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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2009-07-25 00:20:08 UTC

Update Date

2022-03-07 02:51:28 UTC

HMDB ID

HMDB0013117

Secondary Accession Numbers

HMDB13117

Metabolite Identification

Common Name

Vitamin A2

Description

Vitamin A2, also known as 3-dehydoretinol or VA2, 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. Thus, vitamin A2 is considered to be an isoprenoid. Based on a literature review a significant number of articles have been published on Vitamin A2.

Structure

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

HMDB0013117
     RDKit          3D
Vitamin A2
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2418    2.7360    2.1332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9362    1.5488    1.5500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2369    0.6117    0.8880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7985    0.8457    0.7914 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9458    0.0536    0.1877 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5034    0.3938    0.1523 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9231    1.6276    0.8181 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3101   -0.4230   -0.4613 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7389   -0.1522   -0.5350 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5446   -1.0015   -1.1664 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9640   -0.8821   -1.3277 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7710    0.2386   -0.7968 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6295   -1.8330   -1.9967 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0908   -1.7490   -2.1860 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6720   -2.8729   -1.5971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8308   -0.5965    0.2862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1799   -1.8460    0.8827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5499   -0.5436   -1.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3226   -0.7094    0.4287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9795    0.3633    1.1659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3644    1.4001    1.6838 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9959    3.3858    2.6164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7242    3.3412    1.3832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5162    2.4388    2.9144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3577    1.7592    1.2532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2743   -0.8546   -0.2939 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9936    1.8118    0.8964 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4039    2.5365    0.3778 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5532    1.6405    1.8854 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8958   -1.3326   -0.9301 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1959    0.7140   -0.1023 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0403   -1.8793   -1.6009 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1208    0.9280   -0.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5657   -0.1763   -0.1216 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2634    0.7978   -1.6420 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0477   -2.6483   -2.3821 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3535   -1.7643   -3.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4992   -0.7980   -1.8009 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3435   -2.5810   -0.9276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8658   -2.5137    0.0835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9793   -2.3723    1.4616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4170   -1.5608    1.6008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1119   -1.4691   -1.6038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5460   -0.3430   -1.7121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9001    0.3168   -1.4638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5460   -1.6669    0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8310   -0.8294   -0.5736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0652    0.2723    1.2810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9071    2.1754    2.2267 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  1  0
  3 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  2  0
 21  2  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 12 33  1  0
 12 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 14 38  1  0
 15 39  1  0
 17 40  1  0
 17 41  1  0
 17 42  1  0
 18 43  1  0
 18 44  1  0
 18 45  1  0
 19 46  1  0
 19 47  1  0
 20 48  1  0
 21 49  1  0
M  END


  Mrv0541 02251208172D          

 21 21  0  0  0  0            999 V2000
    7.6096  -12.3925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0844  -10.9634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8483  -15.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7854  -14.4251    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0715  -14.8381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2595  -12.3925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7860  -16.6796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8477  -13.1070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0844  -12.3925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6108  -16.6796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6103  -13.8216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0233  -14.5354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3218  -11.6780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3735  -15.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7342  -10.9634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0227  -13.1070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4969  -11.6780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0233  -15.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6108  -15.2499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7854  -15.2505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5591  -10.9634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1 16  1  0  0  0  0
  2 17  1  0  0  0  0
  3 18  1  0  0  0  0
  4 20  1  0  0  0  0
  5 20  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  7 10  2  0  0  0  0
  7 14  1  0  0  0  0
  8 16  2  0  0  0  0
  9 17  1  0  0  0  0
 10 18  1  0  0  0  0
 11 16  1  0  0  0  0
 11 12  2  0  0  0  0
 12 19  1  0  0  0  0
 13 17  2  0  0  0  0
 13 15  1  0  0  0  0
 14 20  1  0  0  0  0
 15 21  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013117

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6-13,21H,14-15H2,1-5H3/b9-6+,12-11+,16-8+,17-13+

> <INCHI_KEY>
XWCYDHJOKKGVHC-OVSJKPMPSA-N

> <FORMULA>
C20H28O

> <MOLECULAR_WEIGHT>
284.4357

> <EXACT_MASS>
284.214015518

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
36.02006678531005

> <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-tetraen-1-ol

> <ALOGPS_LOGP>
5.66

> <JCHEM_LOGP>
4.332171516333333

> <ALOGPS_LOGS>
-4.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.435769749539965

> <JCHEM_PKA_STRONGEST_BASIC>
-2.1707943115512176

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
99.04

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.42e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
vitamin A 2

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0013117
     RDKit          3D
Vitamin A2
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2418    2.7360    2.1332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9362    1.5488    1.5500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2369    0.6117    0.8880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7985    0.8457    0.7914 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9458    0.0536    0.1877 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5034    0.3938    0.1523 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9231    1.6276    0.8181 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3101   -0.4230   -0.4613 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7389   -0.1522   -0.5350 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5446   -1.0015   -1.1664 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9640   -0.8821   -1.3277 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7710    0.2386   -0.7968 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6295   -1.8330   -1.9967 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0908   -1.7490   -2.1860 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6720   -2.8729   -1.5971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8308   -0.5965    0.2862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1799   -1.8460    0.8827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5499   -0.5436   -1.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3226   -0.7094    0.4287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9795    0.3633    1.1659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3644    1.4001    1.6838 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9959    3.3858    2.6164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7242    3.3412    1.3832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5162    2.4388    2.9144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3577    1.7592    1.2532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2743   -0.8546   -0.2939 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9936    1.8118    0.8964 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4039    2.5365    0.3778 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5532    1.6405    1.8854 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8958   -1.3326   -0.9301 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1959    0.7140   -0.1023 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0403   -1.8793   -1.6009 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1208    0.9280   -0.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5657   -0.1763   -0.1216 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2634    0.7978   -1.6420 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0477   -2.6483   -2.3821 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3535   -1.7643   -3.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4992   -0.7980   -1.8009 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3435   -2.5810   -0.9276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8658   -2.5137    0.0835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9793   -2.3723    1.4616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4170   -1.5608    1.6008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1119   -1.4691   -1.6038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5460   -0.3430   -1.7121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9001    0.3168   -1.4638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5460   -1.6669    0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8310   -0.8294   -0.5736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0652    0.2723    1.2810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9071    2.1754    2.2267 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  1  0
  3 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  2  0
 21  2  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 12 33  1  0
 12 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 14 38  1  0
 15 39  1  0
 17 40  1  0
 17 41  1  0
 17 42  1  0
 18 43  1  0
 18 44  1  0
 18 45  1  0
 19 46  1  0
 19 47  1  0
 20 48  1  0
 21 49  1  0
M  END

HEADER    PROTEIN                                 25-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-FEB-12         0                                  
HETATM    1  C   UNK     0      14.205 -23.133   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      18.824 -20.465   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.517 -29.802   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.666 -26.927   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.333 -27.698   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.284 -23.133   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.667 -31.135   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      16.516 -24.466   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      18.824 -23.133   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.207 -31.135   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.206 -25.800   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.977 -27.133   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      21.134 -21.799   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.897 -29.802   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      21.904 -20.465   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      14.976 -24.466   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      19.594 -21.799   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.977 -29.802   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      14.207 -28.466   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.666 -28.468   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      23.444 -20.465   0.000  0.00  0.00           O+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3   18                                                            
CONECT    4   20                                                            
CONECT    5   20                                                            
CONECT    6    8    9                                                       
CONECT    7   10   14                                                       
CONECT    8    6   16                                                       
CONECT    9    6   17                                                       
CONECT   10    7   18                                                       
CONECT   11   16   12                                                       
CONECT   12   11   19                                                       
CONECT   13   17   15                                                       
CONECT   14    7   20                                                       
CONECT   15   13   21                                                       
CONECT   16    1    8   11                                                  
CONECT   17    2    9   13                                                  
CONECT   18    3   10   19                                                  
CONECT   19   12   18   20                                                  
CONECT   20    4    5   14   19                                             
CONECT   21   15                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

COMPND    HMDB0013117
HETATM    1  C1  UNL     1      -3.242   2.736   2.133  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.936   1.549   1.550  1.00  0.00           C  
HETATM    3  C3  UNL     1      -3.237   0.612   0.888  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.799   0.846   0.791  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.946   0.054   0.188  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.503   0.394   0.152  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.923   1.628   0.818  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.310  -0.423  -0.461  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.739  -0.152  -0.535  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.545  -1.001  -1.166  1.00  0.00           C  
HETATM   11  C11 UNL     1       4.964  -0.882  -1.328  1.00  0.00           C  
HETATM   12  C12 UNL     1       5.771   0.239  -0.797  1.00  0.00           C  
HETATM   13  C13 UNL     1       5.630  -1.833  -1.997  1.00  0.00           C  
HETATM   14  C14 UNL     1       7.091  -1.749  -2.186  1.00  0.00           C  
HETATM   15  O1  UNL     1       7.672  -2.873  -1.597  1.00  0.00           O  
HETATM   16  C15 UNL     1      -3.831  -0.596   0.286  1.00  0.00           C  
HETATM   17  C16 UNL     1      -3.180  -1.846   0.883  1.00  0.00           C  
HETATM   18  C17 UNL     1      -3.550  -0.544  -1.210  1.00  0.00           C  
HETATM   19  C18 UNL     1      -5.323  -0.709   0.429  1.00  0.00           C  
HETATM   20  C19 UNL     1      -5.979   0.363   1.166  1.00  0.00           C  
HETATM   21  C20 UNL     1      -5.364   1.400   1.684  1.00  0.00           C  
HETATM   22  H1  UNL     1      -3.996   3.386   2.616  1.00  0.00           H  
HETATM   23  H2  UNL     1      -2.724   3.341   1.383  1.00  0.00           H  
HETATM   24  H3  UNL     1      -2.516   2.439   2.914  1.00  0.00           H  
HETATM   25  H4  UNL     1      -1.358   1.759   1.253  1.00  0.00           H  
HETATM   26  H5  UNL     1      -1.274  -0.855  -0.294  1.00  0.00           H  
HETATM   27  H6  UNL     1       1.994   1.812   0.896  1.00  0.00           H  
HETATM   28  H7  UNL     1       0.404   2.536   0.378  1.00  0.00           H  
HETATM   29  H8  UNL     1       0.553   1.640   1.885  1.00  0.00           H  
HETATM   30  H9  UNL     1       0.896  -1.333  -0.930  1.00  0.00           H  
HETATM   31  H10 UNL     1       3.196   0.714  -0.102  1.00  0.00           H  
HETATM   32  H11 UNL     1       3.040  -1.879  -1.601  1.00  0.00           H  
HETATM   33  H12 UNL     1       5.121   0.928  -0.236  1.00  0.00           H  
HETATM   34  H13 UNL     1       6.566  -0.176  -0.122  1.00  0.00           H  
HETATM   35  H14 UNL     1       6.263   0.798  -1.642  1.00  0.00           H  
HETATM   36  H15 UNL     1       5.048  -2.648  -2.382  1.00  0.00           H  
HETATM   37  H16 UNL     1       7.354  -1.764  -3.271  1.00  0.00           H  
HETATM   38  H17 UNL     1       7.499  -0.798  -1.801  1.00  0.00           H  
HETATM   39  H18 UNL     1       8.344  -2.581  -0.928  1.00  0.00           H  
HETATM   40  H19 UNL     1      -2.866  -2.514   0.083  1.00  0.00           H  
HETATM   41  H20 UNL     1      -3.979  -2.372   1.462  1.00  0.00           H  
HETATM   42  H21 UNL     1      -2.417  -1.561   1.601  1.00  0.00           H  
HETATM   43  H22 UNL     1      -3.112  -1.469  -1.604  1.00  0.00           H  
HETATM   44  H23 UNL     1      -4.546  -0.343  -1.712  1.00  0.00           H  
HETATM   45  H24 UNL     1      -2.900   0.317  -1.464  1.00  0.00           H  
HETATM   46  H25 UNL     1      -5.546  -1.667   0.990  1.00  0.00           H  
HETATM   47  H26 UNL     1      -5.831  -0.829  -0.574  1.00  0.00           H  
HETATM   48  H27 UNL     1      -7.065   0.272   1.281  1.00  0.00           H  
HETATM   49  H28 UNL     1      -5.907   2.175   2.227  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3    3   21
CONECT    3    4   16
CONECT    4    5    5   25
CONECT    5    6   26
CONECT    6    7    8    8
CONECT    7   27   28   29
CONECT    8    9   30
CONECT    9   10   10   31
CONECT   10   11   32
CONECT   11   12   13   13
CONECT   12   33   34   35
CONECT   13   14   36
CONECT   14   15   37   38
CONECT   15   39
CONECT   16   17   18   19
CONECT   17   40   41   42
CONECT   18   43   44   45
CONECT   19   20   46   47
CONECT   20   21   21   48
CONECT   21   49
END

HMDB0013117
     RDKit          3D
Vitamin A2
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2418    2.7360    2.1332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9362    1.5488    1.5500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2369    0.6117    0.8880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7985    0.8457    0.7914 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9458    0.0536    0.1877 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5034    0.3938    0.1523 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9231    1.6276    0.8181 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3101   -0.4230   -0.4613 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7389   -0.1522   -0.5350 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5446   -1.0015   -1.1664 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9640   -0.8821   -1.3277 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7710    0.2386   -0.7968 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6295   -1.8330   -1.9967 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0908   -1.7490   -2.1860 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6720   -2.8729   -1.5971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8308   -0.5965    0.2862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1799   -1.8460    0.8827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5499   -0.5436   -1.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3226   -0.7094    0.4287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9795    0.3633    1.1659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3644    1.4001    1.6838 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9959    3.3858    2.6164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7242    3.3412    1.3832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5162    2.4388    2.9144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3577    1.7592    1.2532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2743   -0.8546   -0.2939 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9936    1.8118    0.8964 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4039    2.5365    0.3778 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5532    1.6405    1.8854 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8958   -1.3326   -0.9301 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1959    0.7140   -0.1023 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0403   -1.8793   -1.6009 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1208    0.9280   -0.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5657   -0.1763   -0.1216 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2634    0.7978   -1.6420 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0477   -2.6483   -2.3821 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3535   -1.7643   -3.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4992   -0.7980   -1.8009 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3435   -2.5810   -0.9276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8658   -2.5137    0.0835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9793   -2.3723    1.4616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4170   -1.5608    1.6008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1119   -1.4691   -1.6038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5460   -0.3430   -1.7121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9001    0.3168   -1.4638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5460   -1.6669    0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8310   -0.8294   -0.5736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0652    0.2723    1.2810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9071    2.1754    2.2267 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  1  0
  3 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  2  0
 21  2  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 12 33  1  0
 12 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 14 38  1  0
 15 39  1  0
 17 40  1  0
 17 41  1  0
 17 42  1  0
 18 43  1  0
 18 44  1  0
 18 45  1  0
 19 46  1  0
 19 47  1  0
 20 48  1  0
 21 49  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(2E,4E,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)nona-2,4,6,8-tetraen-1-ol	ChEBI
3,4-Didehydro-all-trans-retinol	ChEBI
3,4-Didehydro-retinol	ChEBI
3-Dehydoretinol	ChEBI
all-trans-3-Dehydroretinol	ChEBI
Dehydroretinol	ChEBI
all-trans-3,4-Didehydro retinol	HMDB
3,4-Didehydroretinol	HMDB
all-trans-3,4-Didehydroretinol	HMDB
VA2	HMDB
Vitamin a2, (7-cis)-isomer	HMDB
3-Dehydroretinol	HMDB
Vitamin a2	ChEBI

Chemical Formula

C₂₀H₂₈O

Average Molecular Weight

284.4357

Monoisotopic Molecular Weight

284.214015518

IUPAC Name

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

Traditional Name

vitamin A 2

CAS Registry Number

79-80-1

SMILES

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

InChI Identifier

InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6-13,21H,14-15H2,1-5H3/b9-6+,12-11+,16-8+,17-13+

InChI Key

XWCYDHJOKKGVHC-OVSJKPMPSA-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

Retinoid skeleton
Diterpenoid
Fatty alcohol
Fatty acyl
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Retinoids (LMPR01090008 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0013117)
Membrane (HMDB: HMDB0013117)

Fishes (FooDB: FOOD00865)

Fat and oil

Fats and oils (FooDB: FOOD00864)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	< 25 °C	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	0.014 g/L	ALOGPS
logP	5.66	ALOGPS
logP	4.33	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	16.44	ChemAxon
pKa (Strongest Basic)	-2.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	20.23 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	99.04 m³·mol⁻¹	ChemAxon
Polarizability	36.02 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]+	178.005	31661259
DarkChem	[M-H]-	174.312	31661259
DeepCCS	[M+H]+	183.998	30932474
DeepCCS	[M-H]-	181.64	30932474
DeepCCS	[M-2H]-	215.727	30932474
DeepCCS	[M+Na]+	190.954	30932474
AllCCS	[M+H]+	172.1	32859911
AllCCS	[M+H-H2O]+	168.7	32859911
AllCCS	[M+NH4]+	175.2	32859911
AllCCS	[M+Na]+	176.1	32859911
AllCCS	[M-H]-	177.0	32859911
AllCCS	[M+Na-2H]-	177.4	32859911
AllCCS	[M+HCOO]-	177.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Vitamin A2	C\C(=C/CO)\C=C\C=C(/C)\C=C\C1=C(C)C=CCC1(C)C	3251.9	Standard polar	33892256
Vitamin A2	C\C(=C/CO)\C=C\C=C(/C)\C=C\C1=C(C)C=CCC1(C)C	2410.8	Standard non polar	33892256
Vitamin A2	C\C(=C/CO)\C=C\C=C(/C)\C=C\C1=C(C)C=CCC1(C)C	2359.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Vitamin A2,1TMS,isomer #1	CC1=C(/C=C/C(C)=C/C=C/C(C)=C/CO[Si](C)(C)C)C(C)(C)CC=C1	2616.9	Semi standard non polar	33892256
Vitamin A2,1TBDMS,isomer #1	CC1=C(/C=C/C(C)=C/C=C/C(C)=C/CO[Si](C)(C)C(C)(C)C)C(C)(C)CC=C1	2813.2	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 - Vitamin A2 GC-MS (Non-derivatized) - 70eV, Positive	splash10-014i-2190000000-3b869065c87d36ed5099	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Vitamin A2 GC-MS (1 TMS) - 70eV, Positive	splash10-0006-8249000000-a550d49727292f80b946	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Vitamin A2 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 - Vitamin A2 10V, Positive-QTOF	splash10-00kr-1490000000-49ea807dd5aeee7b2838	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 20V, Positive-QTOF	splash10-015a-4920000000-96a6d30e24b05021a4d0	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 40V, Positive-QTOF	splash10-0lei-9820000000-418a688bdad32f088009	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 10V, Negative-QTOF	splash10-001i-0090000000-b56b2d201cdf5f15c840	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 20V, Negative-QTOF	splash10-0ue9-0090000000-f93bb9c048e242947532	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 40V, Negative-QTOF	splash10-00kr-4690000000-10339a6c3a7b2054420e	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 10V, Negative-QTOF	splash10-0udi-0090000000-219cda37112b6df644da	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 20V, Negative-QTOF	splash10-0uei-0190000000-b80f73b4a9625edad010	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 40V, Negative-QTOF	splash10-000i-0690000000-008f73bd4d70cae5d8ac	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 10V, Positive-QTOF	splash10-01bi-0790000000-16543321cc9076d8847c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 20V, Positive-QTOF	splash10-05g0-1910000000-6a3650fca0f7a58e3cfd	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vitamin A2 40V, Positive-QTOF	splash10-05tf-4900000000-b2b2774f095b7867f567	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

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

FDB013830

KNApSAcK ID

C00044897

Chemspider ID

4940721

KEGG Compound ID

Not Available

BioCyc ID

CPD-20073

BiGG ID

Not Available

Wikipedia Link

Dehydroretinal

METLIN ID

Not Available

PubChem Compound

6436043

PDB ID

Not Available

ChEBI ID

132246

Food Biomarker Ontology

Not Available

VMH ID

CE1162

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 Vitamin A2 (HMDB0013117)

MOL for HMDB0013117 (Vitamin A2)

3D MOL for HMDB0013117 (Vitamin A2)

3D SDF for HMDB0013117 (Vitamin A2)

3D-SDF for HMDB0013117 (Vitamin A2)

PDB for HMDB0013117 (Vitamin A2)

3D PDB for HMDB0013117 (Vitamin A2)

SMILES for HMDB0013117 (Vitamin A2)

INCHI for HMDB0013117 (Vitamin A2)

Structure for HMDB0013117 (Vitamin A2)

3D Structure for HMDB0013117 (Vitamin A2)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra