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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 11:47:42 UTC

Update Date

2022-09-22 17:44:24 UTC

HMDB ID

HMDB0253376

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Idebenone

Description

idebenone, also known as BRN 2001459 or CV 2619, belongs to the class of organic compounds known as ubiquinones. These are coenzyme Q derivatives containing a 5, 6-dimethoxy-3-methyl(1,4-benzoquinone) moiety to which an isoprenyl group is attached at ring position 2(or 6). idebenone is an extremely weak basic (essentially neutral) compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). Idebenone is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Idebenone is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0253376
     RDKit          3D
Idebenone
 54 54  0  0  0  0  0  0  0  0999 V2000
    7.2907   -0.0242    0.6070 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1306    0.2617    1.3984 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8938    0.0379    0.8031 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5017    0.8687   -0.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3101    1.9307   -0.5302 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4577    2.9958    0.3914 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1925    0.6669   -0.8062 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8535    1.4805   -1.7077 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3380   -0.4440   -0.4105 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0386   -0.6714   -1.0425 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0840    0.5089   -0.8686 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1942    0.1044   -1.5759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2528    1.1776   -1.4947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4680    0.6807   -2.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0897   -0.5664   -1.7822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6549   -0.7626   -0.4513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8322   -0.6740    0.7596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7231   -0.9854    1.9717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8593   -0.0379    2.1308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3139    1.2573    2.2746 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7423   -1.2664    0.5399 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8687   -2.3831    0.9285 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0394   -1.0943    1.2169 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4242   -1.8796    2.1236 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3030    0.5970   -0.3190 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2186    0.1891    1.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1977   -1.1015    0.3151 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4778    3.4757    0.6356 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0983    3.8048   -0.0115 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8507    2.5820    1.3267 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5206   -1.5687   -0.7075 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1550   -0.7782   -2.1605 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5207    1.4400   -1.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0823    0.6407    0.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9350   -0.0118   -2.6542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5173   -0.8516   -1.1125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3888    1.5864   -0.5087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8432    2.0101   -2.1717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1989    1.5156   -2.4129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0874    0.4837   -3.2817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3698   -1.4096   -2.0439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9388   -0.7819   -2.5232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1308   -1.7985   -0.4455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5806   -0.1045   -0.3164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3675    0.2783    1.0140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0716   -1.5154    0.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1006   -0.9224    2.8861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0439   -2.0386    1.8435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6182   -0.0321    1.3458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4111   -0.2812    3.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2779    1.4797    3.2375 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8688   -2.0279    1.3088 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2987   -2.9809    1.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6760   -3.0604    0.0682 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
  4  5  1  0
  5  6  1  0
  4  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
  9 21  2  0
 21 22  1  0
 21 23  1  0
 23 24  2  0
 23  3  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  6 28  1  0
  6 29  1  0
  6 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 14 40  1  0
 15 41  1  0
 15 42  1  0
 16 43  1  0
 16 44  1  0
 17 45  1  0
 17 46  1  0
 18 47  1  0
 18 48  1  0
 19 49  1  0
 19 50  1  0
 20 51  1  0
 22 52  1  0
 22 53  1  0
 22 54  1  0
M  END


  Mrv1572008281518342D          

 24 24  0  0  0  0            999 V2000
   -1.1721    0.4133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1721   -0.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4544   -0.8267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2589   -0.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2589    0.4133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4544    0.8266    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4534    1.6534    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4534   -1.6534    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9752    0.8261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8879    0.8270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8879   -0.8271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6041   -0.4141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9697   -0.8267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6837   -0.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6041   -0.8267    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5961    0.4187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9697   -0.8267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6837   -0.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9697   -0.8267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6837   -0.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9697   -0.8267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6837   -0.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9697   -0.8267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6837   -0.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 11 12  1  0  0  0  0
  6  1  1  0  0  0  0
  6  7  2  0  0  0  0
  1  2  2  0  0  0  0
  3  8  2  0  0  0  0
  2  3  1  0  0  0  0
  5  9  1  0  0  0  0
  3  4  1  0  0  0  0
  1 10  1  0  0  0  0
  4  5  2  0  0  0  0
  2 11  1  0  0  0  0
  5  6  1  0  0  0  0
 10 16  1  0  0  0  0
  4 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253376

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(OC)C(=O)C(CCCCCCCCCCO)=C(C)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C19H30O5/c1-14-15(12-10-8-6-4-5-7-9-11-13-20)17(22)19(24-3)18(23-2)16(14)21/h20H,4-13H2,1-3H3

