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Showing metabocard for 3-(3'-methylthio)propylmalate (HMDB0304106)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 07:13:37 UTC
Update Date2021-09-24 07:13:38 UTC
HMDB IDHMDB0304106
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-(3'-methylthio)propylmalate
Description3-(3'-methylthio)propylmalate, also known as 3-(3-methylsulfanyl)propylmalic acid, belongs to medium-chain hydroxy acids and derivatives class of compounds. Those are hydroxy acids with a 6 to 12 carbon atoms long side chain. 3-(3'-methylthio)propylmalate is soluble (in water) and a weakly acidic compound (based on its pKa). 3-(3'-methylthio)propylmalate can be found in a number of food items such as elderberry, fig, bitter gourd, and potato, which makes 3-(3'-methylthio)propylmalate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304106 (3-(3'-methylthio)propylmalate)

  Mrv1533005141521392D          

 14 13  0  0  0  0            999 V2000
    6.5704    1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    7.2849    0.9059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    0.9059    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  1 13  2  0  0  0  0
  1 14  1  0  0  0  0
M  CHG  2  12  -1  14  -1
M  END
Download

3D MOL for HMDB0304106 (3-(3'-methylthio)propylmalate)

HMDB0304106
     RDKit          3D
3-(3'-methylthio)propylmalate
 26 25  0  0  0  0  0  0  0  0999 V2000
    4.6209    0.6528   -0.0479 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2939    0.3618    1.1530 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7517   -0.1264    0.3005 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -0.3582    1.2973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6425   -0.7664    0.7917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3785    0.2249    0.0146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8711    0.8115   -1.2051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9404    0.2508   -2.3278 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2647    2.0803   -1.2107 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.6926   -0.5341   -0.5395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4198   -0.9803    0.5263 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3417    0.4981   -1.3662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0653    0.1044   -2.3170 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1764    1.8657   -1.1245 O   0  0  0  0  0  1  0  0  0  0  0  0
    4.3402    1.3718   -0.8323 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8637   -0.3204   -0.5200 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5095    0.9709    0.5082 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5656    0.5979   -0.4712 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0121   -1.1299   -0.1540 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0730   -1.0542    2.0965 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5548    0.6069    1.9032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5772   -1.7761    0.2568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2804   -1.0530    1.6928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8731    0.9949    0.6972 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2550   -1.3105   -1.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4917   -1.9831    0.4407 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  6 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  6 24  1  0
 10 25  1  0
 11 26  1  0
M  CHG  2   9  -1  14  -1
M  END
Download

3D SDF for HMDB0304106 (3-(3'-methylthio)propylmalate)

  Mrv1533005141521392D          

 14 13  0  0  0  0            999 V2000
    6.5704    1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    7.2849    0.9059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    0.9059    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  1 13  2  0  0  0  0
  1 14  1  0  0  0  0
M  CHG  2  12  -1  14  -1
M  END
> <DATABASE_ID>
HMDB0304106

> <DATABASE_NAME>
hmdb

> <SMILES>
CSCCCC(C(O)C([O-])=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H14O5S/c1-14-4-2-3-5(7(10)11)6(9)8(12)13/h5-6,9H,2-4H2,1H3,(H,10,11)(H,12,13)/p-2

> <INCHI_KEY>
SQXVIIOPMYSNCP-UHFFFAOYSA-L

> <FORMULA>
C8H12O5S

> <MOLECULAR_WEIGHT>
220.24

> <EXACT_MASS>
220.04164182

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
20.95295959316767

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-hydroxy-3-[3-(methylsulfanyl)propyl]butanedioate

> <ALOGPS_LOGP>
0.37

> <JCHEM_LOGP>
0.5201821696666667

> <ALOGPS_LOGS>
-1.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.566317251412115

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7478139569182365

> <JCHEM_PKA_STRONGEST_BASIC>
-4.012167421923501

> <JCHEM_POLAR_SURFACE_AREA>
100.49000000000001

> <JCHEM_REFRACTIVITY>
72.9342

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.07e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-3-[3-(methylsulfanyl)propyl]butanedioate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0304106 (3-(3'-methylthio)propylmalate)

HMDB0304106
     RDKit          3D
3-(3'-methylthio)propylmalate
 26 25  0  0  0  0  0  0  0  0999 V2000
    4.6209    0.6528   -0.0479 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2939    0.3618    1.1530 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7517   -0.1264    0.3005 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -0.3582    1.2973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6425   -0.7664    0.7917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3785    0.2249    0.0146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8711    0.8115   -1.2051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9404    0.2508   -2.3278 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2647    2.0803   -1.2107 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.6926   -0.5341   -0.5395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4198   -0.9803    0.5263 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3417    0.4981   -1.3662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0653    0.1044   -2.3170 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1764    1.8657   -1.1245 O   0  0  0  0  0  1  0  0  0  0  0  0
    4.3402    1.3718   -0.8323 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8637   -0.3204   -0.5200 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5095    0.9709    0.5082 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5656    0.5979   -0.4712 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0121   -1.1299   -0.1540 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0730   -1.0542    2.0965 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5548    0.6069    1.9032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5772   -1.7761    0.2568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2804   -1.0530    1.6928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8731    0.9949    0.6972 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2550   -1.3105   -1.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4917   -1.9831    0.4407 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  6 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  6 24  1  0
 10 25  1  0
 11 26  1  0
M  CHG  2   9  -1  14  -1
M  END
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PDB for HMDB0304106 (3-(3'-methylthio)propylmalate)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0      12.265   2.461   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       6.930   4.001   0.000  0.00  0.00           S+0
HETATM    7  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      13.598   6.311   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      14.932   2.461   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0      13.598   1.691   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      10.931   1.691   0.000  0.00  0.00           O-1
CONECT    1    2   13   14                                                  
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    2    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    1                                                            
CONECT   14    1                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for HMDB0304106 (3-(3'-methylthio)propylmalate)

COMPND    HMDB0304106
HETATM    1  C1  UNL     1       4.621   0.653  -0.048  1.00  0.00           C  
HETATM    2  S1  UNL     1       3.294   0.362   1.153  1.00  0.00           S  
HETATM    3  C2  UNL     1       1.752  -0.126   0.301  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.685  -0.358   1.297  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.643  -0.766   0.792  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.379   0.225   0.015  1.00  0.00           C  
HETATM    7  C6  UNL     1      -0.871   0.812  -1.205  1.00  0.00           C  
HETATM    8  O1  UNL     1      -0.940   0.251  -2.328  1.00  0.00           O  
HETATM    9  O2  UNL     1      -0.265   2.080  -1.211  1.00  0.00           O1-
HETATM   10  C7  UNL     1      -2.693  -0.534  -0.539  1.00  0.00           C  
HETATM   11  O3  UNL     1      -3.420  -0.980   0.526  1.00  0.00           O  
HETATM   12  C8  UNL     1      -3.342   0.498  -1.366  1.00  0.00           C  
HETATM   13  O4  UNL     1      -4.065   0.104  -2.317  1.00  0.00           O  
HETATM   14  O5  UNL     1      -3.176   1.866  -1.124  1.00  0.00           O1-
HETATM   15  H1  UNL     1       4.340   1.372  -0.832  1.00  0.00           H  
HETATM   16  H2  UNL     1       4.864  -0.320  -0.520  1.00  0.00           H  
HETATM   17  H3  UNL     1       5.509   0.971   0.508  1.00  0.00           H  
HETATM   18  H4  UNL     1       1.566   0.598  -0.471  1.00  0.00           H  
HETATM   19  H5  UNL     1       2.012  -1.130  -0.154  1.00  0.00           H  
HETATM   20  H6  UNL     1       1.073  -1.054   2.096  1.00  0.00           H  
HETATM   21  H7  UNL     1       0.555   0.607   1.903  1.00  0.00           H  
HETATM   22  H8  UNL     1      -0.577  -1.776   0.257  1.00  0.00           H  
HETATM   23  H9  UNL     1      -1.280  -1.053   1.693  1.00  0.00           H  
HETATM   24  H10 UNL     1      -1.873   0.995   0.697  1.00  0.00           H  
HETATM   25  H11 UNL     1      -2.255  -1.310  -1.188  1.00  0.00           H  
HETATM   26  H12 UNL     1      -3.492  -1.983   0.441  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3
CONECT    3    4   18   19
CONECT    4    5   20   21
CONECT    5    6   22   23
CONECT    6    7   10   24
CONECT    7    8    8    9
CONECT   10   11   12   25
CONECT   11   26
CONECT   12   13   13   14
END
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SMILES for HMDB0304106 (3-(3'-methylthio)propylmalate)

CSCCCC(C(O)C([O-])=O)C([O-])=O
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INCHI for HMDB0304106 (3-(3'-methylthio)propylmalate)

InChI=1S/C8H14O5S/c1-14-4-2-3-5(7(10)11)6(9)8(12)13/h5-6,9H,2-4H2,1H3,(H,10,11)(H,12,13)/p-2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-(3-Methylsulfanyl)propylmalateChEBI
3-(3-Methylsulfanyl)propylmalic acidGenerator
3-(3-Methylsulphanyl)propylmalateGenerator
3-(3-Methylsulphanyl)propylmalic acidGenerator
3-(3-Methylthio)propylmalic acid(2-)Generator
3-(3'-methylthio)Propylmalic acidMetaCyc, Generator
Chemical FormulaC8H12O5S
Average Molecular Weight220.24
Monoisotopic Molecular Weight220.04164182
IUPAC Name2-hydroxy-3-[3-(methylsulfanyl)propyl]butanedioate
Traditional Name2-hydroxy-3-[3-(methylsulfanyl)propyl]butanedioate
CAS Registry NumberNot Available
SMILES
CSCCCC(C(O)C([O-])=O)C([O-])=O
InChI Identifier
InChI=1S/C8H14O5S/c1-14-4-2-3-5(7(10)11)6(9)8(12)13/h5-6,9H,2-4H2,1H3,(H,10,11)(H,12,13)/p-2
InChI KeySQXVIIOPMYSNCP-UHFFFAOYSA-L
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassMedium-chain hydroxy acids and derivatives
Direct ParentMedium-chain hydroxy acids and derivatives
Alternative Parents
Substituents
  • Medium-chain hydroxy acid
  • Medium-chain fatty acid
  • Beta-hydroxy acid
  • Branched fatty acid
  • Thia fatty acid
  • Hydroxy fatty acid
  • Fatty acyl
  • Fatty acid
  • Dicarboxylic acid or derivatives
  • Monosaccharide
  • Secondary alcohol
  • Carboxylic acid derivative
  • Dialkylthioether
  • Carboxylic acid
  • Sulfenyl compound
  • Thioether
  • Alcohol
  • Organic oxygen compound
  • Organooxygen compound
  • Organosulfur compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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 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 IDFDB030393
KNApSAcK IDNot Available
Chemspider ID24785184
KEGG Compound IDNot Available
BioCyc IDCPDQT-36
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44237292
PDB IDNot Available
ChEBI ID133501
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