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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2017-03-21 06:15:41 UTC

Update Date

2021-09-14 15:47:55 UTC

HMDB ID

HMDB0062412

Secondary Accession Numbers

HMDB62412

Metabolite Identification

Common Name

5,8-Epoxy-13-cis-retinoic acid

Description

112018-12-9 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. 112018-12-9 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

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

HMDB0062412
     RDKit          3D
5,8-Epoxy-13-cis-retinoic acid
 51 52  0  0  0  0  0  0  0  0999 V2000
    5.4907    0.7749   -1.2984 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6337    0.1750    0.0916 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8204   -0.0659    0.5673 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0342   -0.6269    1.8612 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2369   -0.8164    2.2157 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0739   -0.9747    2.7428 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3941   -0.0845    0.7897 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2036    0.1974    0.2182 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9487   -0.0615    0.9161 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8127    0.2324    0.3119 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8649    0.8066   -1.0353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4491   -0.0413    1.0487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2379   -0.9847    0.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3880   -0.4155   -0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5444   -0.9114   -0.8061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1743   -1.0915   -2.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0203   -2.2726   -0.2878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7084    0.0372   -0.6179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8533    0.5462    0.7695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6143    0.9962    1.4521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3908    0.9338    0.5597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5361    2.0389   -0.4550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2291    1.0507    1.2644 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4787    1.0077   -1.7023 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8726    1.7093   -1.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9687    0.0664   -1.9636 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6654    0.1952   -0.1038 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1748   -1.7808    3.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2815   -0.5031    1.7770 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2106    0.6178   -0.7650 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9691   -0.4943    1.9271 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4631    0.0848   -1.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1437    0.8034   -1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3622    1.7713   -1.1166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2426   -0.5341    2.0311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8947   -2.0042   -0.0333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0530   -1.1400   -2.9179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4468   -0.3881   -2.6371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6994   -2.1125   -2.3263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4228   -3.0755   -0.7607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0619   -2.3756   -0.6210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9267   -2.2719    0.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6997    0.8410   -1.4008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6338   -0.5610   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3481   -0.2478    1.3912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5880    1.3970    0.7327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6912    2.0573    1.8032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3940    0.3731    2.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4816    2.6117   -0.3345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7243    2.7948   -0.2412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3621    1.7157   -1.4916 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
  4  6  1  0
  2  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 12  1  0
 21 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 11 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 13 36  1  0
 16 37  1  0
 16 38  1  0
 16 39  1  0
 17 40  1  0
 17 41  1  0
 17 42  1  0
 18 43  1  0
 18 44  1  0
 19 45  1  0
 19 46  1  0
 20 47  1  0
 20 48  1  0
 22 49  1  0
 22 50  1  0
 22 51  1  0
M  END

      
  Mrv1652307161819322D          

 23 24  0  0  0  0            999 V2000
    3.5780  -14.0601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5745  -14.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2898  -15.3021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0123  -14.0661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2968  -13.6475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7126  -12.9348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8870  -12.9313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0087  -14.8936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7921  -15.1508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7981  -13.8160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2800  -14.4855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0909  -15.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1050  -14.4892    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5207  -13.7765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5143  -15.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3393  -15.2091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7486  -15.9254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5736  -15.9291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9893  -15.2165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9829  -16.6454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7551  -14.4965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9957  -13.7876    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.5800  -14.5002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  4  5  1  0  0  0  0
  5  1  1  0  0  0  0
  2  3  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  8  4  1  0  0  0  0
  3  8  1  0  0  0  0
  4 10  2  0  0  0  0
  8  9  1  0  0  0  0
  9 11  1  0  0  0  0
 11 10  1  0  0  0  0
  8 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 15 16  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 23 22  2  0  0  0  0
 23 21  1  0  0  0  0
 19 23  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0062412

> <DATABASE_NAME>
hmdb

> <SMILES>
C\C(\C=C\C=C(/C)C1OC2(C)CCCC(C)(C)C2=C1)=C\C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O3/c1-14(12-18(21)22)8-6-9-15(2)16-13-17-19(3,4)10-7-11-20(17,5)23-16/h6,8-9,12-13,16H,7,10-11H2,1-5H3,(H,21,22)/b8-6+,14-12-,15-9+

> <INCHI_KEY>
QDOSIDVGVRAXSE-DYIZZJGFSA-N

> <FORMULA>
C20H28O3

> <MOLECULAR_WEIGHT>
316.441

> <EXACT_MASS>
316.203844762

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
36.55989418355752

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2Z,4E,6E)-7-(4,4,7a-trimethyl-2,4,5,6,7,7a-hexahydro-1-benzofuran-2-yl)-3-methylocta-2,4,6-trienoic acid