> <INCHI_KEY>
JGPMMRGNQUBGND-UHFFFAOYSA-N

> <FORMULA>
C19H30O5

> <MOLECULAR_WEIGHT>
338.444

> <EXACT_MASS>
338.209324066

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
39.55878360573913

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(10-hydroxydecyl)-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione

> <ALOGPS_LOGP>
3.98

> <JCHEM_LOGP>
3.5679935743333338

> <ALOGPS_LOGS>
-4.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.84394282199214

> <JCHEM_PKA_STRONGEST_BASIC>
-1.9914450153462844

> <JCHEM_POLAR_SURFACE_AREA>
72.83000000000001

> <JCHEM_REFRACTIVITY>
96.5179

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.63e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
idebenone

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0253376
     RDKit          3D
Idebenone
 54 54  0  0  0  0  0  0  0  0999 V2000
    7.2907   -0.0242    0.6070 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1306    0.2617    1.3984 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8938    0.0379    0.8031 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5017    0.8687   -0.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3101    1.9307   -0.5302 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4577    2.9958    0.3914 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1925    0.6669   -0.8062 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8535    1.4805   -1.7077 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3380   -0.4440   -0.4105 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0386   -0.6714   -1.0425 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0840    0.5089   -0.8686 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1942    0.1044   -1.5759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2528    1.1776   -1.4947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4680    0.6807   -2.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0897   -0.5664   -1.7822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6549   -0.7626   -0.4513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8322   -0.6740    0.7596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7231   -0.9854    1.9717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8593   -0.0379    2.1308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3139    1.2573    2.2746 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7423   -1.2664    0.5399 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8687   -2.3831    0.9285 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0394   -1.0943    1.2169 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4242   -1.8796    2.1236 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3030    0.5970   -0.3190 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2186    0.1891    1.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1977   -1.1015    0.3151 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4778    3.4757    0.6356 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0983    3.8048   -0.0115 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8507    2.5820    1.3267 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5206   -1.5687   -0.7075 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1550   -0.7782   -2.1605 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5207    1.4400   -1.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0823    0.6407    0.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9350   -0.0118   -2.6542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5173   -0.8516   -1.1125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3888    1.5864   -0.5087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8432    2.0101   -2.1717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1989    1.5156   -2.4129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0874    0.4837   -3.2817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3698   -1.4096   -2.0439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9388   -0.7819   -2.5232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1308   -1.7985   -0.4455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5806   -0.1045   -0.3164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3675    0.2783    1.0140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0716   -1.5154    0.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1006   -0.9224    2.8861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0439   -2.0386    1.8435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6182   -0.0321    1.3458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4111   -0.2812    3.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2779    1.4797    3.2375 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8688   -2.0279    1.3088 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2987   -2.9809    1.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6760   -3.0604    0.0682 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
  4  5  1  0
  5  6  1  0
  4  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
  9 21  2  0
 21 22  1  0
 21 23  1  0
 23 24  2  0
 23  3  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  6 28  1  0
  6 29  1  0
  6 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 14 40  1  0
 15 41  1  0
 15 42  1  0
 16 43  1  0
 16 44  1  0
 17 45  1  0
 17 46  1  0
 18 47  1  0
 18 48  1  0
 19 49  1  0
 19 50  1  0
 20 51  1  0
 22 52  1  0
 22 53  1  0
 22 54  1  0
M  END

HEADER    PROTEIN                                 28-AUG-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-AUG-15         0                                  
HETATM    1  C   UNK     0      -2.188   0.771   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.188  -0.772   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.848  -1.543   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.483  -0.772   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.483   0.771   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.848   1.543   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.846   3.086   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.846  -3.086   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.820   1.542   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.524   1.544   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -3.524  -1.544   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -4.861  -0.773   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.810  -1.543   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.143  -0.772   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.861  -1.543   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -4.846   0.782   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.810  -1.543   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.143  -0.772   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.810  -1.543   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.143  -0.772   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.810  -1.543   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.143  -0.772   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.810  -1.543   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.143  -0.772   0.000  0.00  0.00           C+0
CONECT    1    6    2   10                                                  
CONECT    2    1    3   11                                                  
CONECT    3    8    2    4                                                  
CONECT    4    3    5   13                                                  
CONECT    5    9    4    6                                                  
CONECT    6    1    7    5                                                  
CONECT    7    6                                                            
CONECT    8    3                                                            
CONECT    9    5                                                            
CONECT   10    1   16                                                       
CONECT   11   12    2                                                       
CONECT   12   11                                                            
CONECT   13    4   14                                                       
CONECT   14   13   17                                                       
CONECT   15   24                                                            
CONECT   16   10                                                            
CONECT   17   14   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   15                                                       
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

COMPND    HMDB0253376
HETATM    1  C1  UNL     1       7.291  -0.024   0.607  1.00  0.00           C  
HETATM    2  O1  UNL     1       6.131   0.262   1.398  1.00  0.00           O  
HETATM    3  C2  UNL     1       4.894   0.038   0.803  1.00  0.00           C  
HETATM    4  C3  UNL     1       4.502   0.869  -0.147  1.00  0.00           C  
HETATM    5  O2  UNL     1       5.310   1.931  -0.530  1.00  0.00           O  
HETATM    6  C4  UNL     1       5.458   2.996   0.391  1.00  0.00           C  
HETATM    7  C5  UNL     1       3.193   0.667  -0.806  1.00  0.00           C  
HETATM    8  O3  UNL     1       2.853   1.480  -1.708  1.00  0.00           O  
HETATM    9  C6  UNL     1       2.338  -0.444  -0.410  1.00  0.00           C  
HETATM   10  C7  UNL     1       1.039  -0.671  -1.042  1.00  0.00           C  
HETATM   11  C8  UNL     1       0.084   0.509  -0.869  1.00  0.00           C  
HETATM   12  C9  UNL     1      -1.194   0.104  -1.576  1.00  0.00           C  
HETATM   13  C10 UNL     1      -2.253   1.178  -1.495  1.00  0.00           C  
HETATM   14  C11 UNL     1      -3.468   0.681  -2.220  1.00  0.00           C  
HETATM   15  C12 UNL     1      -4.090  -0.566  -1.782  1.00  0.00           C  
HETATM   16  C13 UNL     1      -4.655  -0.763  -0.451  1.00  0.00           C  
HETATM   17  C14 UNL     1      -3.832  -0.674   0.760  1.00  0.00           C  
HETATM   18  C15 UNL     1      -4.723  -0.985   1.972  1.00  0.00           C  
HETATM   19  C16 UNL     1      -5.859  -0.038   2.131  1.00  0.00           C  
HETATM   20  O4  UNL     1      -5.314   1.257   2.275  1.00  0.00           O  
HETATM   21  C17 UNL     1       2.742  -1.266   0.540  1.00  0.00           C  
HETATM   22  C18 UNL     1       1.869  -2.383   0.928  1.00  0.00           C  
HETATM   23  C19 UNL     1       4.039  -1.094   1.217  1.00  0.00           C  
HETATM   24  O5  UNL     1       4.424  -1.880   2.124  1.00  0.00           O  
HETATM   25  H1  UNL     1       7.303   0.597  -0.319  1.00  0.00           H  
HETATM   26  H2  UNL     1       8.219   0.189   1.155  1.00  0.00           H  
HETATM   27  H3  UNL     1       7.198  -1.101   0.315  1.00  0.00           H  
HETATM   28  H4  UNL     1       4.478   3.476   0.636  1.00  0.00           H  
HETATM   29  H5  UNL     1       6.098   3.805  -0.012  1.00  0.00           H  
HETATM   30  H6  UNL     1       5.851   2.582   1.327  1.00  0.00           H  
HETATM   31  H7  UNL     1       0.521  -1.569  -0.707  1.00  0.00           H  
HETATM   32  H8  UNL     1       1.155  -0.778  -2.160  1.00  0.00           H  
HETATM   33  H9  UNL     1       0.521   1.440  -1.278  1.00  0.00           H  
HETATM   34  H10 UNL     1      -0.082   0.641   0.222  1.00  0.00           H  
HETATM   35  H11 UNL     1      -0.935  -0.012  -2.654  1.00  0.00           H  
HETATM   36  H12 UNL     1      -1.517  -0.852  -1.112  1.00  0.00           H  
HETATM   37  H13 UNL     1      -2.389   1.586  -0.509  1.00  0.00           H  
HETATM   38  H14 UNL     1      -1.843   2.010  -2.172  1.00  0.00           H  
HETATM   39  H15 UNL     1      -4.199   1.516  -2.413  1.00  0.00           H  
HETATM   40  H16 UNL     1      -3.087   0.484  -3.282  1.00  0.00           H  
HETATM   41  H17 UNL     1      -3.370  -1.410  -2.044  1.00  0.00           H  
HETATM   42  H18 UNL     1      -4.939  -0.782  -2.523  1.00  0.00           H  
HETATM   43  H19 UNL     1      -5.131  -1.798  -0.446  1.00  0.00           H  
HETATM   44  H20 UNL     1      -5.581  -0.104  -0.316  1.00  0.00           H  
HETATM   45  H21 UNL     1      -3.367   0.278   1.014  1.00  0.00           H  
HETATM   46  H22 UNL     1      -3.072  -1.515   0.779  1.00  0.00           H  
HETATM   47  H23 UNL     1      -4.101  -0.922   2.886  1.00  0.00           H  
HETATM   48  H24 UNL     1      -5.044  -2.039   1.844  1.00  0.00           H  
HETATM   49  H25 UNL     1      -6.618  -0.032   1.346  1.00  0.00           H  
HETATM   50  H26 UNL     1      -6.411  -0.281   3.097  1.00  0.00           H  
HETATM   51  H27 UNL     1      -5.278   1.480   3.238  1.00  0.00           H  
HETATM   52  H28 UNL     1       0.869  -2.028   1.309  1.00  0.00           H  
HETATM   53  H29 UNL     1       2.299  -2.981   1.760  1.00  0.00           H  
HETATM   54  H30 UNL     1       1.676  -3.060   0.068  1.00  0.00           H  
CONECT    1    2   25   26   27
CONECT    2    3
CONECT    3    4    4   23
CONECT    4    5    7
CONECT    5    6
CONECT    6   28   29   30
CONECT    7    8    8    9
CONECT    9   10   21   21
CONECT   10   11   31   32
CONECT   11   12   33   34
CONECT   12   13   35   36
CONECT   13   14   37   38
CONECT   14   15   39   40
CONECT   15   16   41   42
CONECT   16   17   43   44
CONECT   17   18   45   46
CONECT   18   19   47   48
CONECT   19   20   49   50
CONECT   20   51
CONECT   21   22   23
CONECT   22   52   53   54
CONECT   23   24   24
END

HMDB0253376
     RDKit          3D
Idebenone
 54 54  0  0  0  0  0  0  0  0999 V2000
    7.2907   -0.0242    0.6070 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1306    0.2617    1.3984 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8938    0.0379    0.8031 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5017    0.8687   -0.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3101    1.9307   -0.5302 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4577    2.9958    0.3914 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1925    0.6669   -0.8062 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8535    1.4805   -1.7077 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3380   -0.4440   -0.4105 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0386   -0.6714   -1.0425 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0840    0.5089   -0.8686 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1942    0.1044   -1.5759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2528    1.1776   -1.4947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4680    0.6807   -2.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0897   -0.5664   -1.7822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6549   -0.7626   -0.4513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8322   -0.6740    0.7596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7231   -0.9854    1.9717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8593   -0.0379    2.1308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3139    1.2573    2.2746 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7423   -1.2664    0.5399 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8687   -2.3831    0.9285 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0394   -1.0943    1.2169 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4242   -1.8796    2.1236 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3030    0.5970   -0.3190 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2186    0.1891    1.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1977   -1.1015    0.3151 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4778    3.4757    0.6356 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0983    3.8048   -0.0115 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8507    2.5820    1.3267 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5206   -1.5687   -0.7075 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1550   -0.7782   -2.1605 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5207    1.4400   -1.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0823    0.6407    0.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9350   -0.0118   -2.6542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5173   -0.8516   -1.1125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3888    1.5864   -0.5087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8432    2.0101   -2.1717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1989    1.5156   -2.4129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0874    0.4837   -3.2817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3698   -1.4096   -2.0439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9388   -0.7819   -2.5232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1308   -1.7985   -0.4455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5806   -0.1045   -0.3164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3675    0.2783    1.0140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0716   -1.5154    0.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1006   -0.9224    2.8861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0439   -2.0386    1.8435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6182   -0.0321    1.3458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4111   -0.2812    3.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2779    1.4797    3.2375 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8688   -2.0279    1.3088 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2987   -2.9809    1.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6760   -3.0604    0.0682 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
  4  5  1  0
  5  6  1  0
  4  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
  9 21  2  0
 21 22  1  0
 21 23  1  0
 23 24  2  0
 23  3  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  6 28  1  0
  6 29  1  0
  6 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 14 40  1  0
 15 41  1  0
 15 42  1  0
 16 43  1  0
 16 44  1  0
 17 45  1  0
 17 46  1  0
 18 47  1  0
 18 48  1  0
 19 49  1  0
 19 50  1  0
 20 51  1  0
 22 52  1  0
 22 53  1  0
 22 54  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2,3-Dimethoxy-5-methyl-6-(10'-hydroxydecyl)-1,4-benzoquinone	ChEBI
2-(10-Hydroxydecyl)-5,6-dimethoxy-3-methyl-p-benzoquinone	ChEBI
2-(10-Hydroxydecyl)-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione	ChEBI
6-(10-Hydroxydecyl)-2,3-dimethoxy-5-methyl-1,4-benzoquinone	ChEBI
6-(10-Hydroxydecyl)-2,3-dimethoxy-5-methyl-p-benzoquinone	ChEBI
BRN 2001459	ChEBI
CV 2619	ChEBI
Idebenona	ChEBI
Idebenonum	ChEBI
Raxone	Kegg
Hydroxydecyl ubiquinone	MeSH
Noben	MeSH

Chemical Formula

C₁₉H₃₀O₅

Average Molecular Weight

338.444

Monoisotopic Molecular Weight

338.209324066

IUPAC Name

2-(10-hydroxydecyl)-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione

Traditional Name

idebenone

CAS Registry Number

Not Available

SMILES

COC1=C(OC)C(=O)C(CCCCCCCCCCO)=C(C)C1=O

InChI Identifier

InChI=1S/C19H30O5/c1-14-15(12-10-8-6-4-5-7-9-11-13-20)17(22)19(24-3)18(23-2)16(14)21/h20H,4-13H2,1-3H3

InChI Key

JGPMMRGNQUBGND-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ubiquinones. These are coenzyme Q derivatives containing a 5, 6-dimethoxy-3-methyl(1,4-benzoquinone) moiety to which an isoprenyl group is attached at ring position 2(or 6).

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Quinone and hydroquinone lipids

Direct Parent

Ubiquinones

Alternative Parents

Substituents

Ubiquinone skeleton
Fatty alcohol
P-benzoquinone
Quinone
Fatty acyl
Vinylogous ester
Cyclic ketone
Ketone
Alcohol
Hydrocarbon derivative
Primary alcohol
Organic oxide
Organooxygen compound
Organic oxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

primary alcohol (CHEBI:31687 )
benzoquinones (CHEBI:31687 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (HMDB: HMDB0253376)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	3.98	ALOGPS
logP	3.57	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	16.84	ChemAxon
pKa (Strongest Basic)	-2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	72.83 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	96.52 m³·mol⁻¹	ChemAxon
Polarizability	39.56 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	187.221	30932474
DeepCCS	[M-H]-	184.863	30932474
DeepCCS	[M-2H]-	217.75	30932474
DeepCCS	[M+Na]+	193.314	30932474
AllCCS	[M+H]+	185.6	32859911
AllCCS	[M+H-H2O]+	182.8	32859911
AllCCS	[M+NH4]+	188.2	32859911
AllCCS	[M+Na]+	189.0	32859911
AllCCS	[M-H]-	187.6	32859911
AllCCS	[M+Na-2H]-	188.6	32859911
AllCCS	[M+HCOO]-	189.9	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	16.0282 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.76 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2833.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	317.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	201.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	175.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	153.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	643.1 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	669.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	393.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1492.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	541.1 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	1583.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	358.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	436.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	293.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	280.0 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	10.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Idebenone	COC1=C(OC)C(=O)C(CCCCCCCCCCO)=C(C)C1=O	3764.2	Standard polar	33892256
Idebenone	COC1=C(OC)C(=O)C(CCCCCCCCCCO)=C(C)C1=O	2526.2	Standard non polar	33892256
Idebenone	COC1=C(OC)C(=O)C(CCCCCCCCCCO)=C(C)C1=O	2587.1	Semi standard non polar	33892256

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DBMET01521

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

Idebenone

METLIN ID

Not Available

PubChem Compound

3686

PDB ID

Not Available

ChEBI ID

31687

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Idebenone (HMDB0253376)

MOL for HMDB0253376 (Idebenone)

3D MOL for HMDB0253376 (Idebenone)

3D SDF for HMDB0253376 (Idebenone)

3D-SDF for HMDB0253376 (Idebenone)

PDB for HMDB0253376 (Idebenone)

3D PDB for HMDB0253376 (Idebenone)

SMILES for HMDB0253376 (Idebenone)

INCHI for HMDB0253376 (Idebenone)

Structure for HMDB0253376 (Idebenone)

3D Structure for HMDB0253376 (Idebenone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized