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Showing metabocard for Didesmethyl tocotrienol (HMDB0251224)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 08:33:20 UTC
Update Date2021-09-26 23:03:06 UTC
HMDB IDHMDB0251224
Secondary Accession NumbersNone
Metabolite Identification
Common NameDidesmethyl tocotrienol
Description2-(4,8,12-trimethyltrideca-3,7,11-trien-1-yl)-3,4-dihydro-2H-1-benzopyran-6-ol belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Based on a literature review very few articles have been published on 2-(4,8,12-trimethyltrideca-3,7,11-trien-1-yl)-3,4-dihydro-2H-1-benzopyran-6-ol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Didesmethyl tocotrienol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Didesmethyl tocotrienol 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0251224 (Didesmethyl tocotrienol)


  Mrv1533004201503082D          

 27 28  0  0  0  0            999 V2000
   -7.8592   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  4  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  4  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 17 23  1  0  0  0  0
 23 24  1  0  0  0  0
 14 24  1  0  0  0  0
 10 25  1  0  0  0  0
  6 26  1  0  0  0  0
  2 27  1  0  0  0  0
M  END
Download

3D MOL for HMDB0251224 (Didesmethyl tocotrienol)

HMDB0251224
     RDKit          3D
Didesmethyl tocotrienol
 63 64  0  0  0  0  0  0  0  0999 V2000
   -7.0995   -2.1085   -0.2222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1021   -1.5098   -1.1467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5604   -2.3243   -2.2513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7184   -0.2716   -0.9695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2363    0.5882    0.1294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0808    1.0438    1.0324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1101    1.8090    0.2392 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6301    3.0601   -0.4282 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8373    1.4772    0.0773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1767    0.3003    0.6537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0884    0.5651    1.6407 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493    1.3640    1.1393 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0930    2.7697    0.7053 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2404    0.7914    1.1241 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4221    1.5077    0.6417 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0017    0.7878   -0.5518 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4071   -0.6024   -0.1435 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9923   -1.2532   -1.3986 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9081   -2.3966   -0.9640 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0475   -1.7610   -0.2525 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3474   -2.1436   -0.5083 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3669   -1.4973    0.2031 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6640   -1.8889   -0.0617 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0839   -0.5194    1.1210 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7759   -0.1727    1.3415 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7376   -0.7803    0.6657 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4088   -0.4708    0.8486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2917   -3.1810   -0.4644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7014   -1.9910    0.8161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0374   -1.5320   -0.3127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9269   -1.7701   -2.9440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4100   -2.7441   -2.8186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9832   -3.1662   -1.7844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9918    0.1768   -1.6368 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7109    1.5180   -0.2491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9918    0.0369    0.7181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7183    0.1531    1.5352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5608    1.6798    1.8300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9288    3.7513    0.3622 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8154    3.5441   -1.0184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4253    2.8157   -1.1569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2558    2.1671   -0.5753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7050   -0.2409   -0.2317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8765   -0.4369    1.1003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7487   -0.4452    2.0153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4847    1.0488    2.5825 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6938    3.3939    1.2388 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0248    2.8767   -0.3797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0418    3.2300    1.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3915   -0.2331    1.4807 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1721    1.4822    1.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2748    2.5883    0.4290 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9468    1.3064   -0.8910 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2491    0.7768   -1.3677 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5303   -1.1870    0.2052 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2006   -1.6222   -2.0537 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6552   -0.4920   -1.8594 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2915   -3.0123   -0.2479 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2029   -3.0224   -1.8042 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5956   -2.9154   -1.2306 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2641   -1.4904   -0.7593 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8711   -0.0352    1.6560 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5223    0.6077    2.0719 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  3
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  2  3
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  1  0
 22 24  2  0
 24 25  1  0
 25 26  2  0
 26 27  1  0
 27 17  1  0
 26 20  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
  3 31  1  0
  3 32  1  0
  3 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  6 37  1  0
  6 38  1  0
  8 39  1  0
  8 40  1  0
  8 41  1  0
  9 42  1  0
 10 43  1  0
 10 44  1  0
 11 45  1  0
 11 46  1  0
 13 47  1  0
 13 48  1  0
 13 49  1  0
 14 50  1  0
 15 51  1  0
 15 52  1  0
 16 53  1  0
 16 54  1  0
 17 55  1  0
 18 56  1  0
 18 57  1  0
 19 58  1  0
 19 59  1  0
 21 60  1  0
 23 61  1  0
 24 62  1  0
 25 63  1  0
M  END
Download