> <ALOGPS_LOGP>
5.38

> <JCHEM_LOGP>
4.269493662666666

> <ALOGPS_LOGS>
-4.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.643430277177042

> <JCHEM_PKA_STRONGEST_BASIC>
-4.272741090168912

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
96.39729999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.18e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2Z,4E,6E)-7-(4,4,7a-trimethyl-2,5,6,7-tetrahydro-1-benzofuran-2-yl)-3-methylocta-2,4,6-trienoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0062412
     RDKit          3D
5,8-Epoxy-13-cis-retinoic acid
 51 52  0  0  0  0  0  0  0  0999 V2000
    5.4907    0.7749   -1.2984 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6337    0.1750    0.0916 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8204   -0.0659    0.5673 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0342   -0.6269    1.8612 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2369   -0.8164    2.2157 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0739   -0.9747    2.7428 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3941   -0.0845    0.7897 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2036    0.1974    0.2182 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9487   -0.0615    0.9161 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8127    0.2324    0.3119 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8649    0.8066   -1.0353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4491   -0.0413    1.0487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2379   -0.9847    0.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3880   -0.4155   -0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5444   -0.9114   -0.8061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1743   -1.0915   -2.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0203   -2.2726   -0.2878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7084    0.0372   -0.6179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8533    0.5462    0.7695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6143    0.9962    1.4521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3908    0.9338    0.5597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5361    2.0389   -0.4550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2291    1.0507    1.2644 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4787    1.0077   -1.7023 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8726    1.7093   -1.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9687    0.0664   -1.9636 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6654    0.1952   -0.1038 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1748   -1.7808    3.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2815   -0.5031    1.7770 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2106    0.6178   -0.7650 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9691   -0.4943    1.9271 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4631    0.0848   -1.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1437    0.8034   -1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3622    1.7713   -1.1166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2426   -0.5341    2.0311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8947   -2.0042   -0.0333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0530   -1.1400   -2.9179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4468   -0.3881   -2.6371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6994   -2.1125   -2.3263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4228   -3.0755   -0.7607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0619   -2.3756   -0.6210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9267   -2.2719    0.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6997    0.8410   -1.4008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6338   -0.5610   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3481   -0.2478    1.3912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5880    1.3970    0.7327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6912    2.0573    1.8032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3940    0.3731    2.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4816    2.6117   -0.3345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7243    2.7948   -0.2412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3621    1.7157   -1.4916 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
  4  6  1  0
  2  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 12  1  0
 21 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 11 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 13 36  1  0
 16 37  1  0
 16 38  1  0
 16 39  1  0
 17 40  1  0
 17 41  1  0
 17 42  1  0
 18 43  1  0
 18 44  1  0
 19 45  1  0
 19 46  1  0
 20 47  1  0
 20 48  1  0
 22 49  1  0
 22 50  1  0
 22 51  1  0
M  END

HEADER    PROTEIN                                 16-JUL-18   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-JUL-18         0                                  
HETATM    1  C   UNK     0       6.679 -26.246   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.672 -27.790   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.008 -28.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.356 -26.257   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.021 -25.475   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.797 -24.145   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.256 -24.138   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.350 -27.801   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      10.812 -28.281   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      10.823 -25.790   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.723 -27.040   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.503 -29.334   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.263 -27.047   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      14.039 -25.716   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      14.027 -28.384   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      15.567 -28.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      16.331 -29.727   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      17.871 -29.734   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      18.647 -28.404   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      18.635 -31.071   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      16.343 -27.060   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      18.659 -25.737   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      17.883 -27.067   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    8                                                       
CONECT    4    5    8   10                                                  
CONECT    5    4    1    6    7                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    4    3    9   12                                             
CONECT    9    8   11                                                       
CONECT   10    4   11                                                       
CONECT   11    9   10   13                                                  
CONECT   12    8                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   17   15                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18   23                                                       
CONECT   20   18                                                            
CONECT   21   23                                                            
CONECT   22   23                                                            
CONECT   23   22   21   19                                                  
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

