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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-09 20:53:57 UTC

Update Date

2022-03-07 03:17:38 UTC

HMDB ID

HMDB0060092

Secondary Accession Numbers

HMDB60092

Metabolite Identification

Common Name

all-trans-3,4-Didehydroretinoate

Description

all-trans-3,4-Didehydroretinoate, also known as 3,4-didehydroretinoic acid or vitamin A2 acid, belongs to the class of organic compounds known as retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof. all-trans-3,4-Didehydroretinoate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

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

HMDB0060092
     RDKit          3D
all-trans-3,4-Didehydroretinoate
 48 48  0  0  0  0  0  0  0  0999 V2000
   -3.1014    1.8091   -0.4812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4569    0.6391   -1.3071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5245   -0.3787   -1.4412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3213   -0.2245   -0.7335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3591   -1.1507   -0.6147 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8357   -0.8061    0.1712 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9949    0.7658    0.2306 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8664   -1.3809    0.5817 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8253   -0.5978    1.3273 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6183   -0.0112    1.9349 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5735    0.7444    2.6729 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6045    2.2598    2.5418 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5200    0.1728    3.3773 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4894    1.0285    4.1375 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3924    0.3529    4.7639 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4173    2.3864    4.1655 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9692   -1.3589   -2.4264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1542   -2.4361   -2.9658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4839   -0.5001   -3.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2809   -1.9422   -1.8918 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2751   -0.8633   -1.8145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9132    0.3949   -1.5266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5397    2.5925   -1.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5324    1.5170    0.3887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0427    2.2963   -0.0773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0943    0.7405   -0.2095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4558   -2.0859   -1.0810 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5674    1.0671   -0.8099 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4269    1.1708    0.9859 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0599    1.0208    0.0578 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9046   -2.4637    0.3738 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4615   -1.8030    1.7752 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8457    1.1508    1.7762 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3966    2.7363    3.5032 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5548    2.6146    2.1100 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7648    2.6223    1.8702 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5725   -0.8979    3.4500 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1265    2.8712    5.0740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0780   -2.1993   -3.1313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5737   -2.5984   -4.0509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2742   -3.4513   -2.5280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5844    0.5811   -3.3134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7955   -0.4643   -4.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4601   -0.8715   -3.9738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0561   -2.3337   -0.8465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5939   -2.7689   -2.5202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2910   -1.1370   -1.9985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6071    1.1900   -1.4485 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  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  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
  3 17  1  0
 17 18  1  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  2  0
 22  2  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  9 32  1  0
 10 33  1  0
 12 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 16 38  1  0
 18 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 19 43  1  0
 19 44  1  0
 20 45  1  0
 20 46  1  0
 21 47  1  0
 22 48  1  0
M  END


  Mrv0541 05091313532D          

 22 22  0  0  0  0            999 V2000
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    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
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   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
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    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
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    2.4750    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
    7.1447    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  8  6  1  0  0  0  0
  9  6  2  0  0  0  0
 10  7  2  0  0  0  0
 12 11  2  0  0  0  0
 13  7  1  0  0  0  0
 15  1  1  0  0  0  0
 15  8  2  0  0  0  0
 15 11  1  0  0  0  0
 16  2  1  0  0  0  0
 16  9  1  0  0  0  0
 16 14  2  0  0  0  0
 17  3  1  0  0  0  0
 17 10  1  0  0  0  0
 18 12  1  0  0  0  0
 18 17  2  0  0  0  0
 19 14  1  0  0  0  0
 20  4  1  0  0  0  0
 20  5  1  0  0  0  0
 20 13  1  0  0  0  0
 20 18  1  0  0  0  0
 21 19  2  0  0  0  0
 22 19  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060092

> <DATABASE_NAME>
hmdb

> <SMILES>
C\C(\C=C\C1=C(C)C=CCC1(C)C)=C/C=C/C(/C)=C/C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H26O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6-12,14H,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+

