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Showing metabocard for 1,4-Benzodiazepine (HMDB0244195)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:22:27 UTC
Update Date2021-09-26 22:51:47 UTC
HMDB IDHMDB0244195
Secondary Accession NumbersNone
Metabolite Identification
Common Name1,4-Benzodiazepine
Description1,4-Benzodiazepine belongs to the class of organic compounds known as 1,4-benzodiazepines. These are organic compounds containing a benzene ring fused to a 1,4-azepine. Based on a literature review very few articles have been published on 1,4-Benzodiazepine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1,4-benzodiazepine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1,4-Benzodiazepine 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0244195 (1,4-Benzodiazepine)


  Mrv1652309102123222D          

 11 12  0  0  0  0            999 V2000
   -0.8374   -0.4033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8374   -1.2283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1230   -1.6408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5915   -1.2283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5915   -0.4033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1230    0.0092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2365    0.1111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0408   -0.0725    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3988   -0.8158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0408   -1.5591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2365   -1.7427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
M  END
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3D MOL for HMDB0244195 (1,4-Benzodiazepine)

HMDB0244195
     RDKit          3D
1,4-Benzodiazepine
 19 20  0  0  0  0  0  0  0  0999 V2000
   -2.7837    0.7985    0.3233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5166   -0.4975    0.3586 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2813   -1.1754    0.0942 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0343   -0.6278   -0.0182 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0384   -1.5724    0.0121 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3788   -1.1929   -0.0871 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6729    0.1423   -0.2155 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6488    1.0698   -0.2433 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3265    0.7139   -0.1470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5998    1.8584   -0.1982 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8667    1.8356    0.0032 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8118    1.1160    0.5632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3292   -1.1516    0.6210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2963   -2.2033   -0.0407 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7833   -2.6048    0.1127 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1763   -1.9233   -0.0648 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6810    0.4884   -0.2953 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8467    2.1475   -0.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1013    2.7787   -0.4331 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11  1  1  0
  9  4  1  0
  1 12  1  0
  2 13  1  0
  3 14  1  0
  5 15  1  0
  6 16  1  0
  7 17  1  0
  8 18  1  0
 10 19  1  0
M  END
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3D SDF for HMDB0244195 (1,4-Benzodiazepine)


  Mrv1652309102123222D          

 11 12  0  0  0  0            999 V2000
   -0.8374   -0.4033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8374   -1.2283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1230   -1.6408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5915   -1.2283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5915   -0.4033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1230    0.0092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2365    0.1111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0408   -0.0725    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3988   -0.8158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0408   -1.5591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2365   -1.7427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244195

> <DATABASE_NAME>
hmdb

> <SMILES>
N1C=CN=CC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C9H8N2/c1-2-4-9-8(3-1)7-10-5-6-11-9/h1-7,11H

> <INCHI_KEY>
GUJAGMICFDYKNR-UHFFFAOYSA-N

> <FORMULA>
C9H8N2

> <MOLECULAR_WEIGHT>
144.177

> <EXACT_MASS>
144.068748266

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
15.18501265143175

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1H-1,4-benzodiazepine

> <ALOGPS_LOGP>
1.44

> <JCHEM_LOGP>
1.2974037503333333

> <ALOGPS_LOGS>
-2.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.617610558551186

> <JCHEM_PKA_STRONGEST_BASIC>
19.320364616764127

> <JCHEM_POLAR_SURFACE_AREA>
24.39

> <JCHEM_REFRACTIVITY>
47.1982

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.23e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,4-benzodiazepine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0244195 (1,4-Benzodiazepine)

HMDB0244195
     RDKit          3D
1,4-Benzodiazepine
 19 20  0  0  0  0  0  0  0  0999 V2000
   -2.7837    0.7985    0.3233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5166   -0.4975    0.3586 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2813   -1.1754    0.0942 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0343   -0.6278   -0.0182 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0384   -1.5724    0.0121 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3788   -1.1929   -0.0871 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6729    0.1423   -0.2155 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6488    1.0698   -0.2433 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3265    0.7139   -0.1470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5998    1.8584   -0.1982 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8667    1.8356    0.0032 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8118    1.1160    0.5632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3292   -1.1516    0.6210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2963   -2.2033   -0.0407 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7833   -2.6048    0.1127 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1763   -1.9233   -0.0648 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6810    0.4884   -0.2953 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8467    2.1475   -0.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1013    2.7787   -0.4331 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11  1  1  0
  9  4  1  0
  1 12  1  0
  2 13  1  0
  3 14  1  0
  5 15  1  0
  6 16  1  0
  7 17  1  0
  8 18  1  0
 10 19  1  0
M  END
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PDB for HMDB0244195 (1,4-Benzodiazepine)

HEADER    PROTEIN                                 10-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-21         0                                  
HETATM    1  C   UNK     0      -1.563  -0.753   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.563  -2.293   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.230  -3.063   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.104  -2.293   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.104  -0.753   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.230   0.017   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.308   0.207   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       3.810  -0.135   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       4.478  -1.523   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.810  -2.910   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       2.308  -3.253   0.000  0.00  0.00           N+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    4                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for HMDB0244195 (1,4-Benzodiazepine)

COMPND    HMDB0244195
HETATM    1  C1  UNL     1      -2.784   0.798   0.323  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.517  -0.497   0.359  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.281  -1.175   0.094  1.00  0.00           N  
HETATM    4  C3  UNL     1       0.034  -0.628  -0.018  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.038  -1.572   0.012  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.379  -1.193  -0.087  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.673   0.142  -0.216  1.00  0.00           C  
HETATM    8  C7  UNL     1       1.649   1.070  -0.243  1.00  0.00           C  
HETATM    9  C8  UNL     1       0.326   0.714  -0.147  1.00  0.00           C  
HETATM   10  C9  UNL     1      -0.600   1.858  -0.198  1.00  0.00           C  
HETATM   11  N2  UNL     1      -1.867   1.836   0.003  1.00  0.00           N  
HETATM   12  H1  UNL     1      -3.812   1.116   0.563  1.00  0.00           H  
HETATM   13  H2  UNL     1      -3.329  -1.152   0.621  1.00  0.00           H  
HETATM   14  H3  UNL     1      -1.296  -2.203  -0.041  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.783  -2.605   0.113  1.00  0.00           H  
HETATM   16  H5  UNL     1       3.176  -1.923  -0.065  1.00  0.00           H  
HETATM   17  H6  UNL     1       3.681   0.488  -0.295  1.00  0.00           H  
HETATM   18  H7  UNL     1       1.847   2.147  -0.345  1.00  0.00           H  
HETATM   19  H8  UNL     1      -0.101   2.779  -0.433  1.00  0.00           H  
CONECT    1    2    2   11   12
CONECT    2    3   13
CONECT    3    4   14
CONECT    4    5    5    9
CONECT    5    6   15
CONECT    6    7    7   16
CONECT    7    8   17
CONECT    8    9    9   18
CONECT    9   10
CONECT   10   11   11   19
END
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SMILES for HMDB0244195 (1,4-Benzodiazepine)

N1C=CN=CC2=CC=CC=C12
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INCHI for HMDB0244195 (1,4-Benzodiazepine)

InChI=1S/C9H8N2/c1-2-4-9-8(3-1)7-10-5-6-11-9/h1-7,11H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,4-Benzodiazepine-2,5-dioneHMDB
Chemical FormulaC9H8N2
Average Molecular Weight144.177
Monoisotopic Molecular Weight144.068748266
IUPAC Name1H-1,4-benzodiazepine
Traditional Name1,4-benzodiazepine
CAS Registry NumberNot Available
SMILES
N1C=CN=CC2=CC=CC=C12
InChI Identifier
InChI=1S/C9H8N2/c1-2-4-9-8(3-1)7-10-5-6-11-9/h1-7,11H
InChI KeyGUJAGMICFDYKNR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,4-benzodiazepines. These are organic compounds containing a benzene ring fused to a 1,4-azepine.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzodiazepines
Sub Class1,4-benzodiazepines
Direct Parent1,4-benzodiazepines
Alternative Parents
Substituents
  • 1,4-benzodiazepine
  • Secondary aliphatic/aromatic amine
  • Benzenoid
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Secondary amine
  • Enamine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Imine
  • Amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.44ALOGPS
logP1.3ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)6.62ChemAxon
pKa (Strongest Basic)19.32ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area24.39 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity47.2 m³·mol⁻¹ChemAxon
Polarizability15.19 ųChemAxon
Number of Rings2ChemAxon
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-2H]-161.42230932474
DeepCCS[M+Na]+136.62230932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,4-BenzodiazepineN1C=CN=CC2=CC=CC=C122418.4Standard polar33892256
1,4-BenzodiazepineN1C=CN=CC2=CC=CC=C121604.3Standard non polar33892256
1,4-BenzodiazepineN1C=CN=CC2=CC=CC=C121627.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
1,4-Benzodiazepine,1TMS,isomer #1C[Si](C)(C)N1C=CN=CC2=CC=CC=C211707.2Semi standard non polar33892256
1,4-Benzodiazepine,1TMS,isomer #1C[Si](C)(C)N1C=CN=CC2=CC=CC=C211545.4Standard non polar33892256
1,4-Benzodiazepine,1TMS,isomer #1C[Si](C)(C)N1C=CN=CC2=CC=CC=C212546.7Standard polar33892256
1,4-Benzodiazepine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CN=CC2=CC=CC=C211894.9Semi standard non polar33892256
1,4-Benzodiazepine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CN=CC2=CC=CC=C211747.3Standard non polar33892256
1,4-Benzodiazepine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CN=CC2=CC=CC=C212789.5Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1,4-Benzodiazepine GC-MS (Non-derivatized) - 70eV, Positivesplash10-014l-2900000000-9e8c925446d31b83667c2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,4-Benzodiazepine 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 - 1,4-Benzodiazepine 10V, Positive-QTOFsplash10-0002-0900000000-95bbe2b7dfc9b9638ba02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Benzodiazepine 20V, Positive-QTOFsplash10-0002-0900000000-390c4505208ed84c377c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Benzodiazepine 40V, Positive-QTOFsplash10-00ou-9400000000-1cf529dfb4037d8b97c82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Benzodiazepine 10V, Negative-QTOFsplash10-0006-0900000000-a43e340bb2a95a9ab2aa2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Benzodiazepine 20V, Negative-QTOFsplash10-0006-0900000000-a43e340bb2a95a9ab2aa2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Benzodiazepine 40V, Negative-QTOFsplash10-0006-4900000000-0a79de14d2ea91d6c7192021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
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 ID130847
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound148431
PDB IDNot Available
ChEBI ID38431
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 References
  1. 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 ]