((+)-Epibatidine)

3D PDB for HMDB0242251 ((+)-Epibatidine)

SMILES for HMDB0242251 ((+)-Epibatidine)

INCHI for HMDB0242251 ((+)-Epibatidine)

Structure for HMDB0242251 ((+)-Epibatidine)

3D Structure for HMDB0242251 ((+)-Epibatidine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra