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Showing metabocard for 3,5-Dinitrophenol (HMDB0246070)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:06:32 UTC
Update Date2021-09-26 22:54:55 UTC
HMDB IDHMDB0246070
Secondary Accession NumbersNone
Metabolite Identification
Common Name3,5-Dinitrophenol
Description3,5-Dinitrophenol belongs to the class of organic compounds known as dinitrophenols. These are organic aromatic compounds containing a benzene that carries a single phenol group and exactly two nitro groups. Based on a literature review very few articles have been published on 3,5-Dinitrophenol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3,5-dinitrophenol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3,5-Dinitrophenol 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 HMDB0246070 (3,5-Dinitrophenol)


  Mrv1652311211610322D          

 13 13  0  0  0  0            999 V2000
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  5  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
    1.4289    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
    2.1434   -0.4125    0.0000 O   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    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  5  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  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  9 13  2  0  0  0  0
  4 13  1  0  0  0  0
M  CHG  4   2   1   3  -1  10   1  12  -1
M  END
Download

3D MOL for HMDB0246070 (3,5-Dinitrophenol)

HMDB0246070
     RDKit          3D
3,5-Dinitrophenol
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.6064   -2.1780    0.3729 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4943   -0.9851    0.0711 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.6115   -0.2547   -0.1970 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.2150   -0.3995    0.0089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1059    0.9337   -0.3296 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1417    1.5054   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2056    2.8512   -0.7354 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2676    0.7561   -0.1168 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1568   -0.5768    0.2215 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3282   -1.3218    0.4972 N   0  0  0  0  0  4  0  0  0  0  0  0
    2.2783   -2.5271    0.8067 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5717   -0.7396    0.4333 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.0761   -1.1625    0.2870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0177    1.5130   -0.5441 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1642    3.5234    0.0392 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2477    1.2545   -0.1774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2349   -2.1924    0.5433 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  9 13  2  0
 13  4  1  0
  5 14  1  0
  7 15  1  0
  8 16  1  0
 13 17  1  0
M  CHG  4   2   1   3  -1  10   1  12  -1
M  END
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3D SDF for HMDB0246070 (3,5-Dinitrophenol)


  Mrv1652311211610322D          

 13 13  0  0  0  0            999 V2000
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  5  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
    1.4289    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
    2.1434   -0.4125    0.0000 O   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    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  5  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  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  9 13  2  0  0  0  0
  4 13  1  0  0  0  0
M  CHG  4   2   1   3  -1  10   1  12  -1
M  END
> <DATABASE_ID>
HMDB0246070

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC(=CC(=C1)[N+]([O-])=O)[N+]([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H4N2O5/c9-6-2-4(7(10)11)1-5(3-6)8(12)13/h1-3,9H

> <INCHI_KEY>
UEMBNLWZFIWQFL-UHFFFAOYSA-N

> <FORMULA>
C6H4N2O5

> <MOLECULAR_WEIGHT>
184.107

> <EXACT_MASS>
184.012021237

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
14.636031949101062

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,5-dinitrophenol

> <ALOGPS_LOGP>
1.76

> <JCHEM_LOGP>
1.549648873

> <ALOGPS_LOGS>
-2.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.237725627422958

> <JCHEM_PKA_STRONGEST_BASIC>
-6.242588696855472

> <JCHEM_POLAR_SURFACE_AREA>
106.51000000000002

> <JCHEM_REFRACTIVITY>
40.6799

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.28e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,5-dinitrophenol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0246070 (3,5-Dinitrophenol)

HMDB0246070
     RDKit          3D
3,5-Dinitrophenol
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.6064   -2.1780    0.3729 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4943   -0.9851    0.0711 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.6115   -0.2547   -0.1970 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.2150   -0.3995    0.0089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1059    0.9337   -0.3296 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1417    1.5054   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2056    2.8512   -0.7354 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2676    0.7561   -0.1168 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1568   -0.5768    0.2215 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3282   -1.3218    0.4972 N   0  0  0  0  0  4  0  0  0  0  0  0
    2.2783   -2.5271    0.8067 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5717   -0.7396    0.4333 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.0761   -1.1625    0.2870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0177    1.5130   -0.5441 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1642    3.5234    0.0392 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2477    1.2545   -0.1774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2349   -2.1924    0.5433 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  9 13  2  0
 13  4  1  0
  5 14  1  0
  7 15  1  0
  8 16  1  0
 13 17  1  0
M  CHG  4   2   1   3  -1  10   1  12  -1
M  END
Download

PDB for HMDB0246070 (3,5-Dinitrophenol)

HEADER    PROTEIN                                 21-NOV-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-NOV-16         0                                  
HETATM    1  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM    2  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+1
HETATM    3  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O-1
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334  -0.770   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  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+1
HETATM   11  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O-1
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   13                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    9    4                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for HMDB0246070 (3,5-Dinitrophenol)

COMPND    HMDB0246070
HETATM    1  O1  UNL     1      -2.606  -2.178   0.373  1.00  0.00           O  
HETATM    2  N1  UNL     1      -2.494  -0.985   0.071  1.00  0.00           N1+
HETATM    3  O2  UNL     1      -3.612  -0.255  -0.197  1.00  0.00           O1-
HETATM    4  C1  UNL     1      -1.215  -0.399   0.009  1.00  0.00           C  
HETATM    5  C2  UNL     1      -1.106   0.934  -0.330  1.00  0.00           C  
HETATM    6  C3  UNL     1       0.142   1.505  -0.390  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.206   2.851  -0.735  1.00  0.00           O  
HETATM    8  C4  UNL     1       1.268   0.756  -0.117  1.00  0.00           C  
HETATM    9  C5  UNL     1       1.157  -0.577   0.222  1.00  0.00           C  
HETATM   10  N2  UNL     1       2.328  -1.322   0.497  1.00  0.00           N1+
HETATM   11  O4  UNL     1       2.278  -2.527   0.807  1.00  0.00           O  
HETATM   12  O5  UNL     1       3.572  -0.740   0.433  1.00  0.00           O1-
HETATM   13  C6  UNL     1      -0.076  -1.162   0.287  1.00  0.00           C  
HETATM   14  H1  UNL     1      -2.018   1.513  -0.544  1.00  0.00           H  
HETATM   15  H2  UNL     1       0.164   3.523   0.039  1.00  0.00           H  
HETATM   16  H3  UNL     1       2.248   1.254  -0.177  1.00  0.00           H  
HETATM   17  H4  UNL     1      -0.235  -2.192   0.543  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5   13
CONECT    5    6   14
CONECT    6    7    8    8
CONECT    7   15
CONECT    8    9   16
CONECT    9   10   13   13
CONECT   10   11   11   12
CONECT   13   17
END
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SMILES for HMDB0246070 (3,5-Dinitrophenol)

OC1=CC(=CC(=C1)[N+]([O-])=O)[N+]([O-])=O
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INCHI for HMDB0246070 (3,5-Dinitrophenol)

InChI=1S/C6H4N2O5/c9-6-2-4(7(10)11)1-5(3-6)8(12)13/h1-3,9H
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H4N2O5
Average Molecular Weight184.107
Monoisotopic Molecular Weight184.012021237
IUPAC Name3,5-dinitrophenol
Traditional Name3,5-dinitrophenol
CAS Registry NumberNot Available
SMILES
OC1=CC(=CC(=C1)[N+]([O-])=O)[N+]([O-])=O
InChI Identifier
InChI=1S/C6H4N2O5/c9-6-2-4(7(10)11)1-5(3-6)8(12)13/h1-3,9H
InChI KeyUEMBNLWZFIWQFL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dinitrophenols. These are organic aromatic compounds containing a benzene that carries a single phenol group and exactly two nitro groups.
KingdomOrganic compounds
Super ClassBenzenoids
ClassPhenols
Sub ClassNitrophenols
Direct ParentDinitrophenols
Alternative Parents
Substituents
  • Dinitrophenol
  • Nitrobenzene
  • Nitroaromatic compound
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Monocyclic benzene moiety
  • C-nitro compound
  • Organic nitro compound
  • Organic oxoazanium
  • Allyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic 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
logP1.76ALOGPS
logP1.55ChemAxon
logS-2.6ALOGPS
pKa (Strongest Acidic)6.24ChemAxon
pKa (Strongest Basic)-6.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area106.51 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity40.68 m³·mol⁻¹ChemAxon
Polarizability14.64 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+124.68330932474
DeepCCS[M-H]-121.42130932474
DeepCCS[M-2H]-156.78330932474
DeepCCS[M+Na]+132.74130932474
AllCCS[M+H]+136.332859911
AllCCS[M+H-H2O]+132.032859911
AllCCS[M+NH4]+140.232859911
AllCCS[M+Na]+141.432859911
AllCCS[M-H]-127.932859911
AllCCS[M+Na-2H]-128.432859911
AllCCS[M+HCOO]-128.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3,5-DinitrophenolOC1=CC(=CC(=C1)[N+]([O-])=O)[N+]([O-])=O2887.6Standard polar33892256
3,5-DinitrophenolOC1=CC(=CC(=C1)[N+]([O-])=O)[N+]([O-])=O1680.5Standard non polar33892256
3,5-DinitrophenolOC1=CC(=CC(=C1)[N+]([O-])=O)[N+]([O-])=O1974.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3,5-Dinitrophenol GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-1900000000-33199da40d6729c5070c2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,5-Dinitrophenol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,5-Dinitrophenol GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,5-Dinitrophenol GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,5-Dinitrophenol 10V, Positive-QTOFsplash10-000i-0900000000-bae0a5164cafbc9707132019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,5-Dinitrophenol 20V, Positive-QTOFsplash10-000i-0900000000-950586a9c829b85478bb2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,5-Dinitrophenol 40V, Positive-QTOFsplash10-000i-1900000000-ab13c5f842addffba6ce2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,5-Dinitrophenol 10V, Negative-QTOFsplash10-001i-0900000000-5030a9db78e39500034a2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,5-Dinitrophenol 20V, Negative-QTOFsplash10-001i-0900000000-5030a9db78e39500034a2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,5-Dinitrophenol 40V, Negative-QTOFsplash10-001i-0900000000-5030a9db78e39500034a2019-02-23Wishart 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 ID10975
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11459
PDB IDNot Available
ChEBI ID39360
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 ]