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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2017-03-21 06:15:37 UTC

Update Date

2021-09-14 15:46:22 UTC

HMDB ID

HMDB0062411

Secondary Accession Numbers

HMDB62411

Metabolite Identification

Common Name

5,6-Epoxy-13-cis-retinoic acid

Description

81444-57-7 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. 81444-57-7 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

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

HMDB0062411
     RDKit          3D
5,6-Epoxy-13-cis-retinoic acid
 51 52  0  0  0  0  0  0  0  0999 V2000
    6.2897    2.1632   -0.6260 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7859    0.4078   -0.2069 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9741    0.1236   -0.2297 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0512   -1.3919    0.1046 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0202   -1.9972    0.3011 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2697   -1.9372    0.1567 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4783    0.7206   -0.1819 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4385   -0.1756   -0.1949 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0853    0.3260   -0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0119   -0.4234   -0.1550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0860   -1.8889   -0.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3391    0.1908   -0.2358 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4075   -0.5171   -0.1951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8321   -0.0844   -0.2699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2651   -0.0957   -1.6878 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7381   -1.0152   -0.7577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2019   -2.4370   -1.0643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1494   -1.0280   -0.3943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6204    0.1619    0.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7701    1.3522    0.1870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3168    1.0216    0.5436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3007    0.7976    2.0266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5254    2.3220    0.3330 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7727    1.8645   -1.5232 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2991    2.4812   -0.8122 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7787    2.3175    0.2973 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9331    0.5325   -0.3948 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9798   -1.5976    0.8188 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1166    1.7716   -0.0883 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6739   -1.1899   -0.2376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8741    1.4143   -0.1433 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0674   -2.3223   -0.0259 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5402   -2.3322   -1.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4904   -2.2216    0.7428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4206    1.2508   -0.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2722   -1.6141   -0.0763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3683   -2.4230   -1.7640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0394   -3.0464   -1.5015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9727   -2.8893   -0.0706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3915   -1.9891    0.1672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7847   -1.0938   -1.3005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6649    0.4376    0.1240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6648   -0.1507    1.4736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7691    1.5731   -0.9119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1557    2.2224    0.7609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3048    1.0910    2.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0322    1.5343    2.4737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5935   -0.1979    2.3481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1988    3.1811    0.6728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7115    2.3335    1.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2054    2.4671   -0.6788 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  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 16 14  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
 17 37  1  0
 17 38  1  0
 17 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 19 43  1  0
 20 44  1  0
 20 45  1  0
 22 46  1  0
 22 47  1  0
 22 48  1  0
 23 49  1  0
 23 50  1  0
 23 51  1  0
M  END


  Mrv1652307161819222D          

 23 24  0  0  0  0            999 V2000
    1.5182  -14.4321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5147  -15.2593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2299  -15.6739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9522  -14.4381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2369  -14.0196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6641  -14.0249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3792  -14.4404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0941  -14.0290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8092  -14.4446    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5242  -14.0330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6684  -14.8518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6527  -13.3071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8272  -13.3036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9486  -15.2654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6620  -15.6796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0959  -13.2041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9479  -14.0340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2370  -14.4521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9411  -13.2091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6656  -14.4405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6723  -15.2654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9613  -15.6837    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3900  -15.6721    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  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
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  4 11  1  0  0  0  0
  2  3  1  0  0  0  0
  5 12  1  0  0  0  0
  5 13  1  0  0  0  0
 14 15  1  0  0  0  0
 14 11  1  0  0  0  0
 14  4  1  0  0  0  0
  3 14  1  0  0  0  0
  8 16  1  0  0  0  0
 17 18  1  0  0  0  0
 10 18  2  0  0  0  0
 17 19  1  0  0  0  0
 17 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0062411

> <DATABASE_NAME>
hmdb

> <SMILES>
C\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C\C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O3/c1-15(8-6-9-16(2)14-17(21)22)10-13-20-18(3,4)11-7-12-19(20,5)23-20/h6,8-10,13-14H,7,11-12H2,1-5H3,(H,21,22)/b9-6+,13-10+,15-8+,16-14-

> <INCHI_KEY>
KEEHJLBAOLGBJZ-NJZIYGCESA-N

> <FORMULA>
C20H28O3

> <MOLECULAR_WEIGHT>
316.441

> <EXACT_MASS>
316.203844762

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
36.97495922972524

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2Z,4E,6E,8E)-3,7-dimethyl-9-{2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl}nona-2,4,6,8-tetraenoic acid

> <ALOGPS_LOGP>
5.74

> <JCHEM_LOGP>
4.540570249333333

> <ALOGPS_LOGS>
-4.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.936687619832732

> <JCHEM_PKA_STRONGEST_BASIC>
-4.282240537384268

> <JCHEM_POLAR_SURFACE_AREA>
49.83

> <JCHEM_REFRACTIVITY>
96.52249999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.91e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2Z,4E,6E,8E)-3,7-dimethyl-9-{2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl}nona-2,4,6,8-tetraenoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0062411
     RDKit          3D
5,6-Epoxy-13-cis-retinoic acid
 51 52  0  0  0  0  0  0  0  0999 V2000
    6.2897    2.1632   -0.6260 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7859    0.4078   -0.2069 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9741    0.1236   -0.2297 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0512   -1.3919    0.1046 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0202   -1.9972    0.3011 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2697   -1.9372    0.1567 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4783    0.7206   -0.1819 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4385   -0.1756   -0.1949 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0853    0.3260   -0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0119   -0.4234   -0.1550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0860   -1.8889   -0.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3391    0.1908   -0.2358 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4075   -0.5171   -0.1951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8321   -0.0844   -0.2699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2651   -0.0957   -1.6878 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7381   -1.0152   -0.7577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2019   -2.4370   -1.0643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1494   -1.0280   -0.3943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6204    0.1619    0.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7701    1.3522    0.1870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3168    1.0216    0.5436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3007    0.7976    2.0266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5254    2.3220    0.3330 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7727    1.8645   -1.5232 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2991    2.4812   -0.8122 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7787    2.3175    0.2973 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9331    0.5325   -0.3948 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9798   -1.5976    0.8188 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1166    1.7716   -0.0883 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6739   -1.1899   -0.2376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8741    1.4143   -0.1433 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0674   -2.3223   -0.0259 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5402   -2.3322   -1.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4904   -2.2216    0.7428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4206    1.2508   -0.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2722   -1.6141   -0.0763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3683   -2.4230   -1.7640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0394   -3.0464   -1.5015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9727   -2.8893   -0.0706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3915   -1.9891    0.1672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7847   -1.0938   -1.3005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6649    0.4376    0.1240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6648   -0.1507    1.4736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7691    1.5731   -0.9119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1557    2.2224    0.7609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3048    1.0910    2.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0322    1.5343    2.4737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5935   -0.1979    2.3481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1988    3.1811    0.6728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7115    2.3335    1.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2054    2.4671   -0.6788 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  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 16 14  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
 17 37  1  0
 17 38  1  0
 17 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 19 43  1  0
 20 44  1  0
 20 45  1  0
 22 46  1  0
 22 47  1  0
 22 48  1  0
 23 49  1  0
 23 50  1  0
 23 51  1  0
M  END

HEADER    PROTEIN                                 16-JUL-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-JUL-18         0                                  
HETATM    1  C   UNK     0       2.834 -26.940   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.827 -28.484   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.163 -29.258   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.511 -26.951   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.176 -26.170   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.840 -26.180   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.175 -26.955   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.509 -26.187   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.844 -26.963   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.178 -26.195   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       6.848 -27.723   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.952 -24.840   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.411 -24.833   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.504 -28.495   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.836 -29.269   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.512 -24.648   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      14.836 -26.197   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.509 -26.977   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      14.823 -24.657   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      16.176 -26.956   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      16.188 -28.495   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      14.861 -29.276   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      17.528 -29.255   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2   14                                                       
CONECT    4    5    6   11   14                                             
CONECT    5    4    1   12   13                                             
CONECT    6    4    7                                                       
CONECT    7    8    6                                                       
CONECT    8    7    9   16                                                  
CONECT    9    8   10                                                       
CONECT   10    9   18                                                       
CONECT   11    4   14                                                       
CONECT   12    5                                                            
CONECT   13    5                                                            
CONECT   14   15   11    4    3                                             
CONECT   15   14                                                            
CONECT   16    8                                                            
CONECT   17   18   19   20                                                  
CONECT   18   17   10                                                       
CONECT   19   17                                                            
CONECT   20   17   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

COMPND    HMDB0062411
HETATM    1  C1  UNL     1       6.290   2.163  -0.626  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.786   0.408  -0.207  1.00  0.00           C  
HETATM    3  C3  UNL     1       6.974   0.124  -0.230  1.00  0.00           C  
HETATM    4  C4  UNL     1       7.051  -1.392   0.105  1.00  0.00           C  
HETATM    5  O1  UNL     1       6.020  -1.997   0.301  1.00  0.00           O  
HETATM    6  O2  UNL     1       8.270  -1.937   0.157  1.00  0.00           O  
HETATM    7  C5  UNL     1       4.478   0.721  -0.182  1.00  0.00           C  
HETATM    8  C6  UNL     1       3.438  -0.176  -0.195  1.00  0.00           C  
HETATM    9  C7  UNL     1       2.085   0.326  -0.164  1.00  0.00           C  
HETATM   10  C8  UNL     1       1.012  -0.423  -0.155  1.00  0.00           C  
HETATM   11  C9  UNL     1       1.086  -1.889  -0.163  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.339   0.191  -0.236  1.00  0.00           C  
HETATM   13  C11 UNL     1      -1.408  -0.517  -0.195  1.00  0.00           C  
HETATM   14  C12 UNL     1      -2.832  -0.084  -0.270  1.00  0.00           C  
HETATM   15  O3  UNL     1      -3.265  -0.096  -1.688  1.00  0.00           O  
HETATM   16  C13 UNL     1      -3.738  -1.015  -0.758  1.00  0.00           C  
HETATM   17  C14 UNL     1      -3.202  -2.437  -1.064  1.00  0.00           C  
HETATM   18  C15 UNL     1      -5.149  -1.028  -0.394  1.00  0.00           C  
HETATM   19  C16 UNL     1      -5.620   0.162   0.408  1.00  0.00           C  
HETATM   20  C17 UNL     1      -4.770   1.352   0.187  1.00  0.00           C  
HETATM   21  C18 UNL     1      -3.317   1.022   0.544  1.00  0.00           C  
HETATM   22  C19 UNL     1      -3.301   0.798   2.027  1.00  0.00           C  
HETATM   23  C20 UNL     1      -2.525   2.322   0.333  1.00  0.00           C  
HETATM   24  H1  UNL     1       6.773   1.865  -1.523  1.00  0.00           H  
HETATM   25  H2  UNL     1       5.299   2.481  -0.812  1.00  0.00           H  
HETATM   26  H3  UNL     1       6.779   2.317   0.297  1.00  0.00           H  
HETATM   27  H4  UNL     1       7.933   0.532  -0.395  1.00  0.00           H  
HETATM   28  H5  UNL     1       8.980  -1.598   0.819  1.00  0.00           H  
HETATM   29  H6  UNL     1       4.117   1.772  -0.088  1.00  0.00           H  
HETATM   30  H7  UNL     1       3.674  -1.190  -0.238  1.00  0.00           H  
HETATM   31  H8  UNL     1       1.874   1.414  -0.143  1.00  0.00           H  
HETATM   32  H9  UNL     1       2.067  -2.322  -0.026  1.00  0.00           H  
HETATM   33  H10 UNL     1       0.540  -2.332  -1.041  1.00  0.00           H  
HETATM   34  H11 UNL     1       0.490  -2.222   0.743  1.00  0.00           H  
HETATM   35  H12 UNL     1      -0.421   1.251  -0.355  1.00  0.00           H  
HETATM   36  H13 UNL     1      -1.272  -1.614  -0.076  1.00  0.00           H  
HETATM   37  H14 UNL     1      -2.368  -2.423  -1.764  1.00  0.00           H  
HETATM   38  H15 UNL     1      -4.039  -3.046  -1.501  1.00  0.00           H  
HETATM   39  H16 UNL     1      -2.973  -2.889  -0.071  1.00  0.00           H  
HETATM   40  H17 UNL     1      -5.391  -1.989   0.167  1.00  0.00           H  
HETATM   41  H18 UNL     1      -5.785  -1.094  -1.301  1.00  0.00           H  
HETATM   42  H19 UNL     1      -6.665   0.438   0.124  1.00  0.00           H  
HETATM   43  H20 UNL     1      -5.665  -0.151   1.474  1.00  0.00           H  
HETATM   44  H21 UNL     1      -4.769   1.573  -0.912  1.00  0.00           H  
HETATM   45  H22 UNL     1      -5.156   2.222   0.761  1.00  0.00           H  
HETATM   46  H23 UNL     1      -2.305   1.091   2.454  1.00  0.00           H  
HETATM   47  H24 UNL     1      -4.032   1.534   2.474  1.00  0.00           H  
HETATM   48  H25 UNL     1      -3.593  -0.198   2.348  1.00  0.00           H  
HETATM   49  H26 UNL     1      -3.199   3.181   0.673  1.00  0.00           H  
HETATM   50  H27 UNL     1      -1.711   2.334   1.057  1.00  0.00           H  
HETATM   51  H28 UNL     1      -2.205   2.467  -0.679  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   13   35
CONECT   13   14   36
CONECT   14   15   16   21
CONECT   15   16
CONECT   16   17   18
CONECT   17   37   38   39
CONECT   18   19   40   41
CONECT   19   20   42   43
CONECT   20   21   44   45
CONECT   21   22   23
CONECT   22   46   47   48
CONECT   23   49   50   51
END

HMDB0062411
     RDKit          3D
5,6-Epoxy-13-cis-retinoic acid
 51 52  0  0  0  0  0  0  0  0999 V2000
    6.2897    2.1632   -0.6260 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7859    0.4078   -0.2069 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9741    0.1236   -0.2297 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0512   -1.3919    0.1046 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0202   -1.9972    0.3011 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2697   -1.9372    0.1567 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4783    0.7206   -0.1819 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4385   -0.1756   -0.1949 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0853    0.3260   -0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0119   -0.4234   -0.1550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0860   -1.8889   -0.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3391    0.1908   -0.2358 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4075   -0.5171   -0.1951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8321   -0.0844   -0.2699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2651   -0.0957   -1.6878 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7381   -1.0152   -0.7577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2019   -2.4370   -1.0643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1494   -1.0280   -0.3943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6204    0.1619    0.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7701    1.3522    0.1870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3168    1.0216    0.5436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3007    0.7976    2.0266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5254    2.3220    0.3330 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7727    1.8645   -1.5232 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2991    2.4812   -0.8122 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7787    2.3175    0.2973 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9331    0.5325   -0.3948 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9798   -1.5976    0.8188 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1166    1.7716   -0.0883 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6739   -1.1899   -0.2376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8741    1.4143   -0.1433 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0674   -2.3223   -0.0259 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5402   -2.3322   -1.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4904   -2.2216    0.7428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4206    1.2508   -0.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2722   -1.6141   -0.0763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3683   -2.4230   -1.7640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0394   -3.0464   -1.5015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9727   -2.8893   -0.0706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3915   -1.9891    0.1672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7847   -1.0938   -1.3005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6649    0.4376    0.1240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6648   -0.1507    1.4736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7691    1.5731   -0.9119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1557    2.2224    0.7609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3048    1.0910    2.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0322    1.5343    2.4737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5935   -0.1979    2.3481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1988    3.1811    0.6728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7115    2.3335    1.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2054    2.4671   -0.6788 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  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 16 14  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
 17 37  1  0
 17 38  1  0
 17 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 19 43  1  0
 20 44  1  0
 20 45  1  0
 22 46  1  0
 22 47  1  0
 22 48  1  0
 23 49  1  0
 23 50  1  0
 23 51  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
5,6-Epoxy-13-cis-retinoate	Generator
13-cis-5,6-Epoxy-5,6-dihydroretinoic acid	HMDB

Chemical Formula

C₂₀H₂₈O₃

Average Molecular Weight

316.441

Monoisotopic Molecular Weight

316.203844762

IUPAC Name

(2Z,4E,6E,8E)-3,7-dimethyl-9-{2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl}nona-2,4,6,8-tetraenoic acid

Traditional Name

(2Z,4E,6E,8E)-3,7-dimethyl-9-{2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl}nona-2,4,6,8-tetraenoic acid

CAS Registry Number

81444-57-7

SMILES

C\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C\C(O)=O

InChI Identifier

InChI=1S/C20H28O3/c1-15(8-6-9-16(2)14-17(21)22)10-13-20-18(3,4)11-7-12-19(20,5)23-20/h6,8-10,13-14H,7,11-12H2,1-5H3,(H,21,22)/b9-6+,13-10+,15-8+,16-14-

InChI Key

KEEHJLBAOLGBJZ-NJZIYGCESA-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
Epoxy fatty acid
Heterocyclic fatty acid
Oxepane
Methyl-branched fatty acid
Unsaturated fatty acid
Fatty acyl
Fatty acid
Carboxylic acid derivative
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Ether
Oxacycle
Oxirane
Dialkyl ether
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organooxygen compound
Organic oxide
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	5.74	ALOGPS
logP	4.54	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	4.94	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	49.83 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	96.52 m³·mol⁻¹	ChemAxon
Polarizability	36.97 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-2H]-	228.382	30932474
DeepCCS	[M+Na]+	203.609	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5,6-Epoxy-13-cis-retinoic acid	C\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C\C(O)=O	3855.1	Standard polar	33892256
5,6-Epoxy-13-cis-retinoic acid	C\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C\C(O)=O	2452.8	Standard non polar	33892256
5,6-Epoxy-13-cis-retinoic acid	C\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C\C(O)=O	2591.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5,6-Epoxy-13-cis-retinoic acid,1TMS,isomer #1	CC(=C/C(=O)O[Si](C)(C)C)/C=C/C=C(C)/C=C/C12OC1(C)CCCC2(C)C	2632.5	Semi standard non polar	33892256
5,6-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)/C=C/C12OC1(C)CCCC2(C)C	2846.7	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 - 5,6-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 - 5,6-Epoxy-13-cis-retinoic acid 10V, Positive-QTOF	splash10-0002-0392000000-db71c362cf2ce5f0376b	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 20V, Positive-QTOF	splash10-0a4i-5890000000-8cda60e8ed359a4d3158	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 40V, Positive-QTOF	splash10-0pvi-9400000000-b652752049e9099c4c5f	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 10V, Negative-QTOF	splash10-014i-0089000000-db7b49ec35814d41b146	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 20V, Negative-QTOF	splash10-01ba-0094000000-dc7fa9813bf0f44f3f22	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 40V, Negative-QTOF	splash10-053i-6960000000-b1133bf5dd927a284ac0	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 10V, Positive-QTOF	splash10-00rt-0192000000-861041c7dc974b088a42	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 20V, Positive-QTOF	splash10-0540-0590000000-4f77ff24993914b2af45	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 40V, Positive-QTOF	splash10-0gdu-7910000000-3b294bfc029780e1a389	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 10V, Negative-QTOF	splash10-01b9-0198000000-91d1b99148247a6bd981	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 20V, Negative-QTOF	splash10-00y0-0971000000-29094eb01d6c33d9ba2e	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 40V, Negative-QTOF	splash10-066r-2932000000-86038457c94d4ed88c27	2021-09-24	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

71316381

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 5,6-Epoxy-13-cis-retinoic acid (HMDB0062411)

MOL for HMDB0062411 (5,6-Epoxy-13-cis-retinoic acid)

3D MOL for HMDB0062411 (5,6-Epoxy-13-cis-retinoic acid)

3D SDF for HMDB0062411 (5,6-Epoxy-13-cis-retinoic acid)

3D-SDF for HMDB0062411 (5,6-Epoxy-13-cis-retinoic acid)

PDB for HMDB0062411 (5,6-Epoxy-13-cis-retinoic acid)

3D PDB for HMDB0062411 (5,6-Epoxy-13-cis-retinoic acid)

SMILES for HMDB0062411 (5,6-Epoxy-13-cis-retinoic acid)

INCHI for HMDB0062411 (5,6-Epoxy-13-cis-retinoic acid)

Structure for HMDB0062411 (5,6-Epoxy-13-cis-retinoic acid)

3D Structure for HMDB0062411 (5,6-Epoxy-13-cis-retinoic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra