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Showing metabocard for 2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro- (HMDB0245488)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:33:13 UTC
Update Date2021-09-26 22:53:58 UTC
HMDB IDHMDB0245488
Secondary Accession NumbersNone
Metabolite Identification
Common Name2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-
Description2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-, also known as 1-(2,3-dihydro-2-furanyl)-5-fluoro-2,4(1H,3H)-pyrimidinedione or dehydroftorafur, belongs to the class of organic compounds known as halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Based on a literature review very few articles have been published on 2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2,4(1h,3h)-pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro- is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro- 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 HMDB0245488 (2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-)

  Mrv1652309112100332D          

 14 15  0  0  0  0            999 V2000
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   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   -0.4125    0.0000 N   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
    0.0000    0.8250    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 O   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
    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    1.2375    0.0000 F   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  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  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
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
  6 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0245488 (2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-)

HMDB0245488
     RDKit          3D
2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-
 21 22  0  0  0  0  0  0  0  0999 V2000
    4.0588   -0.5185    0.5125 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8439   -0.3914    0.1869 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4295    0.7955   -0.2811 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1276    0.9409   -0.6327 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7617    2.0636   -1.0693 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2335   -0.0579   -0.5313 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1151    0.1557   -0.9153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8494    1.1900   -0.1318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2257    0.4546    1.0956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2252   -0.8283    0.7867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8762   -1.0143   -0.5579 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6654   -1.2528   -0.0566 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9767   -1.4638    0.3177 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4015   -2.6682    0.7937 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.0852    1.6233   -0.3853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2617    0.2542   -2.0232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2755    2.1077    0.0761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7597    1.4627   -0.7427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4668    0.8454    2.0884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4565   -1.6501    1.4516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0720   -2.0481    0.0182 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
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
  6 12  1  0
 12 13  2  0
 13 14  1  0
 13  2  1  0
 11  7  1  0
  3 15  1  0
  7 16  1  0
  8 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
 12 21  1  0
M  END
Download

3D SDF for HMDB0245488 (2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-)

  Mrv1652309112100332D          

 14 15  0  0  0  0            999 V2000
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   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   -0.4125    0.0000 N   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
    0.0000    0.8250    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 O   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
    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    1.2375    0.0000 F   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  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  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
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
  6 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245488

> <DATABASE_NAME>
hmdb

> <SMILES>
FC1=CN(C2CC=CO2)C(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H7FN2O3/c9-5-4-11(6-2-1-3-14-6)8(13)10-7(5)12/h1,3-4,6H,2H2,(H,10,12,13)

> <INCHI_KEY>
PDLPZZHYCMXDCF-UHFFFAOYSA-N

> <FORMULA>
C8H7FN2O3

> <MOLECULAR_WEIGHT>
198.153

> <EXACT_MASS>
198.044070256

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
16.517959956120066

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(2,3-dihydrofuran-2-yl)-5-fluoro-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
0.17

> <JCHEM_LOGP>
0.03580558333333339

> <ALOGPS_LOGS>
-1.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.07749200888538

> <JCHEM_PKA_STRONGEST_BASIC>
-4.820123027444577

> <JCHEM_POLAR_SURFACE_AREA>
58.64

> <JCHEM_REFRACTIVITY>
44.5945

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.56e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-(2,3-dihydrofuran-2-yl)-5-fluoro-3H-pyrimidine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0245488 (2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-)

HMDB0245488
     RDKit          3D
2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-
 21 22  0  0  0  0  0  0  0  0999 V2000
    4.0588   -0.5185    0.5125 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8439   -0.3914    0.1869 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4295    0.7955   -0.2811 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1276    0.9409   -0.6327 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7617    2.0636   -1.0693 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2335   -0.0579   -0.5313 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1151    0.1557   -0.9153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8494    1.1900   -0.1318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2257    0.4546    1.0956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2252   -0.8283    0.7867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8762   -1.0143   -0.5579 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6654   -1.2528   -0.0566 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9767   -1.4638    0.3177 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4015   -2.6682    0.7937 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.0852    1.6233   -0.3853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2617    0.2542   -2.0232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2755    2.1077    0.0761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7597    1.4627   -0.7427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4668    0.8454    2.0884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4565   -1.6501    1.4516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0720   -2.0481    0.0182 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
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
  6 12  1  0
 12 13  2  0
 13 14  1  0
 13  2  1  0
 11  7  1  0
  3 15  1  0
  7 16  1  0
  8 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
 12 21  1  0
M  END
Download

PDB for HMDB0245488 (2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.088  -3.215   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   14  F   UNK     0      -1.334   2.310   0.000  0.00  0.00           F+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11    6   13                                                  
CONECT   13   12                                                            
CONECT   14    8                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END
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3D PDB for HMDB0245488 (2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-)

COMPND    HMDB0245488
HETATM    1  O1  UNL     1       4.059  -0.519   0.512  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.844  -0.391   0.187  1.00  0.00           C  
HETATM    3  N1  UNL     1       2.429   0.795  -0.281  1.00  0.00           N  
HETATM    4  C2  UNL     1       1.128   0.941  -0.633  1.00  0.00           C  
HETATM    5  O2  UNL     1       0.762   2.064  -1.069  1.00  0.00           O  
HETATM    6  N2  UNL     1       0.234  -0.058  -0.531  1.00  0.00           N  
HETATM    7  C3  UNL     1      -1.115   0.156  -0.915  1.00  0.00           C  
HETATM    8  C4  UNL     1      -1.849   1.190  -0.132  1.00  0.00           C  
HETATM    9  C5  UNL     1      -2.226   0.455   1.096  1.00  0.00           C  
HETATM   10  C6  UNL     1      -2.225  -0.828   0.787  1.00  0.00           C  
HETATM   11  O3  UNL     1      -1.876  -1.014  -0.558  1.00  0.00           O  
HETATM   12  C7  UNL     1       0.665  -1.253  -0.057  1.00  0.00           C  
HETATM   13  C8  UNL     1       1.977  -1.464   0.318  1.00  0.00           C  
HETATM   14  F1  UNL     1       2.402  -2.668   0.794  1.00  0.00           F  
HETATM   15  H1  UNL     1       3.085   1.623  -0.385  1.00  0.00           H  
HETATM   16  H2  UNL     1      -1.262   0.254  -2.023  1.00  0.00           H  
HETATM   17  H3  UNL     1      -1.275   2.108   0.076  1.00  0.00           H  
HETATM   18  H4  UNL     1      -2.760   1.463  -0.743  1.00  0.00           H  
HETATM   19  H5  UNL     1      -2.467   0.845   2.088  1.00  0.00           H  
HETATM   20  H6  UNL     1      -2.457  -1.650   1.452  1.00  0.00           H  
HETATM   21  H7  UNL     1      -0.072  -2.048   0.018  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   13
CONECT    3    4   15
CONECT    4    5    5    6
CONECT    6    7   12
CONECT    7    8   11   16
CONECT    8    9   17   18
CONECT    9   10   10   19
CONECT   10   11   20
CONECT   12   13   13   21
CONECT   13   14
END
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SMILES for HMDB0245488 (2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-)

FC1=CN(C2CC=CO2)C(=O)NC1=O
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INCHI for HMDB0245488 (2,4(1H,3H)-Pyrimidinedione, 1-(2,3-dihydro-2-furanyl)-5-fluoro-)

InChI=1S/C8H7FN2O3/c9-5-4-11(6-2-1-3-14-6)8(13)10-7(5)12/h1,3-4,6H,2H2,(H,10,12,13)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1-(2,3-Dihydro-2-furanyl)-5-fluoro-2,4(1H,3H)-pyrimidinedioneHMDB
DehydroftorafurHMDB
Dehydroftorafur, (R)-isomerHMDB
Dehydroftorafur, (S)-isomerHMDB
Chemical FormulaC8H7FN2O3
Average Molecular Weight198.153
Monoisotopic Molecular Weight198.044070256
IUPAC Name1-(2,3-dihydrofuran-2-yl)-5-fluoro-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name1-(2,3-dihydrofuran-2-yl)-5-fluoro-3H-pyrimidine-2,4-dione
CAS Registry NumberNot Available
SMILES
FC1=CN(C2CC=CO2)C(=O)NC1=O
InChI Identifier
InChI=1S/C8H7FN2O3/c9-5-4-11(6-2-1-3-14-6)8(13)10-7(5)12/h1,3-4,6H,2H2,(H,10,12,13)
InChI KeyPDLPZZHYCMXDCF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentHalopyrimidines
Alternative Parents
Substituents
  • Halopyrimidine
  • Pyrimidone
  • Aryl fluoride
  • Aryl halide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Dihydrofuran
  • Urea
  • Lactam
  • Oxacycle
  • Azacycle
  • Organopnictogen compound
  • Organonitrogen compound
  • Organofluoride
  • Organohalogen compound
  • Organooxygen compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Predicted Chromatographic Properties
Spectra
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 ID111808
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound125711
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 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 ]