3D SDF for HMDB0251224 (Didesmethyl tocotrienol)


  Mrv1533004201503082D          

 27 28  0  0  0  0            999 V2000
   -7.8592   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  4  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  4  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 17 23  1  0  0  0  0
 23 24  1  0  0  0  0
 14 24  1  0  0  0  0
 10 25  1  0  0  0  0
  6 26  1  0  0  0  0
  2 27  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0251224

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCCC(C)=CCCC(C)=CCCC1CCC2=CC(O)=CC=C2O1

> <INCHI_IDENTIFIER>
InChI=1S/C25H36O2/c1-19(2)8-5-9-20(3)10-6-11-21(4)12-7-13-24-16-14-22-18-23(26)15-17-25(22)27-24/h8,10,12,15,17-18,24,26H,5-7,9,11,13-14,16H2,1-4H3

> <INCHI_KEY>
WSTGHGHPTQPFAP-UHFFFAOYSA-N

> <FORMULA>
C25H36O2

> <MOLECULAR_WEIGHT>
368.561

> <EXACT_MASS>
368.271530399

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
45.73701503928244

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(4,8,12-trimethyltrideca-3,7,11-trien-1-yl)-3,4-dihydro-2H-1-benzopyran-6-ol

> <ALOGPS_LOGP>
7.62

> <JCHEM_LOGP>
7.470137979666669

> <ALOGPS_LOGS>
-5.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.020681850149023

> <JCHEM_PKA_STRONGEST_BASIC>
-4.841048425946792

> <JCHEM_POLAR_SURFACE_AREA>
29.46

> <JCHEM_REFRACTIVITY>
118.16229999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.06e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(4,8,12-trimethyltrideca-3,7,11-trien-1-yl)-3,4-dihydro-2H-1-benzopyran-6-ol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0251224 (Didesmethyl tocotrienol)

HMDB0251224
     RDKit          3D
Didesmethyl tocotrienol
 63 64  0  0  0  0  0  0  0  0999 V2000
   -7.0995   -2.1085   -0.2222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1021   -1.5098   -1.1467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5604   -2.3243   -2.2513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7184   -0.2716   -0.9695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2363    0.5882    0.1294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0808    1.0438    1.0324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1101    1.8090    0.2392 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6301    3.0601   -0.4282 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8373    1.4772    0.0773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1767    0.3003    0.6537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0884    0.5651    1.6407 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493    1.3640    1.1393 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0930    2.7697    0.7053 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2404    0.7914    1.1241 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4221    1.5077    0.6417 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0017    0.7878   -0.5518 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4071   -0.6024   -0.1435 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9923   -1.2532   -1.3986 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9081   -2.3966   -0.9640 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0475   -1.7610   -0.2525 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3474   -2.1436   -0.5083 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3669   -1.4973    0.2031 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6640   -1.8889   -0.0617 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0839   -0.5194    1.1210 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7759   -0.1727    1.3415 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7376   -0.7803    0.6657 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4088   -0.4708    0.8486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2917   -3.1810   -0.4644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7014   -1.9910    0.8161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0374   -1.5320   -0.3127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9269   -1.7701   -2.9440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4100   -2.7441   -2.8186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9832   -3.1662   -1.7844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9918    0.1768   -1.6368 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7109    1.5180   -0.2491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9918    0.0369    0.7181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7183    0.1531    1.5352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5608    1.6798    1.8300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9288    3.7513    0.3622 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8154    3.5441   -1.0184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4253    2.8157   -1.1569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2558    2.1671   -0.5753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7050   -0.2409   -0.2317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8765   -0.4369    1.1003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7487   -0.4452    2.0153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4847    1.0488    2.5825 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6938    3.3939    1.2388 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0248    2.8767   -0.3797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0418    3.2300    1.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3915   -0.2331    1.4807 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1721    1.4822    1.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2748    2.5883    0.4290 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9468    1.3064   -0.8910 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2491    0.7768   -1.3677 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5303   -1.1870    0.2052 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2006   -1.6222   -2.0537 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6552   -0.4920   -1.8594 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2915   -3.0123   -0.2479 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2029   -3.0224   -1.8042 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5956   -2.9154   -1.2306 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2641   -1.4904   -0.7593 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8711   -0.0352    1.6560 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5223    0.6077    2.0719 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  3
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  2  3
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  1  0
 22 24  2  0
 24 25  1  0
 25 26  2  0
 26 27  1  0
 27 17  1  0
 26 20  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
  3 31  1  0
  3 32  1  0
  3 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  6 37  1  0
  6 38  1  0
  8 39  1  0
  8 40  1  0
  8 41  1  0
  9 42  1  0
 10 43  1  0
 10 44  1  0
 11 45  1  0
 11 46  1  0
 13 47  1  0
 13 48  1  0
 13 49  1  0
 14 50  1  0
 15 51  1  0
 15 52  1  0
 16 53  1  0
 16 54  1  0
 17 55  1  0
 18 56  1  0
 18 57  1  0
 19 58  1  0
 19 59  1  0
 21 60  1  0
 23 61  1  0
 24 62  1  0
 25 63  1  0
M  END
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PDB for HMDB0251224 (Didesmethyl tocotrienol)

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  C   UNK     0     -14.670  -5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -13.337  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -12.003  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -10.669  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       6.668  -2.310   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  -2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -13.337  -3.080   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   27                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   26                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   25                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   24                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   23                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   17   24                                                  
CONECT   24   23   14                                                       
CONECT   25   10                                                            
CONECT   26    6                                                            
CONECT   27    2                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   56    0
END
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3D PDB for HMDB0251224 (Didesmethyl tocotrienol)

COMPND    HMDB0251224
HETATM    1  C1  UNL     1      -7.100  -2.109  -0.222  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.102  -1.510  -1.147  1.00  0.00           C  
HETATM    3  C3  UNL     1      -5.560  -2.324  -2.251  1.00  0.00           C  
HETATM    4  C4  UNL     1      -5.718  -0.272  -0.970  1.00  0.00           C  
HETATM    5  C5  UNL     1      -6.236   0.588   0.129  1.00  0.00           C  
HETATM    6  C6  UNL     1      -5.081   1.044   1.032  1.00  0.00           C  
HETATM    7  C7  UNL     1      -4.110   1.809   0.239  1.00  0.00           C  
HETATM    8  C8  UNL     1      -4.630   3.060  -0.428  1.00  0.00           C  
HETATM    9  C9  UNL     1      -2.837   1.477   0.077  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.177   0.300   0.654  1.00  0.00           C  
HETATM   11  C11 UNL     1      -1.088   0.565   1.641  1.00  0.00           C  
HETATM   12  C12 UNL     1       0.049   1.364   1.139  1.00  0.00           C  
HETATM   13  C13 UNL     1      -0.093   2.770   0.705  1.00  0.00           C  
HETATM   14  C14 UNL     1       1.240   0.791   1.124  1.00  0.00           C  
HETATM   15  C15 UNL     1       2.422   1.508   0.642  1.00  0.00           C  
HETATM   16  C16 UNL     1       3.002   0.788  -0.552  1.00  0.00           C  
HETATM   17  C17 UNL     1       3.407  -0.602  -0.144  1.00  0.00           C  
HETATM   18  C18 UNL     1       3.992  -1.253  -1.399  1.00  0.00           C  
HETATM   19  C19 UNL     1       4.908  -2.397  -0.964  1.00  0.00           C  
HETATM   20  C20 UNL     1       6.048  -1.761  -0.253  1.00  0.00           C  
HETATM   21  C21 UNL     1       7.347  -2.144  -0.508  1.00  0.00           C  
HETATM   22  C22 UNL     1       8.367  -1.497   0.203  1.00  0.00           C  
HETATM   23  O1  UNL     1       9.664  -1.889  -0.062  1.00  0.00           O  
HETATM   24  C23 UNL     1       8.084  -0.519   1.121  1.00  0.00           C  
HETATM   25  C24 UNL     1       6.776  -0.173   1.342  1.00  0.00           C  
HETATM   26  C25 UNL     1       5.738  -0.780   0.666  1.00  0.00           C  
HETATM   27  O2  UNL     1       4.409  -0.471   0.849  1.00  0.00           O  
HETATM   28  H1  UNL     1      -7.292  -3.181  -0.464  1.00  0.00           H  
HETATM   29  H2  UNL     1      -6.701  -1.991   0.816  1.00  0.00           H  
HETATM   30  H3  UNL     1      -8.037  -1.532  -0.313  1.00  0.00           H  
HETATM   31  H4  UNL     1      -4.927  -1.770  -2.944  1.00  0.00           H  
HETATM   32  H5  UNL     1      -6.410  -2.744  -2.819  1.00  0.00           H  
HETATM   33  H6  UNL     1      -4.983  -3.166  -1.784  1.00  0.00           H  
HETATM   34  H7  UNL     1      -4.992   0.177  -1.637  1.00  0.00           H  
HETATM   35  H8  UNL     1      -6.711   1.518  -0.249  1.00  0.00           H  
HETATM   36  H9  UNL     1      -6.992   0.037   0.718  1.00  0.00           H  
HETATM   37  H10 UNL     1      -4.718   0.153   1.535  1.00  0.00           H  
HETATM   38  H11 UNL     1      -5.561   1.680   1.830  1.00  0.00           H  
HETATM   39  H12 UNL     1      -4.929   3.751   0.362  1.00  0.00           H  
HETATM   40  H13 UNL     1      -3.815   3.544  -1.018  1.00  0.00           H  
HETATM   41  H14 UNL     1      -5.425   2.816  -1.157  1.00  0.00           H  
HETATM   42  H15 UNL     1      -2.256   2.167  -0.575  1.00  0.00           H  
HETATM   43  H16 UNL     1      -1.705  -0.241  -0.232  1.00  0.00           H  
HETATM   44  H17 UNL     1      -2.877  -0.437   1.100  1.00  0.00           H  
HETATM   45  H18 UNL     1      -0.749  -0.445   2.015  1.00  0.00           H  
HETATM   46  H19 UNL     1      -1.485   1.049   2.583  1.00  0.00           H  
HETATM   47  H20 UNL     1       0.694   3.394   1.239  1.00  0.00           H  
HETATM   48  H21 UNL     1       0.025   2.877  -0.380  1.00  0.00           H  
HETATM   49  H22 UNL     1      -1.042   3.230   1.079  1.00  0.00           H  
HETATM   50  H23 UNL     1       1.391  -0.233   1.481  1.00  0.00           H  
HETATM   51  H24 UNL     1       3.172   1.482   1.480  1.00  0.00           H  
HETATM   52  H25 UNL     1       2.275   2.588   0.429  1.00  0.00           H  
HETATM   53  H26 UNL     1       3.947   1.306  -0.891  1.00  0.00           H  
HETATM   54  H27 UNL     1       2.249   0.777  -1.368  1.00  0.00           H  
HETATM   55  H28 UNL     1       2.530  -1.187   0.205  1.00  0.00           H  
HETATM   56  H29 UNL     1       3.201  -1.622  -2.054  1.00  0.00           H  
HETATM   57  H30 UNL     1       4.655  -0.492  -1.859  1.00  0.00           H  
HETATM   58  H31 UNL     1       4.292  -3.012  -0.248  1.00  0.00           H  
HETATM   59  H32 UNL     1       5.203  -3.022  -1.804  1.00  0.00           H  
HETATM   60  H33 UNL     1       7.596  -2.915  -1.231  1.00  0.00           H  
HETATM   61  H34 UNL     1      10.264  -1.490  -0.759  1.00  0.00           H  
HETATM   62  H35 UNL     1       8.871  -0.035   1.656  1.00  0.00           H  
HETATM   63  H36 UNL     1       6.522   0.608   2.072  1.00  0.00           H  
CONECT    1    2   28   29   30
CONECT    2    3    4    4
CONECT    3   31   32   33
CONECT    4    5   34
CONECT    5    6   35   36
CONECT    6    7   37   38
CONECT    7    8    9    9
CONECT    8   39   40   41
CONECT    9   10   42
CONECT   10   11   43   44
CONECT   11   12   45   46
CONECT   12   13   14   14
CONECT   13   47   48   49
CONECT   14   15   50
CONECT   15   16   51   52
CONECT   16   17   53   54
CONECT   17   18   27   55
CONECT   18   19   56   57
CONECT   19   20   58   59
CONECT   20   21   21   26
CONECT   21   22   60
CONECT   22   23   24   24
CONECT   23   61
CONECT   24   25   62
CONECT   25   26   26   63
CONECT   26   27
END
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SMILES for HMDB0251224 (Didesmethyl tocotrienol)

CC(C)=CCCC(C)=CCCC(C)=CCCC1CCC2=CC(O)=CC=C2O1
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INCHI for HMDB0251224 (Didesmethyl tocotrienol)

InChI=1S/C25H36O2/c1-19(2)8-5-9-20(3)10-6-11-21(4)12-7-13-24-16-14-22-18-23(26)15-17-25(22)27-24/h8,10,12,15,17-18,24,26H,5-7,9,11,13-14,16H2,1-4H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC25H36O2
Average Molecular Weight368.561
Monoisotopic Molecular Weight368.271530399
IUPAC Name2-(4,8,12-trimethyltrideca-3,7,11-trien-1-yl)-3,4-dihydro-2H-1-benzopyran-6-ol
Traditional Name2-(4,8,12-trimethyltrideca-3,7,11-trien-1-yl)-3,4-dihydro-2H-1-benzopyran-6-ol
CAS Registry NumberNot Available
SMILES
CC(C)=CCCC(C)=CCCC(C)=CCCC1CCC2=CC(O)=CC=C2O1
InChI Identifier
InChI=1S/C25H36O2/c1-19(2)8-5-9-20(3)10-6-11-21(4)12-7-13-24-16-14-22-18-23(26)15-17-25(22)27-24/h8,10,12,15,17-18,24,26H,5-7,9,11,13-14,16H2,1-4H3
InChI KeyWSTGHGHPTQPFAP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassDiterpenoids
Direct ParentDiterpenoids
Alternative Parents
Substituents
  • Diterpenoid
  • 1-benzopyran
  • Benzopyran
  • Chromane
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Alkyl aryl ether
  • Benzenoid
  • Oxacycle
  • Organoheterocyclic compound
  • Ether
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP7.62ALOGPS
logP7.47ChemAxon
logS-5.5ALOGPS
pKa (Strongest Acidic)10.02ChemAxon
pKa (Strongest Basic)-4.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area29.46 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity118.16 m³·mol⁻¹ChemAxon
Polarizability45.74 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+186.74730932474
DeepCCS[M-H]-184.37130932474
DeepCCS[M-2H]-217.89130932474
DeepCCS[M+Na]+193.5530932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202225.404 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.25 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3628.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid729.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid308.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid382.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid441.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1124.4 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid981.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)88.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid2292.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid843.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1678.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid821.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid575.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate333.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA576.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water8.7 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Didesmethyl tocotrienolCC(C)=CCCC(C)=CCCC(C)=CCCC1CCC2=CC(O)=CC=C2O13814.3Standard polar33892256
Didesmethyl tocotrienolCC(C)=CCCC(C)=CCCC(C)=CCCC1CCC2=CC(O)=CC=C2O12929.7Standard non polar33892256
Didesmethyl tocotrienolCC(C)=CCCC(C)=CCCC(C)=CCCC1CCC2=CC(O)=CC=C2O13054.0Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound54447752
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]