COMPND    HMDB0062412
HETATM    1  C1  UNL     1       5.491   0.775  -1.298  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.634   0.175   0.092  1.00  0.00           C  
HETATM    3  C3  UNL     1       6.820  -0.066   0.567  1.00  0.00           C  
HETATM    4  C4  UNL     1       7.034  -0.627   1.861  1.00  0.00           C  
HETATM    5  O1  UNL     1       8.237  -0.816   2.216  1.00  0.00           O  
HETATM    6  O2  UNL     1       6.074  -0.975   2.743  1.00  0.00           O  
HETATM    7  C5  UNL     1       4.394  -0.084   0.790  1.00  0.00           C  
HETATM    8  C6  UNL     1       3.204   0.197   0.218  1.00  0.00           C  
HETATM    9  C7  UNL     1       1.949  -0.061   0.916  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.813   0.232   0.312  1.00  0.00           C  
HETATM   11  C9  UNL     1       0.865   0.807  -1.035  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.449  -0.041   1.049  1.00  0.00           C  
HETATM   13  C11 UNL     1      -1.238  -0.985   0.256  1.00  0.00           C  
HETATM   14  C12 UNL     1      -2.388  -0.416  -0.038  1.00  0.00           C  
HETATM   15  C13 UNL     1      -3.544  -0.911  -0.806  1.00  0.00           C  
HETATM   16  C14 UNL     1      -3.174  -1.091  -2.236  1.00  0.00           C  
HETATM   17  C15 UNL     1      -4.020  -2.273  -0.288  1.00  0.00           C  
HETATM   18  C16 UNL     1      -4.708   0.037  -0.618  1.00  0.00           C  
HETATM   19  C17 UNL     1      -4.853   0.546   0.770  1.00  0.00           C  
HETATM   20  C18 UNL     1      -3.614   0.996   1.452  1.00  0.00           C  
HETATM   21  C19 UNL     1      -2.391   0.934   0.560  1.00  0.00           C  
HETATM   22  C20 UNL     1      -2.536   2.039  -0.455  1.00  0.00           C  
HETATM   23  O3  UNL     1      -1.229   1.051   1.264  1.00  0.00           O  
HETATM   24  H1  UNL     1       6.479   1.008  -1.702  1.00  0.00           H  
HETATM   25  H2  UNL     1       4.873   1.709  -1.219  1.00  0.00           H  
HETATM   26  H3  UNL     1       4.969   0.066  -1.964  1.00  0.00           H  
HETATM   27  H4  UNL     1       7.665   0.195  -0.104  1.00  0.00           H  
HETATM   28  H5  UNL     1       6.175  -1.781   3.326  1.00  0.00           H  
HETATM   29  H6  UNL     1       4.282  -0.503   1.777  1.00  0.00           H  
HETATM   30  H7  UNL     1       3.211   0.618  -0.765  1.00  0.00           H  
HETATM   31  H8  UNL     1       1.969  -0.494   1.927  1.00  0.00           H  
HETATM   32  H9  UNL     1       1.463   0.085  -1.667  1.00  0.00           H  
HETATM   33  H10 UNL     1      -0.144   0.803  -1.521  1.00  0.00           H  
HETATM   34  H11 UNL     1       1.362   1.771  -1.117  1.00  0.00           H  
HETATM   35  H12 UNL     1      -0.243  -0.534   2.031  1.00  0.00           H  
HETATM   36  H13 UNL     1      -0.895  -2.004  -0.033  1.00  0.00           H  
HETATM   37  H14 UNL     1      -4.053  -1.140  -2.918  1.00  0.00           H  
HETATM   38  H15 UNL     1      -2.447  -0.388  -2.637  1.00  0.00           H  
HETATM   39  H16 UNL     1      -2.699  -2.112  -2.326  1.00  0.00           H  
HETATM   40  H17 UNL     1      -3.423  -3.076  -0.761  1.00  0.00           H  
HETATM   41  H18 UNL     1      -5.062  -2.376  -0.621  1.00  0.00           H  
HETATM   42  H19 UNL     1      -3.927  -2.272   0.815  1.00  0.00           H  
HETATM   43  H20 UNL     1      -4.700   0.841  -1.401  1.00  0.00           H  
HETATM   44  H21 UNL     1      -5.634  -0.561  -0.856  1.00  0.00           H  
HETATM   45  H22 UNL     1      -5.348  -0.248   1.391  1.00  0.00           H  
HETATM   46  H23 UNL     1      -5.588   1.397   0.733  1.00  0.00           H  
HETATM   47  H24 UNL     1      -3.691   2.057   1.803  1.00  0.00           H  
HETATM   48  H25 UNL     1      -3.394   0.373   2.354  1.00  0.00           H  
HETATM   49  H26 UNL     1      -3.482   2.612  -0.334  1.00  0.00           H  
HETATM   50  H27 UNL     1      -1.724   2.795  -0.241  1.00  0.00           H  
HETATM   51  H28 UNL     1      -2.362   1.716  -1.492  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3    3    7
CONECT    3    4   27
CONECT    4    5    5    6
CONECT    6   28
CONECT    7    8    8   29
CONECT    8    9   30
CONECT    9   10   10   31
CONECT   10   11   12
CONECT   11   32   33   34
CONECT   12   13   23   35
CONECT   13   14   14   36
CONECT   14   15   21
CONECT   15   16   17   18
CONECT   16   37   38   39
CONECT   17   40   41   42
CONECT   18   19   43   44
CONECT   19   20   45   46
CONECT   20   21   47   48
CONECT   21   22   23
CONECT   22   49   50   51
END

HMDB0062412
     RDKit          3D
5,8-Epoxy-13-cis-retinoic acid
 51 52  0  0  0  0  0  0  0  0999 V2000
    5.4907    0.7749   -1.2984 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6337    0.1750    0.0916 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8204   -0.0659    0.5673 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0342   -0.6269    1.8612 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2369   -0.8164    2.2157 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0739   -0.9747    2.7428 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3941   -0.0845    0.7897 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2036    0.1974    0.2182 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9487   -0.0615    0.9161 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8127    0.2324    0.3119 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8649    0.8066   -1.0353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4491   -0.0413    1.0487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2379   -0.9847    0.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3880   -0.4155   -0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5444   -0.9114   -0.8061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1743   -1.0915   -2.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0203   -2.2726   -0.2878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7084    0.0372   -0.6179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8533    0.5462    0.7695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6143    0.9962    1.4521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3908    0.9338    0.5597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5361    2.0389   -0.4550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2291    1.0507    1.2644 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4787    1.0077   -1.7023 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8726    1.7093   -1.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9687    0.0664   -1.9636 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6654    0.1952   -0.1038 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1748   -1.7808    3.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2815   -0.5031    1.7770 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2106    0.6178   -0.7650 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9691   -0.4943    1.9271 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4631    0.0848   -1.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1437    0.8034   -1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3622    1.7713   -1.1166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2426   -0.5341    2.0311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8947   -2.0042   -0.0333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0530   -1.1400   -2.9179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4468   -0.3881   -2.6371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6994   -2.1125   -2.3263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4228   -3.0755   -0.7607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0619   -2.3756   -0.6210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9267   -2.2719    0.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6997    0.8410   -1.4008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6338   -0.5610   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3481   -0.2478    1.3912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5880    1.3970    0.7327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6912    2.0573    1.8032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3940    0.3731    2.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4816    2.6117   -0.3345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7243    2.7948   -0.2412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3621    1.7157   -1.4916 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
  4  6  1  0
  2  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 12  1  0
 21 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 11 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 13 36  1  0
 16 37  1  0
 16 38  1  0
 16 39  1  0
 17 40  1  0
 17 41  1  0
 17 42  1  0
 18 43  1  0
 18 44  1  0
 19 45  1  0
 19 46  1  0
 20 47  1  0
 20 48  1  0
 22 49  1  0
 22 50  1  0
 22 51  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
5,8-Epoxy-13-cis-retinoate	Generator
5,8-Oxy-13-cis-retinoic acid	HMDB
5,8-Oxy-13-cis-retinoate	Generator, HMDB

Chemical Formula

C₂₀H₂₈O₃

Average Molecular Weight

316.441

Monoisotopic Molecular Weight

316.203844762

IUPAC Name

(2Z,4E,6E)-7-(4,4,7a-trimethyl-2,4,5,6,7,7a-hexahydro-1-benzofuran-2-yl)-3-methylocta-2,4,6-trienoic acid

Traditional Name

(2Z,4E,6E)-7-(4,4,7a-trimethyl-2,5,6,7-tetrahydro-1-benzofuran-2-yl)-3-methylocta-2,4,6-trienoic acid

CAS Registry Number

112018-12-9

SMILES

C\C(\C=C\C=C(/C)C1OC2(C)CCCC(C)(C)C2=C1)=C\C(O)=O

InChI Identifier

InChI=1S/C20H28O3/c1-14(12-18(21)22)8-6-9-15(2)16-13-17-19(3,4)10-7-11-20(17,5)23-16/h6,8-9,12-13,16H,7,10-11H2,1-5H3,(H,21,22)/b8-6+,14-12-,15-9+

InChI Key

QDOSIDVGVRAXSE-DYIZZJGFSA-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

Diterpenoid
Retinoid skeleton
Benzofuran
Medium-chain fatty acid
Branched fatty acid
Heterocyclic fatty acid
Methyl-branched fatty acid
Fatty acyl
Fatty acid
Unsaturated fatty acid
Dihydrofuran
Carboxylic acid derivative
Carboxylic acid
Dialkyl ether
Oxacycle
Ether
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Carbonyl group
Organic oxygen compound
Organic oxide
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Not Available

Not Available

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	5.38	ALOGPS
logP	4.27	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	4.64	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	46.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	96.4 m³·mol⁻¹	ChemAxon
Polarizability	36.56 Å³	ChemAxon
Number of Rings	2	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
DeepCCS	[M+H]+	195.915	30932474
DeepCCS	[M-H]-	193.557	30932474
DeepCCS	[M-2H]-	227.849	30932474
DeepCCS	[M+Na]+	203.81	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5,8-Epoxy-13-cis-retinoic acid	C\C(\C=C\C=C(/C)C1OC2(C)CCCC(C)(C)C2=C1)=C\C(O)=O	3808.5	Standard polar	33892256
5,8-Epoxy-13-cis-retinoic acid	C\C(\C=C\C=C(/C)C1OC2(C)CCCC(C)(C)C2=C1)=C\C(O)=O	2382.4	Standard non polar	33892256
5,8-Epoxy-13-cis-retinoic acid	C\C(\C=C\C=C(/C)C1OC2(C)CCCC(C)(C)C2=C1)=C\C(O)=O	2529.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5,8-Epoxy-13-cis-retinoic acid,1TMS,isomer #1	CC(=C/C(=O)O[Si](C)(C)C)/C=C/C=C(\C)C1C=C2C(C)(C)CCCC2(C)O1	2470.6	Semi standard non polar	33892256
5,8-Epoxy-13-cis-retinoic acid,1TBDMS,isomer #1	CC(=C/C(=O)O[Si](C)(C)C(C)(C)C)/C=C/C=C(\C)C1C=C2C(C)(C)CCCC2(C)O1	2688.0	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 - 5,8-Epoxy-13-cis-retinoic acid 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 - 5,8-Epoxy-13-cis-retinoic acid 10V, Positive-QTOF	splash10-0002-0392000000-9dbf7bb10fa1601a2a3b	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 20V, Positive-QTOF	splash10-0a4i-4690000000-55827767de361993d164	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 40V, Positive-QTOF	splash10-0540-9500000000-e21d5e898eeee23951f1	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 10V, Negative-QTOF	splash10-01b9-0079000000-1e7ad2193ee79b949971	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 20V, Negative-QTOF	splash10-00xs-0194000000-b6ec0ebfb3b7d59dc1b1	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 40V, Negative-QTOF	splash10-0pca-1960000000-4cf6ae66ac38055d1d47	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 10V, Negative-QTOF	splash10-00xr-0096000000-336c0053a8a2b4772a60	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 20V, Negative-QTOF	splash10-00di-0091000000-7814b454b97c52c4406c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 40V, Negative-QTOF	splash10-0pb9-0091000000-7d63ae1d92a28d525431	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 10V, Positive-QTOF	splash10-00r2-0292000000-1679c201b7c84fa8a3cb	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 20V, Positive-QTOF	splash10-0a4i-0950000000-0984ed17e4ee97f3bd25	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,8-Epoxy-13-cis-retinoic acid 40V, Positive-QTOF	splash10-05p6-7910000000-866e21fd9e2444093971	2021-09-23	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

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

71316382

PDB ID

Not Available

ChEBI ID

Not Available

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

Samokyszyn VM, Marnett LJ: Hydroperoxide-dependent cooxidation of 13-cis-retinoic acid by prostaglandin H synthase. J Biol Chem. 1987 Oct 15;262(29):14119-33. [PubMed:3115987 ]

Showing metabocard for 5,8-Epoxy-13-cis-retinoic acid (HMDB0062412)

MOL for HMDB0062412 (5,8-Epoxy-13-cis-retinoic acid)

3D MOL for HMDB0062412 (5,8-Epoxy-13-cis-retinoic acid)

3D SDF for HMDB0062412 (5,8-Epoxy-13-cis-retinoic acid)

3D-SDF for HMDB0062412 (5,8-Epoxy-13-cis-retinoic acid)

PDB for HMDB0062412 (5,8-Epoxy-13-cis-retinoic acid)

3D PDB for HMDB0062412 (5,8-Epoxy-13-cis-retinoic acid)

SMILES for HMDB0062412 (5,8-Epoxy-13-cis-retinoic acid)

INCHI for HMDB0062412 (5,8-Epoxy-13-cis-retinoic acid)

Structure for HMDB0062412 (5,8-Epoxy-13-cis-retinoic acid)

3D Structure for HMDB0062412 (5,8-Epoxy-13-cis-retinoic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra