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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-24 06:07:05 UTC

Update Date

2021-09-24 06:07:05 UTC

HMDB ID

HMDB0303974

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al

Description

(3s,5r,6s)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al is a member of the class of compounds known as diterpenoids. Diterpenoids are terpene compounds formed by four isoprene units. Thus, (3s,5r,6s)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al is considered to be an isoprenoid lipid molecule (3s,5r,6s)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al is practically insoluble (in water) and an extremely weak acidic compound (based on its pKa). (3s,5r,6s)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al can be found in a number of food items such as sweet cherry, jute, sunburst squash (pattypan squash), and atlantic herring, which makes (3s,5r,6s)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al a potential biomarker for the consumption of these food products.

Structure

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


  Mrv1533007131514022D          

 38 39  0  0  1  0            999 V2000
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    1.4289   -2.0329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 36 14  1  0  0  0  0
 37 15  1  0  0  0  0
 22 38  1  6  0  0  0
M  END

HMDB0303974
     RDKit          3D
(3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al
 62 63  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1533007131514022D          

 38 39  0  0  1  0            999 V2000
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 35 13  1  0  0  0  0
 36 14  1  0  0  0  0
 37 15  1  0  0  0  0
 22 38  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0303974

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]/C(=C(/[H])\C(\[H])=C(/C)\C(\[H])=C(/[H])\C(\[H])=C(/C)\C(\[H])=C(/[H])[C@@]12O[C@]1(C)C[C@@]([H])(O)CC2(C)C)/C(/[H])=C(\C)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H34O3/c1-19(10-7-8-11-21(3)18-26)12-9-13-20(2)14-15-25-23(4,5)16-22(27)17-24(25,6)28-25/h7-15,18,22,27H,16-17H2,1-6H3/b8-7+,12-9+,15-14+,19-10+,20-13+,21-11+/t22-,24+,25-/m0/s1

> <INCHI_KEY>
CAXVJDRXJFKYQP-LKODNMENSA-N

> <FORMULA>
C25H34O3

> <MOLECULAR_WEIGHT>
382.544

> <EXACT_MASS>
382.250794955

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
46.58020647041809

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,4E,6E,8E,10E,12E)-13-[(1S,4S,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl]-2,7,11-trimethyltrideca-2,4,6,8,10,12-hexaenal

> <ALOGPS_LOGP>
5.84

> <JCHEM_LOGP>
4.372423300000001

> <ALOGPS_LOGS>
-5.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.139684034106125

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7377022034819802

> <JCHEM_POLAR_SURFACE_AREA>
49.83

> <JCHEM_REFRACTIVITY>
122.2173

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.42e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
C25-epoxy-apo-aldehyde

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0303974
     RDKit          3D
(3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al
 62 63  0  0  0  0  0  0  0  0999 V2000
    9.1034   -2.7351    2.4514 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5558   -1.7756    1.4143 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9769   -1.5950    1.1780 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8142   -2.2423    1.8418 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6336   -1.1048    0.7280 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2247   -1.2934    0.9734 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3465   -0.6172    0.2788 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9162   -0.7810    0.4981 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9764   -0.1343   -0.1644 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4195    0.8246   -1.2041 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5911   -0.3797    0.1431 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5633    0.1938   -0.4385 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2012   -0.1369   -0.0404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8924    0.3855   -0.5640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7685    1.3849   -1.6359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1933   -0.0346   -0.0760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3140    0.4394   -0.5537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6564    0.0203   -0.0646 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7368   -0.8256    1.0319 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9708    0.5144    1.3064 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8377    1.1411    2.1310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3402    1.0418    1.5031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8572    1.8576    0.3486 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.3563    3.1677    0.5030 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5151    1.3144   -0.9920 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8288   -0.0248   -0.9827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7734   -1.1671   -0.6761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3458   -0.2508   -2.4205 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5238   -3.5735    1.9989 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9567   -3.1685    3.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4711   -2.2193    3.2283 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3362   -0.9072    0.4342 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9801   -0.4150   -0.0183 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8455   -1.9800    1.7177 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6586    0.0857   -0.4793 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5931   -1.4864    1.2624 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9164    1.6929   -0.7290 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6359    1.1650   -1.8839 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2086    0.3674   -1.8661 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3343   -1.1060    0.9300 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7610    0.9096   -1.2155 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0362   -0.8807    0.7609 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1546    2.0235   -1.5323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5910    2.1572   -1.6350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8058    0.9329   -2.6602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3021   -0.7731    0.7202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2703    1.1687   -1.3458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1737    1.6852    1.4279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2266    0.3731    2.6285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2935    1.8147    2.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3164    1.7459    2.3877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0896    0.2625    1.8250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9601    1.9479    0.4205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3913    3.1557    0.7511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7950    2.0282   -1.4900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3976    1.3078   -1.6965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5869   -1.5618    0.3530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6932   -1.9954   -1.4339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8390   -0.8571   -0.6944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8278    0.6172   -2.8293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6114   -1.0819   -2.3571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1767   -0.6221   -3.0540 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  2  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 14 16  1  0
 16 17  2  0
 18 17  1  6
 18 19  1  0
 19 20  1  0
 20 21  1  1
 20 22  1  0
 22 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
 26 27  1  0
 26 28  1  0
 20 18  1  0
 26 18  1  0
  1 29  1  0
  1 30  1  0
  1 31  1  0
  3 32  1  0
  5 33  1  0
  6 34  1  0
  7 35  1  0
  8 36  1  0
 10 37  1  0
 10 38  1  0
 10 39  1  0
 11 40  1  0
 12 41  1  0
 13 42  1  0
 15 43  1  0
 15 44  1  0
 15 45  1  0
 16 46  1  0
 17 47  1  0
 21 48  1  0
 21 49  1  0
 21 50  1  0
 22 51  1  0
 22 52  1  0
 23 53  1  1
 24 54  1  0
 25 55  1  0
 25 56  1  0
 27 57  1  0
 27 58  1  0
 27 59  1  0
 28 60  1  0
 28 61  1  0
 28 62  1  0
M  END

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0      -1.953  -6.462   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -3.795   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -9.653  -6.462   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.991  -0.410   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.011  -0.410   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.897   4.414   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.033  -6.462   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.573  -6.462   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.413  -3.795   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.263  -5.128   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -7.343  -7.796   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.953  -3.795   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.357  -2.461   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -1.127   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.897   0.206   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -9.653  -9.129   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.723  -5.128   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.897  -2.461   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -8.883  -7.796   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0     -11.193  -9.129   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   29  H   UNK     0      -4.263  -7.796   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0      -7.343  -5.128   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0       0.357  -5.128   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0      -5.033  -3.795   0.000  0.00  0.00           H+0
HETATM   33  H   UNK     0      -6.573  -9.129   0.000  0.00  0.00           H+0
HETATM   34  H   UNK     0      -2.723  -2.461   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0      -0.413  -1.127   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0       4.030  -1.846   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       0.357   0.206   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0       5.335   4.620   0.000  0.00  0.00           H+0
CONECT    1   19                                                            
CONECT    2   20                                                            
CONECT    3   21                                                            
CONECT    4   23                                                            
CONECT    5   23                                                            
CONECT    6   24                                                            
CONECT    7    8   10   29                                                  
CONECT    8    7   11   30                                                  
CONECT    9   12   13   31                                                  
CONECT   10    7   19   32                                                  
CONECT   11    8   21   33                                                  
CONECT   12    9   19   34                                                  
CONECT   13    9   20   35                                                  
CONECT   14   15   20   36                                                  
CONECT   15   14   25   37                                                  
CONECT   16   22   23                                                       
CONECT   17   22   24                                                       
CONECT   18   21   26                                                       
CONECT   19    1   10   12                                                  
CONECT   20    2   13   14                                                  
CONECT   21    3   11   18                                                  
CONECT   22   16   17   27   38                                             
CONECT   23    4    5   16   25                                             
CONECT   24    6   17   25   28                                             
CONECT   25   15   23   24   28                                             
CONECT   26   18                                                            
CONECT   27   22                                                            
CONECT   28   24   25                                                       
CONECT   29    7                                                            
CONECT   30    8                                                            
CONECT   31    9                                                            
CONECT   32   10                                                            
CONECT   33   11                                                            
CONECT   34   12                                                            
CONECT   35   13                                                            
CONECT   36   14                                                            
CONECT   37   15                                                            
CONECT   38   22                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   78    0
END

COMPND    HMDB0303974
HETATM    1  C1  UNL     1       9.103  -2.735   2.451  1.00  0.00           C  
HETATM    2  C2  UNL     1       9.556  -1.776   1.414  1.00  0.00           C  
HETATM    3  C3  UNL     1      10.977  -1.595   1.178  1.00  0.00           C  
HETATM    4  O1  UNL     1      11.814  -2.242   1.842  1.00  0.00           O  
HETATM    5  C4  UNL     1       8.634  -1.105   0.728  1.00  0.00           C  
HETATM    6  C5  UNL     1       7.225  -1.293   0.973  1.00  0.00           C  
HETATM    7  C6  UNL     1       6.346  -0.617   0.279  1.00  0.00           C  
HETATM    8  C7  UNL     1       4.916  -0.781   0.498  1.00  0.00           C  
HETATM    9  C8  UNL     1       3.976  -0.134  -0.164  1.00  0.00           C  
HETATM   10  C9  UNL     1       4.419   0.825  -1.204  1.00  0.00           C  
HETATM   11  C10 UNL     1       2.591  -0.380   0.143  1.00  0.00           C  
HETATM   12  C11 UNL     1       1.563   0.194  -0.438  1.00  0.00           C  
HETATM   13  C12 UNL     1       0.201  -0.137  -0.040  1.00  0.00           C  
HETATM   14  C13 UNL     1      -0.892   0.385  -0.564  1.00  0.00           C  
HETATM   15  C14 UNL     1      -0.769   1.385  -1.636  1.00  0.00           C  
HETATM   16  C15 UNL     1      -2.193  -0.035  -0.076  1.00  0.00           C  
HETATM   17  C16 UNL     1      -3.314   0.439  -0.554  1.00  0.00           C  
HETATM   18  C17 UNL     1      -4.656   0.020  -0.065  1.00  0.00           C  
HETATM   19  O2  UNL     1      -4.737  -0.826   1.032  1.00  0.00           O  
HETATM   20  C18 UNL     1      -4.971   0.514   1.306  1.00  0.00           C  
HETATM   21  C19 UNL     1      -3.838   1.141   2.131  1.00  0.00           C  
HETATM   22  C20 UNL     1      -6.340   1.042   1.503  1.00  0.00           C  
HETATM   23  C21 UNL     1      -6.857   1.858   0.349  1.00  0.00           C  
HETATM   24  O3  UNL     1      -6.356   3.168   0.503  1.00  0.00           O  
HETATM   25  C22 UNL     1      -6.515   1.314  -0.992  1.00  0.00           C  
HETATM   26  C23 UNL     1      -5.829  -0.025  -0.983  1.00  0.00           C  
HETATM   27  C24 UNL     1      -6.773  -1.167  -0.676  1.00  0.00           C  
HETATM   28  C25 UNL     1      -5.346  -0.251  -2.421  1.00  0.00           C  
HETATM   29  H1  UNL     1       8.524  -3.573   1.999  1.00  0.00           H  
HETATM   30  H2  UNL     1       9.957  -3.169   3.005  1.00  0.00           H  
HETATM   31  H3  UNL     1       8.471  -2.219   3.228  1.00  0.00           H  
HETATM   32  H4  UNL     1      11.336  -0.907   0.434  1.00  0.00           H  
HETATM   33  H5  UNL     1       8.980  -0.415  -0.018  1.00  0.00           H  
HETATM   34  H6  UNL     1       6.845  -1.980   1.718  1.00  0.00           H  
HETATM   35  H7  UNL     1       6.659   0.086  -0.479  1.00  0.00           H  
HETATM   36  H8  UNL     1       4.593  -1.486   1.262  1.00  0.00           H  
HETATM   37  H9  UNL     1       4.916   1.693  -0.729  1.00  0.00           H  
HETATM   38  H10 UNL     1       3.636   1.165  -1.884  1.00  0.00           H  
HETATM   39  H11 UNL     1       5.209   0.367  -1.866  1.00  0.00           H  
HETATM   40  H12 UNL     1       2.334  -1.106   0.930  1.00  0.00           H  
HETATM   41  H13 UNL     1       1.761   0.910  -1.215  1.00  0.00           H  
HETATM   42  H14 UNL     1       0.036  -0.881   0.761  1.00  0.00           H  
HETATM   43  H15 UNL     1       0.155   2.024  -1.532  1.00  0.00           H  
HETATM   44  H16 UNL     1      -1.591   2.157  -1.635  1.00  0.00           H  
HETATM   45  H17 UNL     1      -0.806   0.933  -2.660  1.00  0.00           H  
HETATM   46  H18 UNL     1      -2.302  -0.773   0.720  1.00  0.00           H  
HETATM   47  H19 UNL     1      -3.270   1.169  -1.346  1.00  0.00           H  
HETATM   48  H20 UNL     1      -3.174   1.685   1.428  1.00  0.00           H  
HETATM   49  H21 UNL     1      -3.227   0.373   2.629  1.00  0.00           H  
HETATM   50  H22 UNL     1      -4.294   1.815   2.880  1.00  0.00           H  
HETATM   51  H23 UNL     1      -6.316   1.746   2.388  1.00  0.00           H  
HETATM   52  H24 UNL     1      -7.090   0.262   1.825  1.00  0.00           H  
HETATM   53  H25 UNL     1      -7.960   1.948   0.420  1.00  0.00           H  
HETATM   54  H26 UNL     1      -5.391   3.156   0.751  1.00  0.00           H  
HETATM   55  H27 UNL     1      -5.795   2.028  -1.490  1.00  0.00           H  
HETATM   56  H28 UNL     1      -7.398   1.308  -1.696  1.00  0.00           H  
HETATM   57  H29 UNL     1      -6.587  -1.562   0.353  1.00  0.00           H  
HETATM   58  H30 UNL     1      -6.693  -1.995  -1.434  1.00  0.00           H  
HETATM   59  H31 UNL     1      -7.839  -0.857  -0.694  1.00  0.00           H  
HETATM   60  H32 UNL     1      -4.828   0.617  -2.829  1.00  0.00           H  
HETATM   61  H33 UNL     1      -4.611  -1.082  -2.357  1.00  0.00           H  
HETATM   62  H34 UNL     1      -6.177  -0.622  -3.054  1.00  0.00           H  
CONECT    1    2   29   30   31
CONECT    2    3    5    5
CONECT    3    4    4   32
CONECT    5    6   33
CONECT    6    7    7   34
CONECT    7    8   35
CONECT    8    9    9   36
CONECT    9   10   11
CONECT   10   37   38   39
CONECT   11   12   12   40
CONECT   12   13   41
CONECT   13   14   14   42
CONECT   14   15   16
CONECT   15   43   44   45
CONECT   16   17   17   46
CONECT   17   18   47
CONECT   18   19   20   26
CONECT   19   20
CONECT   20   21   22
CONECT   21   48   49   50
CONECT   22   23   51   52
CONECT   23   24   25   53
CONECT   24   54
CONECT   25   26   55   56
CONECT   26   27   28
CONECT   27   57   58   59
CONECT   28   60   61   62
END

HMDB0303974
     RDKit          3D
(3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al
 62 63  0  0  0  0  0  0  0  0999 V2000
    9.1034   -2.7351    2.4514 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5558   -1.7756    1.4143 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9769   -1.5950    1.1780 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8142   -2.2423    1.8418 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6336   -1.1048    0.7280 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2247   -1.2934    0.9734 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3465   -0.6172    0.2788 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9162   -0.7810    0.4981 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9764   -0.1343   -0.1644 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4195    0.8246   -1.2041 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5911   -0.3797    0.1431 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5633    0.1938   -0.4385 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2012   -0.1369   -0.0404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8924    0.3855   -0.5640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7685    1.3849   -1.6359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1933   -0.0346   -0.0760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3140    0.4394   -0.5537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6564    0.0203   -0.0646 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7368   -0.8256    1.0319 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9708    0.5144    1.3064 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8377    1.1411    2.1310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3402    1.0418    1.5031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8572    1.8576    0.3486 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.3563    3.1677    0.5030 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5151    1.3144   -0.9920 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8288   -0.0248   -0.9827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7734   -1.1671   -0.6761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3458   -0.2508   -2.4205 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5238   -3.5735    1.9989 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9567   -3.1685    3.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4711   -2.2193    3.2283 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3362   -0.9072    0.4342 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9801   -0.4150   -0.0183 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8455   -1.9800    1.7177 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6586    0.0857   -0.4793 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5931   -1.4864    1.2624 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9164    1.6929   -0.7290 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6359    1.1650   -1.8839 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2086    0.3674   -1.8661 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3343   -1.1060    0.9300 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7610    0.9096   -1.2155 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0362   -0.8807    0.7609 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1546    2.0235   -1.5323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5910    2.1572   -1.6350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8058    0.9329   -2.6602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3021   -0.7731    0.7202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2703    1.1687   -1.3458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1737    1.6852    1.4279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2266    0.3731    2.6285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2935    1.8147    2.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3164    1.7459    2.3877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0896    0.2625    1.8250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9601    1.9479    0.4205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3913    3.1557    0.7511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7950    2.0282   -1.4900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3976    1.3078   -1.6965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5869   -1.5618    0.3530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6932   -1.9954   -1.4339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8390   -0.8571   -0.6944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8278    0.6172   -2.8293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6114   -1.0819   -2.3571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1767   -0.6221   -3.0540 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  2  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 14 16  1  0
 16 17  2  0
 18 17  1  6
 18 19  1  0
 19 20  1  0
 20 21  1  1
 20 22  1  0
 22 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
 26 27  1  0
 26 28  1  0
 20 18  1  0
 26 18  1  0
  1 29  1  0
  1 30  1  0
  1 31  1  0
  3 32  1  0
  5 33  1  0
  6 34  1  0
  7 35  1  0
  8 36  1  0
 10 37  1  0
 10 38  1  0
 10 39  1  0
 11 40  1  0
 12 41  1  0
 13 42  1  0
 15 43  1  0
 15 44  1  0
 15 45  1  0
 16 46  1  0
 17 47  1  0
 21 48  1  0
 21 49  1  0
 21 50  1  0
 22 51  1  0
 22 52  1  0
 23 53  1  1
 24 54  1  0
 25 55  1  0
 25 56  1  0
 27 57  1  0
 27 58  1  0
 27 59  1  0
 28 60  1  0
 28 61  1  0
 28 62  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(3S,5R,6S)-5,6-Epoxy-3-hydroxy-5,6-dihydro-12'-apo-b-caroten-12'-al	Generator
(3S,5R,6S)-5,6-Epoxy-3-hydroxy-5,6-dihydro-12'-apo-β-caroten-12'-al	Generator
(3S,5R,6S)-5,6-Epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al	KEGG

Chemical Formula

C₂₅H₃₄O₃

Average Molecular Weight

382.544

Monoisotopic Molecular Weight

382.250794955

IUPAC Name

(2E,4E,6E,8E,10E,12E)-13-[(1S,4S,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl]-2,7,11-trimethyltrideca-2,4,6,8,10,12-hexaenal

Traditional Name

C25-epoxy-apo-aldehyde

CAS Registry Number

Not Available

SMILES

[H]/C(=C(/[H])\C(\[H])=C(/C)\C(\[H])=C(/[H])\C(\[H])=C(/C)\C(\[H])=C(/[H])[C@@]12O[C@]1(C)C[C@@]([H])(O)CC2(C)C)/C(/[H])=C(\C)C=O

InChI Identifier

InChI=1S/C25H34O3/c1-19(10-7-8-11-21(3)18-26)12-9-13-20(2)14-15-25-23(4,5)16-22(27)17-24(25,6)28-25/h7-15,18,22,27H,16-17H2,1-6H3/b8-7+,12-9+,15-14+,19-10+,20-13+,21-11+/t22-,24+,25-/m0/s1

InChI Key

CAXVJDRXJFKYQP-LKODNMENSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Oxepane
Alpha,beta-unsaturated aldehyde
Cyclic alcohol
Enal
Secondary alcohol
Dialkyl ether
Oxacycle
Oxirane
Ether
Organoheterocyclic compound
Hydrocarbon derivative
Alcohol
Organic oxide
Aldehyde
Organic oxygen compound
Organooxygen compound
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

12'-apo-carotenal (CHEBI:34597 )
C40 isoprenoids (tetraterpenes) (LMPR01070294 )

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	5.84	ALOGPS
logP	4.37	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	15.14	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	49.83 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	122.22 m³·mol⁻¹	ChemAxon
Polarizability	46.58 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
AllCCS	[M+H]+	202.086	32859911
AllCCS	[M+H-H2O]+	199.589	32859911
AllCCS	[M+Na]+	205.054	32859911
AllCCS	[M+NH4]+	204.393	32859911
AllCCS	[M-H]-	200.426	32859911
AllCCS	[M+Na-2H]-	201.734	32859911
AllCCS	[M+HCOO]-	203.335	32859911
DeepCCS	[M-2H]-	259.863	30932474
DeepCCS	[M+Na]+	233.923	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	18.2577 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.49 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	3252.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	330.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	205.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	200.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	116.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	1012.7 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	609.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	84.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1627.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	597.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1278.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	706.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	419.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	221.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	486.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	9.0 seconds	40023050

Predicted Kovats Retention Indices

Not Available

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 10V, Positive-QTOF	splash10-0159-1239000000-4f02a7be8b3bf1783756	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 20V, Positive-QTOF	splash10-02ta-4955000000-60da21711a9a7edb38cb	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 40V, Positive-QTOF	splash10-066r-9720000000-7db904a21612daea4e2d	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 10V, Negative-QTOF	splash10-001i-0009000000-bee26f983c9e4ec1982a	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 20V, Negative-QTOF	splash10-0gx9-0009000000-b4bdb58d8c578577c040	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 40V, Negative-QTOF	splash10-052r-5958000000-cb558debd50889da69c8	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 10V, Positive-QTOF	splash10-016r-0029000000-16bd70db285a67dcd4f6	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 20V, Positive-QTOF	splash10-000t-0249000000-e58ccd5af6485173aede	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 40V, Positive-QTOF	splash10-017i-2901000000-8913618e2c42f2bc3604	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 10V, Negative-QTOF	splash10-0udi-0009000000-e36cfdbd258a7e45a8d6	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 20V, Negative-QTOF	splash10-0udj-0109000000-9f766a2e320167d057cf	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al 40V, Negative-QTOF	splash10-000i-0938000000-5e6449f152747989ded3	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030121

KNApSAcK ID

Not Available

Chemspider ID

4445489

KEGG Compound ID

C14045

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5282320

PDB ID

Not Available

ChEBI ID

34597

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al (HMDB0303974)

MOL for HMDB0303974 ((3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al)

3D MOL for HMDB0303974 ((3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al)

3D SDF for HMDB0303974 ((3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al)

3D-SDF for HMDB0303974 ((3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al)

PDB for HMDB0303974 ((3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al)

3D PDB for HMDB0303974 ((3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al)

SMILES for HMDB0303974 ((3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al)

INCHI for HMDB0303974 ((3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al)

Structure for HMDB0303974 ((3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al)

3D Structure for HMDB0303974 ((3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

MS/MS Spectra