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Showing metabocard for 1-Methyl-4-nitroimidazole (HMDB0060659)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-06-18 17:47:59 UTC
Update Date2023-02-21 17:30:08 UTC
HMDB IDHMDB0060659
Secondary Accession Numbers
  • HMDB60659
Metabolite Identification
Common Name1-Methyl-4-nitroimidazole
Description1-Methyl-4-nitroimidazole is a metabolite of azathioprine. Azathioprine is a purine analogue immunosuppressive drug. It is used to prevent rejection following organ transplantation, and to treat a vast array of autoimmune diseases, including rheumatoid arthritis, pemphigus, inflammatory bowel disease, multiple sclerosis, autoimmune hepatitis, atopic dermatitis, myasthenia gravis, neuromyelitis optica or Devic's disease, restrictive lung disease, and others. (Wikipedia)
Structure
Data?1677000608
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060659 (1-Methyl-4-nitroimidazole)

 
  Mrv0541 06181310472D          
 
  9  9  0  0  0  0            999 V2000
   14.7248  -11.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7248  -10.6429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1686  -10.6429    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   15.4261  -10.2304    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   13.9411  -10.3954    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.4461  -11.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9411  -11.7154    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.4261   -9.4054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.2266  -12.1279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  4  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  4  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  CHG  2   3  -1   4   1
M  END
Download

3D MOL for HMDB0060659 (1-Methyl-4-nitroimidazole)

HMDB0060659
     RDKit          3D
1-Methyl-4-nitroimidazole
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.1836    0.2963   -0.2428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8438   -0.1103    0.1452 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4620   -1.0039    1.0731 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8755   -1.0153    1.0457 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3599   -0.1729    0.1462 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6951    0.1405   -0.2225 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.6469   -0.4385    0.3580 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9810    1.0622   -1.1994 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.2566    0.4139   -0.4381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2248    1.4101   -0.2282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2972    0.0155   -1.3167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9436   -0.1752    0.4014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1433   -1.5852    1.7041 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2832    1.1629   -1.2261 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  2  0
  9  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  9 14  1  0
M  CHG  2   6   1   8  -1
M  END
Download

3D SDF for HMDB0060659 (1-Methyl-4-nitroimidazole)

 
  Mrv0541 06181310472D          
 
  9  9  0  0  0  0            999 V2000
   14.7248  -11.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7248  -10.6429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1686  -10.6429    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   15.4261  -10.2304    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   13.9411  -10.3954    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.4461  -11.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9411  -11.7154    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.4261   -9.4054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.2266  -12.1279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  4  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  4  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  CHG  2   3  -1   4   1
M  END
> <DATABASE_ID>
HMDB0060659

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C=NC(=C1)[N+]([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H5N3O2/c1-6-2-4(5-3-6)7(8)9/h2-3H,1H3

> <INCHI_KEY>
HSCOLDQJZRZQMV-UHFFFAOYSA-N

> <FORMULA>
C4H5N3O2

> <MOLECULAR_WEIGHT>
127.1014

> <EXACT_MASS>
127.038176419

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.088315516818561

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-methyl-4-nitro-1H-imidazole

> <ALOGPS_LOGP>
-0.23

> <JCHEM_LOGP>
0.6128935780000001

> <ALOGPS_LOGS>
-1.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-0.3412685475326954

> <JCHEM_POLAR_SURFACE_AREA>
63.64

> <JCHEM_REFRACTIVITY>
31.5477

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.14e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-methyl-4-nitroimidazole

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0060659 (1-Methyl-4-nitroimidazole)

HMDB0060659
     RDKit          3D
1-Methyl-4-nitroimidazole
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.1836    0.2963   -0.2428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8438   -0.1103    0.1452 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4620   -1.0039    1.0731 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8755   -1.0153    1.0457 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3599   -0.1729    0.1462 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6951    0.1405   -0.2225 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.6469   -0.4385    0.3580 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9810    1.0622   -1.1994 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.2566    0.4139   -0.4381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2248    1.4101   -0.2282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2972    0.0155   -1.3167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9436   -0.1752    0.4014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1433   -1.5852    1.7041 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2832    1.1629   -1.2261 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  2  0
  9  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  9 14  1  0
M  CHG  2   6   1   8  -1
M  END
Download

PDB for HMDB0060659 (1-Methyl-4-nitroimidazole)

HEADER    PROTEIN                                 18-JUN-13   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-JUN-13         0                                  
HETATM    1  C   UNK     0      27.486 -21.407   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      27.486 -19.867   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      30.181 -19.867   0.000  0.00  0.00           O-1
HETATM    4  N   UNK     0      28.795 -19.097   0.000  0.00  0.00           N+1
HETATM    5  N   UNK     0      26.023 -19.405   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      25.099 -20.637   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      26.023 -21.869   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      28.795 -17.557   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      24.690 -22.639   0.000  0.00  0.00           C+0
CONECT    1    2    7                                                       
CONECT    2    1    4    5                                                  
CONECT    3    4                                                            
CONECT    4    3    2    8                                                  
CONECT    5    2    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    1    9                                                  
CONECT    8    4                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0060659 (1-Methyl-4-nitroimidazole)

COMPND    HMDB0060659
HETATM    1  C1  UNL     1      -2.184   0.296  -0.243  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.844  -0.110   0.145  1.00  0.00           N  
HETATM    3  C2  UNL     1      -0.462  -1.004   1.073  1.00  0.00           C  
HETATM    4  N2  UNL     1       0.875  -1.015   1.046  1.00  0.00           N  
HETATM    5  C3  UNL     1       1.360  -0.173   0.146  1.00  0.00           C  
HETATM    6  N3  UNL     1       2.695   0.141  -0.222  1.00  0.00           N1+
HETATM    7  O1  UNL     1       3.647  -0.439   0.358  1.00  0.00           O  
HETATM    8  O2  UNL     1       2.981   1.062  -1.199  1.00  0.00           O1-
HETATM    9  C4  UNL     1       0.257   0.414  -0.438  1.00  0.00           C  
HETATM   10  H1  UNL     1      -2.225   1.410  -0.228  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.297   0.016  -1.317  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.944  -0.175   0.401  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.143  -1.585   1.704  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.283   1.163  -1.226  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    9
CONECT    3    4    4   13
CONECT    4    5
CONECT    5    6    9    9
CONECT    6    7    7    8
CONECT    9   14
END
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SMILES for HMDB0060659 (1-Methyl-4-nitroimidazole)

CN1C=NC(=C1)[N+]([O-])=O
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INCHI for HMDB0060659 (1-Methyl-4-nitroimidazole)

InChI=1S/C4H5N3O2/c1-6-2-4(5-3-6)7(8)9/h2-3H,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC4H5N3O2
Average Molecular Weight127.1014
Monoisotopic Molecular Weight127.038176419
IUPAC Name1-methyl-4-nitro-1H-imidazole
Traditional Name1-methyl-4-nitroimidazole
CAS Registry NumberNot Available
SMILES
CN1C=NC(=C1)[N+]([O-])=O
InChI Identifier
InChI=1S/C4H5N3O2/c1-6-2-4(5-3-6)7(8)9/h2-3H,1H3
InChI KeyHSCOLDQJZRZQMV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitroimidazoles. Nitroimidazoles are compounds containing an imidazole ring which bears a nitro group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzoles
Sub ClassImidazoles
Direct ParentNitroimidazoles
Alternative Parents
Substituents
  • Nitroaromatic compound
  • Nitroimidazole
  • N-substituted imidazole
  • Imidolactam
  • Heteroaromatic compound
  • C-nitro compound
  • Organic nitro compound
  • Organic oxoazanium
  • Allyl-type 1,3-dipolar organic compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Azacycle
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
Process
Naturally occurring process
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
Water Solubility3.14 g/LALOGPS
logP-0.23ALOGPS
logP0.61ChemAxon
logS-1.6ALOGPS
pKa (Strongest Basic)-0.34ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area63.64 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity31.55 m³·mol⁻¹ChemAxon
Polarizability11.09 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
DarkChem[M+H]+125.85731661259
DarkChem[M-H]-122.88431661259
DeepCCS[M+H]+124.1130932474
DeepCCS[M-H]-121.12930932474
DeepCCS[M-2H]-158.33630932474
DeepCCS[M+Na]+132.80930932474
AllCCS[M+H]+127.432859911
AllCCS[M+H-H2O]+122.832859911
AllCCS[M+NH4]+131.832859911
AllCCS[M+Na]+133.032859911
AllCCS[M-H]-121.432859911
AllCCS[M+Na-2H]-123.532859911
AllCCS[M+HCOO]-125.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1-Methyl-4-nitroimidazoleCN1C=NC(=C1)[N+]([O-])=O1875.5Standard polar33892256
1-Methyl-4-nitroimidazoleCN1C=NC(=C1)[N+]([O-])=O1162.6Standard non polar33892256
1-Methyl-4-nitroimidazoleCN1C=NC(=C1)[N+]([O-])=O1476.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1-Methyl-4-nitroimidazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9500000000-5572508a2c2c51823d132017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-Methyl-4-nitroimidazole 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-Methyl-4-nitroimidazole 10V, Positive-QTOFsplash10-004i-1900000000-d877350c3caef4c843442017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methyl-4-nitroimidazole 20V, Positive-QTOFsplash10-0il0-4900000000-c8ce22a6a8141005a4672017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methyl-4-nitroimidazole 40V, Positive-QTOFsplash10-0a59-9100000000-40b7719a2cb99667331d2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methyl-4-nitroimidazole 10V, Negative-QTOFsplash10-004i-0900000000-bf396a90d19c67b3089a2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methyl-4-nitroimidazole 20V, Negative-QTOFsplash10-0002-9000000000-088fbb049b50fa3022862017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methyl-4-nitroimidazole 40V, Negative-QTOFsplash10-0ul1-9000000000-6cc95eb36814b01901d42017-10-06Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
 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 IDNot Available
KEGG Compound IDC16621
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound18209
PDB IDNot Available
ChEBI IDNot Available
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