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Showing metabocard for 12,13-epoxy-9-alkoxy-10E-octadecenoate (HMDB0062289)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-03-16 03:41:49 UTC
Update Date2023-02-21 17:30:48 UTC
HMDB IDHMDB0062289
Secondary Accession Numbers
  • HMDB62289
Metabolite Identification
Common Name12,13-epoxy-9-alkoxy-10E-octadecenoate
Description2-bromopyridine, also known as 2-pyridyl bromide, belongs to the class of organic compounds known as 2-halopyridines. These are organic compounds containing a pyridine ring substituted at the 2-position by a halogen atom. It is a colorless liquid that is used as an intermediate in organic synthesis. 2-bromopyridine is a moderately basic compound (based on its pKa). 2-Bromopyridine is an organic compound with the formula BrC5H4N. Pyrithione can be prepared in a two-step synthesis from 2-bromopyridine by oxidation to the N-oxide with a suitable peracid followed by substitution using either sodium dithionite or sodium sulfide with sodium hydroxide to introduce the thiol functional group. It reacts with butyllithium to give 2-lithiopyridine, a versatile reagent. It can be prepared from 2-aminopyridine via diazotization followed by bromination.
Structure
Data?1677000648
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0062289 (12,13-epoxy-9-alkoxy-10E-octadecenoate)


  Mrv1572004221606472D          

  7  7  0  0  0  0            999 V2000
   -0.0000    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  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
    1.4289   -0.0000    0.0000 C   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
    0.7145    2.0625    0.0000 Br  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
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  6  5  1  0  0  0  0
  7  4  2  0  0  0  0
  7  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0062289 (12,13-epoxy-9-alkoxy-10E-octadecenoate)

HMDB0062289
     RDKit          3D
12,13-epoxy-9-alkoxy-10E-octadecenoate
 11 11  0  0  0  0  0  0  0  0999 V2000
    3.2251   -0.8605    0.0846 Br  0  0  0  0  0  0  0  0  0  0  0  0
    1.3433   -0.4943    0.0484 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8903    0.8032   -0.0778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4577    1.1225   -0.1092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3488    0.0779   -0.0080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8881   -1.2173    0.1180 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4217   -1.4625    0.1422 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6465    1.5935   -0.1543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7934    2.1633   -0.2104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4073    0.3008   -0.0300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6316   -2.0266    0.1964 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  2  1  0
  3  8  1  0
  4  9  1  0
  5 10  1  0
  6 11  1  0
M  END
Download

3D SDF for HMDB0062289 (12,13-epoxy-9-alkoxy-10E-octadecenoate)


  Mrv1572004221606472D          

  7  7  0  0  0  0            999 V2000
   -0.0000    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  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
    1.4289   -0.0000    0.0000 C   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
    0.7145    2.0625    0.0000 Br  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
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  6  5  1  0  0  0  0
  7  4  2  0  0  0  0
  7  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0062289

> <DATABASE_NAME>
hmdb

> <SMILES>
BrC1=CC=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H4BrN/c6-5-3-1-2-4-7-5/h1-4H

> <INCHI_KEY>
IMRWILPUOVGIMU-UHFFFAOYSA-N

> <FORMULA>
C5H4BrN

> <MOLECULAR_WEIGHT>
157.998

> <EXACT_MASS>
156.952712

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
11.625292804619416

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-bromopyridine

> <ALOGPS_LOGP>
1.62

> <JCHEM_LOGP>
1.7298480286666664

> <ALOGPS_LOGS>
-0.39

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
1.4740985609818051

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
32.366099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.39e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-bromopyridine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0062289 (12,13-epoxy-9-alkoxy-10E-octadecenoate)

HMDB0062289
     RDKit          3D
12,13-epoxy-9-alkoxy-10E-octadecenoate
 11 11  0  0  0  0  0  0  0  0999 V2000
    3.2251   -0.8605    0.0846 Br  0  0  0  0  0  0  0  0  0  0  0  0
    1.3433   -0.4943    0.0484 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8903    0.8032   -0.0778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4577    1.1225   -0.1092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3488    0.0779   -0.0080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8881   -1.2173    0.1180 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4217   -1.4625    0.1422 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6465    1.5935   -0.1543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7934    2.1633   -0.2104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4073    0.3008   -0.0300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6316   -2.0266    0.1964 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  2  1  0
  3  8  1  0
  4  9  1  0
  5 10  1  0
  6 11  1  0
M  END
Download

PDB for HMDB0062289 (12,13-epoxy-9-alkoxy-10E-octadecenoate)

HEADER    PROTEIN                                 22-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-APR-16         0                                  
HETATM    1  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+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   2.310   0.000  0.00  0.00           C+0
HETATM    6 Br   UNK     0       1.334   3.850   0.000  0.00  0.00          Br+0
HETATM    7  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    7                                                       
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    4    5                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0062289 (12,13-epoxy-9-alkoxy-10E-octadecenoate)

COMPND    HMDB0062289
HETATM    1 BR1  UNL     1       3.225  -0.860   0.085  1.00  0.00          BR  
HETATM    2  C1  UNL     1       1.343  -0.494   0.048  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.890   0.803  -0.078  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.458   1.122  -0.109  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.349   0.078  -0.008  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.888  -1.217   0.118  1.00  0.00           C  
HETATM    7  N1  UNL     1       0.422  -1.463   0.142  1.00  0.00           N  
HETATM    8  H1  UNL     1       1.646   1.593  -0.154  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.793   2.163  -0.210  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.407   0.301  -0.030  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.632  -2.027   0.196  1.00  0.00           H  
CONECT    1    2
CONECT    2    3    3    7
CONECT    3    4    8
CONECT    4    5    5    9
CONECT    5    6   10
CONECT    6    7    7   11
END
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SMILES for HMDB0062289 (12,13-epoxy-9-alkoxy-10E-octadecenoate)

BrC1=CC=CC=N1
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INCHI for HMDB0062289 (12,13-epoxy-9-alkoxy-10E-octadecenoate)

InChI=1S/C5H4BrN/c6-5-3-1-2-4-7-5/h1-4H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Pyridyl bromideChEBI
alpha-BromopyridineChEBI
O-BromopyridineChEBI
a-BromopyridineGenerator
Α-bromopyridineGenerator
12,13-Epoxy-9-alkoxy-10E-octadecenoic acidGenerator
Chemical FormulaC5H4BrN
Average Molecular Weight157.998
Monoisotopic Molecular Weight156.952712
IUPAC Name2-bromopyridine
Traditional Name2-bromopyridine
CAS Registry Number109-04-6
SMILES
BrC1=CC=CC=N1
InChI Identifier
InChI=1S/C5H4BrN/c6-5-3-1-2-4-7-5/h1-4H
InChI KeyIMRWILPUOVGIMU-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 2-halopyridines. These are organic compounds containing a pyridine ring substituted at the 2-position by a halogen atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassHalopyridines
Direct Parent2-halopyridines
Alternative Parents
Substituents
  • 2-halopyridine
  • Aryl halide
  • Aryl bromide
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organobromide
  • Organohalogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility63.9 g/lALOGPS
LogP1.62ALOGPS
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.62ALOGPS
logP1.73ChemAxon
logS-0.39ALOGPS
pKa (Strongest Basic)1.47ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.89 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity32.37 m³·mol⁻¹ChemAxon
Polarizability11.63 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+122.78630932474
DeepCCS[M-H]-119.98730932474
DeepCCS[M-2H]-156.3230932474
DeepCCS[M+Na]+131.14430932474
AllCCS[M+H]+130.832859911
AllCCS[M+H-H2O]+125.932859911
AllCCS[M+NH4]+135.432859911
AllCCS[M+Na]+136.732859911
AllCCS[M-H]-128.132859911
AllCCS[M+Na-2H]-131.232859911
AllCCS[M+HCOO]-134.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
12,13-epoxy-9-alkoxy-10E-octadecenoateBrC1=CC=CC=N11512.0Standard polar33892256
12,13-epoxy-9-alkoxy-10E-octadecenoateBrC1=CC=CC=N1975.6Standard non polar33892256
12,13-epoxy-9-alkoxy-10E-octadecenoateBrC1=CC=CC=N11021.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4i-4900000000-7cc2e49efc604ad170f42017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 10V, Positive-QTOFsplash10-0a4i-0900000000-b44345810f60580f81ab2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 20V, Positive-QTOFsplash10-0a4i-0900000000-34976ebea62781f99a352016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 40V, Positive-QTOFsplash10-0kcr-4900000000-4e904fa4201e333ddcd82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 10V, Negative-QTOFsplash10-0a4i-0900000000-a4c936c9aad5ac71a1672016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 20V, Negative-QTOFsplash10-0a4i-0900000000-99f2016205194a347ed22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 40V, Negative-QTOFsplash10-0zi0-6900000000-63da9ce37f15cd3d96362016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 10V, Negative-QTOFsplash10-0a4i-0900000000-083389b8b2a38ee935e82021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 20V, Negative-QTOFsplash10-0a4i-0900000000-083389b8b2a38ee935e82021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 40V, Negative-QTOFsplash10-0zfr-9800000000-eefa70a8b3d063ea9a212021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 10V, Positive-QTOFsplash10-0a4i-0900000000-132dc1ec168be09e6e792021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 20V, Positive-QTOFsplash10-0a4i-0900000000-ae79753eb5c3f39873f72021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 12,13-epoxy-9-alkoxy-10E-octadecenoate 40V, Positive-QTOFsplash10-0kbf-2900000000-a9d8958f08fb33912e152021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2-Bromopyridine
METLIN IDNot Available
PubChem Compound7973
PDB IDNot Available
ChEBI ID51574
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available