> <INCHI_KEY>
SYESMXTWOAQFET-YCNIQYBTSA-N

> <FORMULA>
C20H26O2

> <MOLECULAR_WEIGHT>
298.4192

> <EXACT_MASS>
298.193280076

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
35.72469083346676

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)nona-2,4,6,8-tetraenoic acid

> <ALOGPS_LOGP>
6.00

> <JCHEM_LOGP>
4.652446054333334

> <ALOGPS_LOGS>
-4.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.996647744997455

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
98.9074

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.37e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)nona-2,4,6,8-tetraenoic acid

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0060092
     RDKit          3D
all-trans-3,4-Didehydroretinoate
 48 48  0  0  0  0  0  0  0  0999 V2000
   -3.1014    1.8091   -0.4812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4569    0.6391   -1.3071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5245   -0.3787   -1.4412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3213   -0.2245   -0.7335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3591   -1.1507   -0.6147 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8357   -0.8061    0.1712 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9949    0.7658    0.2306 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8664   -1.3809    0.5817 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8253   -0.5978    1.3273 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6183   -0.0112    1.9349 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5735    0.7444    2.6729 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6045    2.2598    2.5418 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5200    0.1728    3.3773 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4894    1.0285    4.1375 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3924    0.3529    4.7639 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4173    2.3864    4.1655 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9692   -1.3589   -2.4264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1542   -2.4361   -2.9658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4839   -0.5001   -3.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2809   -1.9422   -1.8918 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2751   -0.8633   -1.8145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9132    0.3949   -1.5266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5397    2.5925   -1.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5324    1.5170    0.3887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0427    2.2963   -0.0773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0943    0.7405   -0.2095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4558   -2.0859   -1.0810 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5674    1.0671   -0.8099 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4269    1.1708    0.9859 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0599    1.0208    0.0578 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9046   -2.4637    0.3738 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4615   -1.8030    1.7752 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8457    1.1508    1.7762 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3966    2.7363    3.5032 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5548    2.6146    2.1100 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7648    2.6223    1.8702 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5725   -0.8979    3.4500 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1265    2.8712    5.0740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0780   -2.1993   -3.1313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5737   -2.5984   -4.0509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2742   -3.4513   -2.5280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5844    0.5811   -3.3134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7955   -0.4643   -4.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4601   -0.8715   -3.9738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0561   -2.3337   -0.8465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5939   -2.7689   -2.5202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2910   -1.1370   -1.9985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6071    1.1900   -1.4485 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  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  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
  3 17  1  0
 17 18  1  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  2  0
 22  2  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  9 32  1  0
 10 33  1  0
 12 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 16 38  1  0
 18 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 19 43  1  0
 19 44  1  0
 20 45  1  0
 20 46  1  0
 21 47  1  0
 22 48  1  0
M  END

HEADER    PROTEIN                                 09-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-MAY-13         0                                  
HETATM    1  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      13.337   6.160   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      14.671   3.850   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2   16                                                            
CONECT    3   17                                                            
CONECT    4   20                                                            
CONECT    5   20                                                            
CONECT    6    8    9                                                       
CONECT    7   10   13                                                       
CONECT    8    6   15                                                       
CONECT    9    6   16                                                       
CONECT   10    7   17                                                       
CONECT   11   12   15                                                       
CONECT   12   11   18                                                       
CONECT   13    7   20                                                       
CONECT   14   16   19                                                       
CONECT   15    1    8   11                                                  
CONECT   16    2    9   14                                                  
CONECT   17    3   10   18                                                  
CONECT   18   12   17   20                                                  
CONECT   19   14   21   22                                                  
CONECT   20    4    5   13   18                                             
CONECT   21   19                                                            
CONECT   22   19                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

COMPND    HMDB0060092
HETATM    1  C1  UNL     1      -3.101   1.809  -0.481  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.457   0.639  -1.307  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.525  -0.379  -1.441  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.321  -0.224  -0.734  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.359  -1.151  -0.615  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.836  -0.806   0.171  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.995   0.766   0.231  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.866  -1.381   0.582  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.825  -0.598   1.327  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.618  -0.011   1.935  1.00  0.00           C  
HETATM   11  C11 UNL     1       4.573   0.744   2.673  1.00  0.00           C  
HETATM   12  C12 UNL     1       4.605   2.260   2.542  1.00  0.00           C  
HETATM   13  C13 UNL     1       5.520   0.173   3.377  1.00  0.00           C  
HETATM   14  C14 UNL     1       6.489   1.029   4.137  1.00  0.00           C  
HETATM   15  O1  UNL     1       7.392   0.353   4.764  1.00  0.00           O  
HETATM   16  O2  UNL     1       6.417   2.386   4.166  1.00  0.00           O  
HETATM   17  C15 UNL     1      -2.969  -1.359  -2.426  1.00  0.00           C  
HETATM   18  C16 UNL     1      -2.154  -2.436  -2.966  1.00  0.00           C  
HETATM   19  C17 UNL     1      -3.484  -0.500  -3.650  1.00  0.00           C  
HETATM   20  C18 UNL     1      -4.281  -1.942  -1.892  1.00  0.00           C  
HETATM   21  C19 UNL     1      -5.275  -0.863  -1.815  1.00  0.00           C  
HETATM   22  C20 UNL     1      -4.913   0.395  -1.527  1.00  0.00           C  
HETATM   23  H1  UNL     1      -2.540   2.593  -1.058  1.00  0.00           H  
HETATM   24  H2  UNL     1      -2.532   1.517   0.389  1.00  0.00           H  
HETATM   25  H3  UNL     1      -4.043   2.296  -0.077  1.00  0.00           H  
HETATM   26  H4  UNL     1      -1.094   0.741  -0.210  1.00  0.00           H  
HETATM   27  H5  UNL     1      -0.456  -2.086  -1.081  1.00  0.00           H  
HETATM   28  H6  UNL     1       0.567   1.067  -0.810  1.00  0.00           H  
HETATM   29  H7  UNL     1       0.427   1.171   0.986  1.00  0.00           H  
HETATM   30  H8  UNL     1       2.060   1.021   0.058  1.00  0.00           H  
HETATM   31  H9  UNL     1       1.905  -2.464   0.374  1.00  0.00           H  
HETATM   32  H10 UNL     1       3.461  -1.803   1.775  1.00  0.00           H  
HETATM   33  H11 UNL     1       2.846   1.151   1.776  1.00  0.00           H  
HETATM   34  H12 UNL     1       4.397   2.736   3.503  1.00  0.00           H  
HETATM   35  H13 UNL     1       5.555   2.615   2.110  1.00  0.00           H  
HETATM   36  H14 UNL     1       3.765   2.622   1.870  1.00  0.00           H  
HETATM   37  H15 UNL     1       5.573  -0.898   3.450  1.00  0.00           H  
HETATM   38  H16 UNL     1       6.127   2.871   5.074  1.00  0.00           H  
HETATM   39  H17 UNL     1      -1.078  -2.199  -3.131  1.00  0.00           H  
HETATM   40  H18 UNL     1      -2.574  -2.598  -4.051  1.00  0.00           H  
HETATM   41  H19 UNL     1      -2.274  -3.451  -2.528  1.00  0.00           H  
HETATM   42  H20 UNL     1      -3.584   0.581  -3.313  1.00  0.00           H  
HETATM   43  H21 UNL     1      -2.796  -0.464  -4.469  1.00  0.00           H  
HETATM   44  H22 UNL     1      -4.460  -0.871  -3.974  1.00  0.00           H  
HETATM   45  H23 UNL     1      -4.056  -2.334  -0.846  1.00  0.00           H  
HETATM   46  H24 UNL     1      -4.594  -2.769  -2.520  1.00  0.00           H  
HETATM   47  H25 UNL     1      -6.291  -1.137  -1.998  1.00  0.00           H  
HETATM   48  H26 UNL     1      -5.607   1.190  -1.449  1.00  0.00           H  
CONECT    1    2   23   24   25
CONECT    2    3    3   22
CONECT    3    4   17
CONECT    4    5    5   26
CONECT    5    6   27
CONECT    6    7    8    8
CONECT    7   28   29   30
CONECT    8    9   31
CONECT    9   10   10   32
CONECT   10   11   33
CONECT   11   12   13   13
CONECT   12   34   35   36
CONECT   13   14   37
CONECT   14   15   15   16
CONECT   16   38
CONECT   17   18   19   20
CONECT   18   39   40   41
CONECT   19   42   43   44
CONECT   20   21   45   46
CONECT   21   22   22   47
CONECT   22   48
END

HMDB0060092
     RDKit          3D
all-trans-3,4-Didehydroretinoate
 48 48  0  0  0  0  0  0  0  0999 V2000
   -3.1014    1.8091   -0.4812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4569    0.6391   -1.3071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5245   -0.3787   -1.4412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3213   -0.2245   -0.7335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3591   -1.1507   -0.6147 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8357   -0.8061    0.1712 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9949    0.7658    0.2306 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8664   -1.3809    0.5817 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8253   -0.5978    1.3273 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6183   -0.0112    1.9349 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5735    0.7444    2.6729 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6045    2.2598    2.5418 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5200    0.1728    3.3773 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4894    1.0285    4.1375 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3924    0.3529    4.7639 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4173    2.3864    4.1655 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9692   -1.3589   -2.4264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1542   -2.4361   -2.9658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4839   -0.5001   -3.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2809   -1.9422   -1.8918 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2751   -0.8633   -1.8145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9132    0.3949   -1.5266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5397    2.5925   -1.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5324    1.5170    0.3887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0427    2.2963   -0.0773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0943    0.7405   -0.2095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4558   -2.0859   -1.0810 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5674    1.0671   -0.8099 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4269    1.1708    0.9859 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0599    1.0208    0.0578 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9046   -2.4637    0.3738 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4615   -1.8030    1.7752 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8457    1.1508    1.7762 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3966    2.7363    3.5032 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5548    2.6146    2.1100 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7648    2.6223    1.8702 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5725   -0.8979    3.4500 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1265    2.8712    5.0740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0780   -2.1993   -3.1313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5737   -2.5984   -4.0509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2742   -3.4513   -2.5280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5844    0.5811   -3.3134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7955   -0.4643   -4.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4601   -0.8715   -3.9738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0561   -2.3337   -0.8465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5939   -2.7689   -2.5202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2910   -1.1370   -1.9985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6071    1.1900   -1.4485 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  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  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
  3 17  1  0
 17 18  1  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  2  0
 22  2  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  9 32  1  0
 10 33  1  0
 12 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 16 38  1  0
 18 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 19 43  1  0
 19 44  1  0
 20 45  1  0
 20 46  1  0
 21 47  1  0
 22 48  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3,4-Didehydroretinoic acid	ChEBI
all-trans-3,4-Didehydro-retinoic acid	ChEBI
Didehydroretinoic acid	ChEBI
Vitamin a2 acid	ChEBI
3,4-Didehydroretinoate	Generator
all-trans-3,4-Didehydro-retinoate	Generator
Didehydroretinoate	Generator
all-trans-3,4-Didehydroretinoic acid	Generator
3,4-Didehydroretinoic acid, sodium salt	HMDB

Chemical Formula

C₂₀H₂₆O₂

Average Molecular Weight

298.4192

Monoisotopic Molecular Weight

298.193280076

IUPAC Name

(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)nona-2,4,6,8-tetraenoic acid

Traditional Name

(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)nona-2,4,6,8-tetraenoic acid

CAS Registry Number

Not Available

SMILES

C\C(\C=C\C1=C(C)C=CCC1(C)C)=C/C=C/C(/C)=C/C(O)=O

InChI Identifier

InChI=1S/C20H26O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6-12,14H,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+

InChI Key

SYESMXTWOAQFET-YCNIQYBTSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Retinoids

Direct Parent

Retinoids

Alternative Parents

Substituents

Retinoic acid
Diterpenoid
Retinoid skeleton
Medium-chain fatty acid
Branched fatty acid
Methyl-branched fatty acid
Fatty acyl
Unsaturated fatty acid
Fatty acid
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Organic oxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Retinoids (LMPR01090020 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0060092)

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
Water Solubility	0.0074 g/L	ALOGPS
logP	6	ALOGPS
logP	4.65	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.3 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	98.91 m³·mol⁻¹	ChemAxon
Polarizability	35.72 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	179.119	31661259
DarkChem	[M-H]-	177.89	31661259
DeepCCS	[M+H]+	198.072	30932474
DeepCCS	[M-H]-	195.714	30932474
DeepCCS	[M-2H]-	229.899	30932474
DeepCCS	[M+Na]+	205.196	30932474
AllCCS	[M+H]+	175.4	32859911
AllCCS	[M+H-H2O]+	172.1	32859911
AllCCS	[M+NH4]+	178.5	32859911
AllCCS	[M+Na]+	179.4	32859911
AllCCS	[M-H]-	178.0	32859911
AllCCS	[M+Na-2H]-	178.3	32859911
AllCCS	[M+HCOO]-	178.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
all-trans-3,4-Didehydroretinoate	C\C(\C=C\C1=C(C)C=CCC1(C)C)=C/C=C/C(/C)=C/C(O)=O	3810.3	Standard polar	33892256
all-trans-3,4-Didehydroretinoate	C\C(\C=C\C1=C(C)C=CCC1(C)C)=C/C=C/C(/C)=C/C(O)=O	2453.9	Standard non polar	33892256
all-trans-3,4-Didehydroretinoate	C\C(\C=C\C1=C(C)C=CCC1(C)C)=C/C=C/C(/C)=C/C(O)=O	2496.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
all-trans-3,4-Didehydroretinoate,1TMS,isomer #1	CC1=C(/C=C/C(C)=C/C=C/C(C)=C/C(=O)O[Si](C)(C)C)C(C)(C)CC=C1	2701.7	Semi standard non polar	33892256
all-trans-3,4-Didehydroretinoate,1TBDMS,isomer #1	CC1=C(/C=C/C(C)=C/C=C/C(C)=C/C(=O)O[Si](C)(C)C(C)(C)C)C(C)(C)CC=C1	2912.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - all-trans-3,4-Didehydroretinoate GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-2190000000-c6f9f2351a8952470f3b	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - all-trans-3,4-Didehydroretinoate GC-MS (1 TMS) - 70eV, Positive	splash10-0a4i-6259000000-3eef7c5898196604bf75	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - all-trans-3,4-Didehydroretinoate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 10V, Positive-QTOF	splash10-001i-0290000000-bff7adf141bbcb7a77c5	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 20V, Positive-QTOF	splash10-0f80-2960000000-55281f0b8495de384ae0	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 40V, Positive-QTOF	splash10-059i-7900000000-0394e4380528d9fb243a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 10V, Negative-QTOF	splash10-0f6t-0090000000-4ee06be0f46d388dee15	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 20V, Negative-QTOF	splash10-0ufs-0090000000-c5ee27afefaca27f4874	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 40V, Negative-QTOF	splash10-0019-3490000000-3f59ab9cc9e6a95fef88	2017-10-06	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

447276

PDB ID

Not Available

ChEBI ID

133794

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

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]
Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for all-trans-3,4-Didehydroretinoate (HMDB0060092)

MOL for HMDB0060092 (all-trans-3,4-Didehydroretinoate)

3D MOL for HMDB0060092 (all-trans-3,4-Didehydroretinoate)

3D SDF for HMDB0060092 (all-trans-3,4-Didehydroretinoate)

3D-SDF for HMDB0060092 (all-trans-3,4-Didehydroretinoate)

PDB for HMDB0060092 (all-trans-3,4-Didehydroretinoate)

3D PDB for HMDB0060092 (all-trans-3,4-Didehydroretinoate)

SMILES for HMDB0060092 (all-trans-3,4-Didehydroretinoate)

INCHI for HMDB0060092 (all-trans-3,4-Didehydroretinoate)

Structure for HMDB0060092 (all-trans-3,4-Didehydroretinoate)

3D Structure for HMDB0060092 (all-trans-3,4-Didehydroretinoate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra