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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 06:53:03 UTC

Update Date

2021-09-23 06:53:03 UTC

HMDB ID

HMDB0302131

Secondary Accession Numbers

None

Metabolite Identification

Common Name

1-Dehydro-[6]-gingerdione

Description

1-dehydro-[6]-gingerdione belongs to hydroxycinnamic acids and derivatives class of compounds. Those are compounds containing an cinnamic acid (or a derivative thereof) where the benzene ring is hydroxylated. 1-dehydro-[6]-gingerdione is practically insoluble (in water) and a very weakly acidic compound (based on its pKa). 1-dehydro-[6]-gingerdione can be found in ginger, which makes 1-dehydro-[6]-gingerdione a potential biomarker for the consumption of this food product.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0302131
     RDKit          3D
1-Dehydro-[6]-gingerdione
 43 43  0  0  0  0  0  0  0  0999 V2000
   -6.8198    0.3745    0.1921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8608   -0.3658   -0.7246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9644   -1.2130    0.1599 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1874   -0.3854    1.1269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3084    0.6324    0.4715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3246   -0.0213   -0.4026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7455   -0.7467   -1.4961 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0256    0.0817   -0.1500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0268   -0.5547   -0.9978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3990   -1.2283   -2.0080 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3892   -0.4554   -0.7416 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8660    0.2145    0.2714 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2784    0.3492    0.5790 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7024    1.0863    1.6856 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0370    1.2215    1.9878 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0078    0.6250    1.1959 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3550    0.7555    1.4922 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6008   -0.0952    0.1153 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5222   -0.7137   -0.7124 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1478   -1.4718   -1.8457 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2499   -0.2306   -0.1884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7589    0.6404   -0.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9838   -0.2302    1.0905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3311    1.3276    0.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4270   -1.0777   -1.3878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3075    0.2970   -1.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3228   -1.9119   -0.3788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7051   -1.7992    0.8017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8657    0.0810    1.8837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5763   -1.1104    1.7424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8064    1.2333    1.2725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8941    1.3733   -0.1166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6077   -0.4970   -2.4534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7637    0.6567    0.7078 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0686   -0.9550   -1.4153 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1901    0.7330    0.9730 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9568    1.5655    2.3245 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3964    1.7885    2.8417 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0416    0.3206    0.9134 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1098   -1.6798   -2.3976 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4623   -0.8997   -2.5238 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6460   -2.4190   -1.5913 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9843   -0.8184   -1.0651 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
  6  8  2  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 18 21  2  0
 21 13  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  7 33  1  0
  8 34  1  0
 11 35  1  0
 12 36  1  0
 14 37  1  0
 15 38  1  0
 17 39  1  0
 20 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
M  END

 
  Mrv0541 02241220432D          
 
 21 21  0  0  0  0            999 V2000
   15.1840  -17.1918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1840  -18.0284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8951  -18.4467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6062  -18.0284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6062  -17.1918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8951  -16.7735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4729  -18.4467    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3591  -16.7735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0702  -17.1918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8231  -16.7735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.5342  -17.1918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.2453  -16.7735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.9982  -17.1918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.7093  -16.7735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.4204  -17.1918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.1734  -16.7735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.8845  -17.1918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8231  -15.9369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.2453  -15.9369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.4311  -16.7735    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.7136  -17.2037    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
  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
  2  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 10 18  2  0  0  0  0
 12 19  1  0  0  0  0
  1 20  1  0  0  0  0
 20 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302131

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC\C(O)=C\C(=O)\C=C\C1=CC(OC)=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C17H22O4/c1-3-4-5-6-14(18)12-15(19)9-7-13-8-10-16(20)17(11-13)21-2/h7-12,18,20H,3-6H2,1-2H3/b9-7+,14-12-

> <INCHI_KEY>
GPNSDXAINXYRNZ-YYKRUEADSA-N

> <FORMULA>
C17H22O4

> <MOLECULAR_WEIGHT>
290.3542

> <EXACT_MASS>
290.151809192

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
33.177616189700814

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1E,4Z)-5-hydroxy-1-(4-hydroxy-3-methoxyphenyl)deca-1,4-dien-3-one

> <ALOGPS_LOGP>
3.83

> <JCHEM_LOGP>
4.098923498

> <ALOGPS_LOGS>
-3.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.576189734007528

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.189727665708386

> <JCHEM_PKA_STRONGEST_BASIC>
-4.8135607775323495

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
85.82659999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.28e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1E,4Z)-5-hydroxy-1-(4-hydroxy-3-methoxyphenyl)deca-1,4-dien-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0302131
     RDKit          3D
1-Dehydro-[6]-gingerdione
 43 43  0  0  0  0  0  0  0  0999 V2000
   -6.8198    0.3745    0.1921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8608   -0.3658   -0.7246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9644   -1.2130    0.1599 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1874   -0.3854    1.1269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3084    0.6324    0.4715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3246   -0.0213   -0.4026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7455   -0.7467   -1.4961 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0256    0.0817   -0.1500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0268   -0.5547   -0.9978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3990   -1.2283   -2.0080 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3892   -0.4554   -0.7416 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8660    0.2145    0.2714 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2784    0.3492    0.5790 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7024    1.0863    1.6856 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0370    1.2215    1.9878 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0078    0.6250    1.1959 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3550    0.7555    1.4922 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6008   -0.0952    0.1153 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5222   -0.7137   -0.7124 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1478   -1.4718   -1.8457 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2499   -0.2306   -0.1884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7589    0.6404   -0.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9838   -0.2302    1.0905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3311    1.3276    0.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4270   -1.0777   -1.3878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3075    0.2970   -1.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3228   -1.9119   -0.3788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7051   -1.7992    0.8017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8657    0.0810    1.8837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5763   -1.1104    1.7424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8064    1.2333    1.2725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8941    1.3733   -0.1166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6077   -0.4970   -2.4534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7637    0.6567    0.7078 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0686   -0.9550   -1.4153 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1901    0.7330    0.9730 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9568    1.5655    2.3245 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3964    1.7885    2.8417 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0416    0.3206    0.9134 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1098   -1.6798   -2.3976 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4623   -0.8997   -2.5238 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6460   -2.4190   -1.5913 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9843   -0.8184   -1.0651 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
  6  8  2  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 18 21  2  0
 21 13  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  7 33  1  0
  8 34  1  0
 11 35  1  0
 12 36  1  0
 14 37  1  0
 15 38  1  0
 17 39  1  0
 20 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      28.343 -32.091   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      28.343 -33.653   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      29.671 -34.434   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      30.998 -33.653   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      30.998 -32.091   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      29.671 -31.311   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      27.016 -34.434   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      32.404 -31.311   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      33.731 -32.091   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      35.136 -31.311   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      36.464 -32.091   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      37.791 -31.311   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      39.197 -32.091   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      40.524 -31.311   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      41.851 -32.091   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      43.257 -31.311   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      44.584 -32.091   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      35.136 -29.749   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      37.791 -29.749   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      26.938 -31.311   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      25.599 -32.114   0.000  0.00  0.00           C+0
CONECT    1    2    6   20                                                  
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    1                                                       
CONECT    7    2                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   18                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   10                                                            
CONECT   19   12                                                            
CONECT   20    1   21                                                       
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

COMPND    HMDB0302131
HETATM    1  C1  UNL     1      -6.820   0.374   0.192  1.00  0.00           C  
HETATM    2  C2  UNL     1      -5.861  -0.366  -0.725  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.964  -1.213   0.160  1.00  0.00           C  
HETATM    4  C4  UNL     1      -4.187  -0.385   1.127  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.308   0.632   0.472  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.325  -0.021  -0.403  1.00  0.00           C  
HETATM    7  O1  UNL     1      -2.746  -0.747  -1.496  1.00  0.00           O  
HETATM    8  C7  UNL     1      -1.026   0.082  -0.150  1.00  0.00           C  
HETATM    9  C8  UNL     1      -0.027  -0.555  -0.998  1.00  0.00           C  
HETATM   10  O2  UNL     1      -0.399  -1.228  -2.008  1.00  0.00           O  
HETATM   11  C9  UNL     1       1.389  -0.455  -0.742  1.00  0.00           C  
HETATM   12  C10 UNL     1       1.866   0.214   0.271  1.00  0.00           C  
HETATM   13  C11 UNL     1       3.278   0.349   0.579  1.00  0.00           C  
HETATM   14  C12 UNL     1       3.702   1.086   1.686  1.00  0.00           C  
HETATM   15  C13 UNL     1       5.037   1.221   1.988  1.00  0.00           C  
HETATM   16  C14 UNL     1       6.008   0.625   1.196  1.00  0.00           C  
HETATM   17  O3  UNL     1       7.355   0.755   1.492  1.00  0.00           O  
HETATM   18  C15 UNL     1       5.601  -0.095   0.115  1.00  0.00           C  
HETATM   19  O4  UNL     1       6.522  -0.714  -0.712  1.00  0.00           O  
HETATM   20  C16 UNL     1       6.148  -1.472  -1.846  1.00  0.00           C  
HETATM   21  C17 UNL     1       4.250  -0.231  -0.188  1.00  0.00           C  
HETATM   22  H1  UNL     1      -7.759   0.640  -0.322  1.00  0.00           H  
HETATM   23  H2  UNL     1      -6.984  -0.230   1.090  1.00  0.00           H  
HETATM   24  H3  UNL     1      -6.331   1.328   0.483  1.00  0.00           H  
HETATM   25  H4  UNL     1      -6.427  -1.078  -1.388  1.00  0.00           H  
HETATM   26  H5  UNL     1      -5.308   0.297  -1.393  1.00  0.00           H  
HETATM   27  H6  UNL     1      -4.323  -1.912  -0.379  1.00  0.00           H  
HETATM   28  H7  UNL     1      -5.705  -1.799   0.802  1.00  0.00           H  
HETATM   29  H8  UNL     1      -4.866   0.081   1.884  1.00  0.00           H  
HETATM   30  H9  UNL     1      -3.576  -1.110   1.742  1.00  0.00           H  
HETATM   31  H10 UNL     1      -2.806   1.233   1.273  1.00  0.00           H  
HETATM   32  H11 UNL     1      -3.894   1.373  -0.117  1.00  0.00           H  
HETATM   33  H12 UNL     1      -2.608  -0.497  -2.453  1.00  0.00           H  
HETATM   34  H13 UNL     1      -0.764   0.657   0.708  1.00  0.00           H  
HETATM   35  H14 UNL     1       2.069  -0.955  -1.415  1.00  0.00           H  
HETATM   36  H15 UNL     1       1.190   0.733   0.973  1.00  0.00           H  
HETATM   37  H16 UNL     1       2.957   1.566   2.324  1.00  0.00           H  
HETATM   38  H17 UNL     1       5.396   1.789   2.842  1.00  0.00           H  
HETATM   39  H18 UNL     1       8.042   0.321   0.913  1.00  0.00           H  
HETATM   40  H19 UNL     1       7.110  -1.680  -2.398  1.00  0.00           H  
HETATM   41  H20 UNL     1       5.462  -0.900  -2.524  1.00  0.00           H  
HETATM   42  H21 UNL     1       5.646  -2.419  -1.591  1.00  0.00           H  
HETATM   43  H22 UNL     1       3.984  -0.818  -1.065  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3   25   26
CONECT    3    4   27   28
CONECT    4    5   29   30
CONECT    5    6   31   32
CONECT    6    7    8    8
CONECT    7   33
CONECT    8    9   34
CONECT    9   10   10   11
CONECT   11   12   12   35
CONECT   12   13   36
CONECT   13   14   14   21
CONECT   14   15   37
CONECT   15   16   16   38
CONECT   16   17   18
CONECT   17   39
CONECT   18   19   21   21
CONECT   19   20
CONECT   20   40   41   42
CONECT   21   43
END

HMDB0302131
     RDKit          3D
1-Dehydro-[6]-gingerdione
 43 43  0  0  0  0  0  0  0  0999 V2000
   -6.8198    0.3745    0.1921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8608   -0.3658   -0.7246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9644   -1.2130    0.1599 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1874   -0.3854    1.1269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3084    0.6324    0.4715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3246   -0.0213   -0.4026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7455   -0.7467   -1.4961 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0256    0.0817   -0.1500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0268   -0.5547   -0.9978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3990   -1.2283   -2.0080 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3892   -0.4554   -0.7416 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8660    0.2145    0.2714 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2784    0.3492    0.5790 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7024    1.0863    1.6856 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0370    1.2215    1.9878 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0078    0.6250    1.1959 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3550    0.7555    1.4922 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6008   -0.0952    0.1153 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5222   -0.7137   -0.7124 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1478   -1.4718   -1.8457 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2499   -0.2306   -0.1884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7589    0.6404   -0.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9838   -0.2302    1.0905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3311    1.3276    0.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4270   -1.0777   -1.3878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3075    0.2970   -1.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3228   -1.9119   -0.3788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7051   -1.7992    0.8017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8657    0.0810    1.8837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5763   -1.1104    1.7424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8064    1.2333    1.2725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8941    1.3733   -0.1166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6077   -0.4970   -2.4534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7637    0.6567    0.7078 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0686   -0.9550   -1.4153 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1901    0.7330    0.9730 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9568    1.5655    2.3245 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3964    1.7885    2.8417 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0416    0.3206    0.9134 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1098   -1.6798   -2.3976 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4623   -0.8997   -2.5238 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6460   -2.4190   -1.5913 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9843   -0.8184   -1.0651 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
  6  8  2  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 18 21  2  0
 21 13  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  7 33  1  0
  8 34  1  0
 11 35  1  0
 12 36  1  0
 14 37  1  0
 15 38  1  0
 17 39  1  0
 20 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₇H₂₂O₄

Average Molecular Weight

290.3542

Monoisotopic Molecular Weight

290.151809192

IUPAC Name

(1E,4Z)-5-hydroxy-1-(4-hydroxy-3-methoxyphenyl)deca-1,4-dien-3-one

Traditional Name

(1E,4Z)-5-hydroxy-1-(4-hydroxy-3-methoxyphenyl)deca-1,4-dien-3-one

CAS Registry Number

Not Available

SMILES

CCCCC\C(O)=C\C(=O)\C=C\C1=CC(OC)=C(O)C=C1

InChI Identifier

InChI=1S/C17H22O4/c1-3-4-5-6-14(18)12-15(19)9-7-13-8-10-16(20)17(11-13)21-2/h7-12,18,20H,3-6H2,1-2H3/b9-7+,14-12-

InChI Key

GPNSDXAINXYRNZ-YYKRUEADSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxycinnamic acids and derivatives. Hydroxycinnamic acids and derivatives are compounds containing an cinnamic acid (or a derivative thereof) where the benzene ring is hydroxylated.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Cinnamic acids and derivatives

Sub Class

Hydroxycinnamic acids and derivatives

Direct Parent

Hydroxycinnamic acids and derivatives

Alternative Parents

Substituents

Hydroxycinnamic acid or derivatives
Methoxyphenol
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
Styrene
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Monocyclic benzene moiety
Benzenoid
Enone
Vinylogous acid
Alpha,beta-unsaturated ketone
Acryloyl-group
Ketone
Enol
Ether
Carbonyl group
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

hydroxycinnamic acid (CHEBI:81311 )

Ontology

Not Available

Exogenous (HMDB: HMDB0302131)

Food

Herb and spice

Spice

Ginger (FooDB: FOOD00206)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	3.83	ALOGPS
logP	4.1	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	8.19	ChemAxon
pKa (Strongest Basic)	-4.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	85.83 m³·mol⁻¹	ChemAxon
Polarizability	33.18 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	172.711	32859911
AllCCS	[M+H-H2O]+	169.305	32859911
AllCCS	[M+Na]+	176.777	32859911
AllCCS	[M+NH4]+	175.869	32859911
AllCCS	[M-H]-	173.704	32859911
AllCCS	[M+Na-2H]-	174.364	32859911
AllCCS	[M+HCOO]-	175.228	32859911
DeepCCS	[M+H]+	181.739	30932474
DeepCCS	[M-H]-	179.381	30932474
DeepCCS	[M-2H]-	212.267	30932474
DeepCCS	[M+Na]+	187.832	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	13.9492 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.83 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2425.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	315.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	183.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	179.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	232.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	746.3 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	561.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	85.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1414.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	483.7 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1445.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	416.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	456.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	350.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	276.2 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	10.3 seconds	40023050

Predicted Kovats Retention Indices

Not Available

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 10V, Positive-QTOF	splash10-0006-1490000000-051d1da916ff6d6e723e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 20V, Positive-QTOF	splash10-00bd-6920000000-5538e2d5e6deb32f5805	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 40V, Positive-QTOF	splash10-059f-9600000000-f262694e0315418eea3a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 10V, Negative-QTOF	splash10-000i-1790000000-6765948d72f302b50add	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 20V, Negative-QTOF	splash10-009g-3930000000-740cfe9682300f4390a2	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 40V, Negative-QTOF	splash10-05xu-5910000000-e6bc59f9928b5e9cb3bf	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 10V, Positive-QTOF	splash10-0006-0590000000-417b070f8d82f60e523a	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 20V, Positive-QTOF	splash10-0096-6940000000-3551a34a0049706221eb	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 40V, Positive-QTOF	splash10-0002-5910000000-347f51bd7973203a03de	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 10V, Negative-QTOF	splash10-000i-0590000000-ff3d3ebc677848b27845	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 20V, Negative-QTOF	splash10-0081-2920000000-4eaa0b7f09a8355dcee9	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Dehydro-[6]-gingerdione 40V, Negative-QTOF	splash10-015a-9810000000-07e2eb1ea0f2fdc30993	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB001892

KNApSAcK ID

Not Available

Chemspider ID

24673323

KEGG Compound ID

C17746

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

81311

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 1-Dehydro-[6]-gingerdione (HMDB0302131)

MOL for HMDB0302131 (1-Dehydro-[6]-gingerdione)

3D MOL for HMDB0302131 (1-Dehydro-[6]-gingerdione)

3D SDF for HMDB0302131 (1-Dehydro-[6]-gingerdione)

3D-SDF for HMDB0302131 (1-Dehydro-[6]-gingerdione)

PDB for HMDB0302131 (1-Dehydro-[6]-gingerdione)

3D PDB for HMDB0302131 (1-Dehydro-[6]-gingerdione)

SMILES for HMDB0302131 (1-Dehydro-[6]-gingerdione)

INCHI for HMDB0302131 (1-Dehydro-[6]-gingerdione)

Structure for HMDB0302131 (1-Dehydro-[6]-gingerdione)

3D Structure for HMDB0302131 (1-Dehydro-[6]-gingerdione)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

MS/MS Spectra