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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2009-07-25 00:07:34 UTC

Update Date

2021-09-14 15:41:20 UTC

HMDB ID

HMDB0012799

Secondary Accession Numbers

HMDB12799

Metabolite Identification

Common Name

5'-Carboxy-gamma-chromanol

Description

5'-Carboxy-gamma-tocopherol is a dehydrogenation carboxylate product of 5'-hydroxy-r-tocopherol by an unidentified microsomal enzyme(s) probably via an aldehyde intermediate. r-Tocopherol provides different antioxidant activities in food and in-vitro studies and showed higher activity in trapping lipophilic electrophiles and reactive nitrogen and oxygen species. From the metabolism end product, only that of r-tocopherol (2,7,8-trimethyl-2-(b-carboxyethyl)-6-hydroxychroman), but not that of a-tocopherol, was identified to provide natriuretic activity. Only the r-tocopherol plasma level served as biomarker for cancer and cardiovascular risk.

Structure

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

HMDB0012799
     RDKit          3D
5'-Carboxy-gamma-chromanol
 48 49  0  0  0  0  0  0  0  0999 V2000
    4.9826   -1.0126   -1.7589 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0236   -0.2437   -0.9270 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4561    0.9262   -0.3253 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7860    1.3284   -0.5332 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6312    1.7068    0.4671 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3334    1.3201    0.6738 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8886    0.1412    0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7238   -0.6210   -0.7137 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2216   -1.8652   -1.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5756   -0.2069    0.3066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1761    0.1072    1.4532 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3984   -1.1785    2.2071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4551    0.8276    1.1318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3774    0.0303    0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6082    0.8787    0.0110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6356    0.2282   -0.8565 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.1355   -1.0850   -0.2545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2498    0.0596   -2.2644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8719    0.5845   -3.2230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1430   -0.7169   -2.5687 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6419    1.0095    2.3455 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3557    2.0842    1.5136 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5228   -1.8986   -2.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8624   -1.3272   -1.1615 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3576   -0.3315   -2.5648 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4052    0.7920   -1.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9782    2.6248    0.9366 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4712   -1.9358   -2.4209 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1637   -2.0554   -1.1277 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7917   -2.7064   -0.8468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2623   -1.1243    2.8985 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4850   -1.4180    2.8395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5182   -2.0368    1.5133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9270    1.1449    2.0795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1844    1.7488    0.5771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7199   -0.9072    0.7161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8750   -0.1432   -0.7072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1076    1.1121    0.9856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3581    1.8602   -0.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5397    0.9043   -0.8245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4526   -1.9172   -0.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1276   -1.2946   -0.7217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3431   -0.8845    0.8226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2125   -1.7169   -2.7330 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0219    1.4717    3.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4780    0.3973    2.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8972    2.7119    2.2512 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6239    2.6268    0.9171 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  7 10  1  0
 10 11  1  0
 11 12  1  1
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 18 20  1  0
 11 21  1  0
 21 22  1  0
  8  2  1  0
 22  6  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  9 28  1  0
  9 29  1  0
  9 30  1  0
 12 31  1  0
 12 32  1  0
 12 33  1  0
 13 34  1  0
 13 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
 16 40  1  6
 17 41  1  0
 17 42  1  0
 17 43  1  0
 20 44  1  0
 21 45  1  0
 21 46  1  0
 22 47  1  0
 22 48  1  0
M  END

                  
  Mrv1652303102016462D          

 22 23  0  0  0  0            999 V2000
 9979.6434 9984.1056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9978.2142 9983.2765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9978.2142 9981.6198    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9982.4960 9983.2765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9983.2100 9982.8641    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9983.9258 9983.2765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9984.6393 9982.8641    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9985.3550 9983.2765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9986.0687 9982.8641    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9984.6393 9982.0397    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9981.7814 9983.6911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.6434 9983.2740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9978.9290 9982.8612    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9978.9289 9982.0364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.6434 9981.6239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9981.0695 9983.2741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9980.3548 9982.8614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9980.3548 9982.0364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9981.0695 9981.6240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9981.7838 9982.0364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9981.7838 9982.8614    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9985.3554 9984.1008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  8  1  0  0  0  0
  7 10  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 13  2  1  0  0  0  0
 14  3  1  0  0  0  0
  1 12  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
 16 17  1  0  0  0  0
 16 21  1  0  0  0  0
 21 11  1  1  0  0  0
 21  4  1  0  0  0  0
 17 12  2  0  0  0  0
 15 18  2  0  0  0  0
  8 22  2  0  0  0  0
  8  9  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0012799

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@@H](CCC[C@]1(C)CCC2=CC(O)=C(C)C(C)=C2O1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C18H26O4/c1-11(17(20)21)6-5-8-18(4)9-7-14-10-15(19)12(2)13(3)16(14)22-18/h10-11,19H,5-9H2,1-4H3,(H,20,21)/t11-,18+/m0/s1

> <INCHI_KEY>
CNGKBUHOCIWLHJ-BBATYDOGSA-N

> <FORMULA>
C18H26O4

> <MOLECULAR_WEIGHT>
306.402

> <EXACT_MASS>
306.183109317

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
35.017076665988704

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-5-[(2R)-6-hydroxy-2,7,8-trimethyl-3,4-dihydro-2H-1-benzopyran-2-yl]-2-methylpentanoic acid

> <ALOGPS_LOGP>
3.92

> <JCHEM_LOGP>
4.799433774999999

> <ALOGPS_LOGS>
-3.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.470460777184186

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.271517092767854

> <JCHEM_PKA_STRONGEST_BASIC>
-4.852416284607269

> <JCHEM_POLAR_SURFACE_AREA>
66.75999999999999

> <JCHEM_REFRACTIVITY>
86.11899999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.31e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-5-[(2R)-6-hydroxy-2,7,8-trimethyl-3,4-dihydro-1-benzopyran-2-yl]-2-methylpentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0012799
     RDKit          3D
5'-Carboxy-gamma-chromanol
 48 49  0  0  0  0  0  0  0  0999 V2000
    4.9826   -1.0126   -1.7589 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0236   -0.2437   -0.9270 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4561    0.9262   -0.3253 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7860    1.3284   -0.5332 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6312    1.7068    0.4671 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3334    1.3201    0.6738 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8886    0.1412    0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7238   -0.6210   -0.7137 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2216   -1.8652   -1.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5756   -0.2069    0.3066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1761    0.1072    1.4532 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3984   -1.1785    2.2071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4551    0.8276    1.1318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3774    0.0303    0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6082    0.8787    0.0110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6356    0.2282   -0.8565 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.1355   -1.0850   -0.2545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2498    0.0596   -2.2644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8719    0.5845   -3.2230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1430   -0.7169   -2.5687 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6419    1.0095    2.3455 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3557    2.0842    1.5136 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5228   -1.8986   -2.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8624   -1.3272   -1.1615 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3576   -0.3315   -2.5648 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4052    0.7920   -1.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9782    2.6248    0.9366 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4712   -1.9358   -2.4209 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1637   -2.0554   -1.1277 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7917   -2.7064   -0.8468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2623   -1.1243    2.8985 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4850   -1.4180    2.8395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5182   -2.0368    1.5133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9270    1.1449    2.0795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1844    1.7488    0.5771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7199   -0.9072    0.7161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8750   -0.1432   -0.7072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1076    1.1121    0.9856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3581    1.8602   -0.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5397    0.9043   -0.8245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4526   -1.9172   -0.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1276   -1.2946   -0.7217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3431   -0.8845    0.8226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2125   -1.7169   -2.7330 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0219    1.4717    3.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4780    0.3973    2.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8972    2.7119    2.2512 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6239    2.6268    0.9171 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  7 10  1  0
 10 11  1  0
 11 12  1  1
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 18 20  1  0
 11 21  1  0
 21 22  1  0
  8  2  1  0
 22  6  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  9 28  1  0
  9 29  1  0
  9 30  1  0
 12 31  1  0
 12 32  1  0
 12 33  1  0
 13 34  1  0
 13 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
 16 40  1  6
 17 41  1  0
 17 42  1  0
 17 43  1  0
 20 44  1  0
 21 45  1  0
 21 46  1  0
 22 47  1  0
 22 48  1  0
M  END

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0    8628.6688636.997   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8626.0008635.449   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8626.0008632.357   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0    8633.9938635.449   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8635.3258634.680   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8636.6618635.449   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8637.9938634.680   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8639.3298635.449   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0    8640.6628634.680   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0    8637.9938633.141   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8632.6598636.223   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8628.6688635.445   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8627.3348634.674   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8627.3348633.135   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8628.6688632.365   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0    8631.3308635.445   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0    8629.9968634.675   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8629.9968633.135   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8631.3308632.365   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8632.6638633.135   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8632.6638634.675   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0    8639.3308636.988   0.000  0.00  0.00           O+0
CONECT    1   12                                                            
CONECT    2   13                                                            
CONECT    3   14                                                            
CONECT    4    5   21                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    8   10    6                                                  
CONECT    8    7   22    9                                                  
CONECT    9    8                                                            
CONECT   10    7                                                            
CONECT   11   21                                                            
CONECT   12   13    1   17                                                  
CONECT   13   12   14    2                                                  
CONECT   14   13   15    3                                                  
CONECT   15   14   18                                                       
CONECT   16   17   21                                                       
CONECT   17   18   16   12                                                  
CONECT   18   17   19   15                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   16   11    4                                             
CONECT   22    8                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

COMPND    HMDB0012799
HETATM    1  C1  UNL     1       4.983  -1.013  -1.759  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.024  -0.244  -0.927  1.00  0.00           C  
HETATM    3  C3  UNL     1       4.456   0.926  -0.325  1.00  0.00           C  
HETATM    4  O1  UNL     1       5.786   1.328  -0.533  1.00  0.00           O  
HETATM    5  C4  UNL     1       3.631   1.707   0.467  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.333   1.320   0.674  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.889   0.141   0.070  1.00  0.00           C  
HETATM    8  C7  UNL     1       2.724  -0.621  -0.714  1.00  0.00           C  
HETATM    9  C8  UNL     1       2.222  -1.865  -1.339  1.00  0.00           C  
HETATM   10  O2  UNL     1       0.576  -0.207   0.307  1.00  0.00           O  
HETATM   11  C9  UNL     1      -0.176   0.107   1.453  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.398  -1.178   2.207  1.00  0.00           C  
HETATM   13  C11 UNL     1      -1.455   0.828   1.132  1.00  0.00           C  
HETATM   14  C12 UNL     1      -2.377   0.030   0.243  1.00  0.00           C  
HETATM   15  C13 UNL     1      -3.608   0.879   0.011  1.00  0.00           C  
HETATM   16  C14 UNL     1      -4.636   0.228  -0.856  1.00  0.00           C  
HETATM   17  C15 UNL     1      -5.135  -1.085  -0.255  1.00  0.00           C  
HETATM   18  C16 UNL     1      -4.250   0.060  -2.264  1.00  0.00           C  
HETATM   19  O3  UNL     1      -4.872   0.584  -3.223  1.00  0.00           O  
HETATM   20  O4  UNL     1      -3.143  -0.717  -2.569  1.00  0.00           O  
HETATM   21  C17 UNL     1       0.642   1.010   2.345  1.00  0.00           C  
HETATM   22  C18 UNL     1       1.356   2.084   1.514  1.00  0.00           C  
HETATM   23  H1  UNL     1       4.523  -1.899  -2.199  1.00  0.00           H  
HETATM   24  H2  UNL     1       5.862  -1.327  -1.162  1.00  0.00           H  
HETATM   25  H3  UNL     1       5.358  -0.332  -2.565  1.00  0.00           H  
HETATM   26  H4  UNL     1       6.405   0.792  -1.096  1.00  0.00           H  
HETATM   27  H5  UNL     1       3.978   2.625   0.937  1.00  0.00           H  
HETATM   28  H6  UNL     1       2.471  -1.936  -2.421  1.00  0.00           H  
HETATM   29  H7  UNL     1       1.164  -2.055  -1.128  1.00  0.00           H  
HETATM   30  H8  UNL     1       2.792  -2.706  -0.847  1.00  0.00           H  
HETATM   31  H9  UNL     1      -1.262  -1.124   2.899  1.00  0.00           H  
HETATM   32  H10 UNL     1       0.485  -1.418   2.840  1.00  0.00           H  
HETATM   33  H11 UNL     1      -0.518  -2.037   1.513  1.00  0.00           H  
HETATM   34  H12 UNL     1      -1.927   1.145   2.080  1.00  0.00           H  
HETATM   35  H13 UNL     1      -1.184   1.749   0.577  1.00  0.00           H  
HETATM   36  H14 UNL     1      -2.720  -0.907   0.716  1.00  0.00           H  
HETATM   37  H15 UNL     1      -1.875  -0.143  -0.707  1.00  0.00           H  
HETATM   38  H16 UNL     1      -4.108   1.112   0.986  1.00  0.00           H  
HETATM   39  H17 UNL     1      -3.358   1.860  -0.441  1.00  0.00           H  
HETATM   40  H18 UNL     1      -5.540   0.904  -0.825  1.00  0.00           H  
HETATM   41  H19 UNL     1      -4.453  -1.917  -0.430  1.00  0.00           H  
HETATM   42  H20 UNL     1      -6.128  -1.295  -0.722  1.00  0.00           H  
HETATM   43  H21 UNL     1      -5.343  -0.884   0.823  1.00  0.00           H  
HETATM   44  H22 UNL     1      -3.212  -1.717  -2.733  1.00  0.00           H  
HETATM   45  H23 UNL     1       0.022   1.472   3.145  1.00  0.00           H  
HETATM   46  H24 UNL     1       1.478   0.397   2.793  1.00  0.00           H  
HETATM   47  H25 UNL     1       1.897   2.712   2.251  1.00  0.00           H  
HETATM   48  H26 UNL     1       0.624   2.627   0.917  1.00  0.00           H  
CONECT    1    2   23   24   25
CONECT    2    3    3    8
CONECT    3    4    5
CONECT    4   26
CONECT    5    6    6   27
CONECT    6    7   22
CONECT    7    8    8   10
CONECT    8    9
CONECT    9   28   29   30
CONECT   10   11
CONECT   11   12   13   21
CONECT   12   31   32   33
CONECT   13   14   34   35
CONECT   14   15   36   37
CONECT   15   16   38   39
CONECT   16   17   18   40
CONECT   17   41   42   43
CONECT   18   19   19   20
CONECT   20   44
CONECT   21   22   45   46
CONECT   22   47   48
END

HMDB0012799
     RDKit          3D
5'-Carboxy-gamma-chromanol
 48 49  0  0  0  0  0  0  0  0999 V2000
    4.9826   -1.0126   -1.7589 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0236   -0.2437   -0.9270 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4561    0.9262   -0.3253 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7860    1.3284   -0.5332 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6312    1.7068    0.4671 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3334    1.3201    0.6738 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8886    0.1412    0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7238   -0.6210   -0.7137 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2216   -1.8652   -1.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5756   -0.2069    0.3066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1761    0.1072    1.4532 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3984   -1.1785    2.2071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4551    0.8276    1.1318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3774    0.0303    0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6082    0.8787    0.0110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6356    0.2282   -0.8565 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.1355   -1.0850   -0.2545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2498    0.0596   -2.2644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8719    0.5845   -3.2230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1430   -0.7169   -2.5687 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6419    1.0095    2.3455 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3557    2.0842    1.5136 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5228   -1.8986   -2.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8624   -1.3272   -1.1615 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3576   -0.3315   -2.5648 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4052    0.7920   -1.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9782    2.6248    0.9366 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4712   -1.9358   -2.4209 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1637   -2.0554   -1.1277 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7917   -2.7064   -0.8468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2623   -1.1243    2.8985 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4850   -1.4180    2.8395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5182   -2.0368    1.5133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9270    1.1449    2.0795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1844    1.7488    0.5771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7199   -0.9072    0.7161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8750   -0.1432   -0.7072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1076    1.1121    0.9856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3581    1.8602   -0.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5397    0.9043   -0.8245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4526   -1.9172   -0.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1276   -1.2946   -0.7217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3431   -0.8845    0.8226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2125   -1.7169   -2.7330 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0219    1.4717    3.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4780    0.3973    2.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8972    2.7119    2.2512 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6239    2.6268    0.9171 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  7 10  1  0
 10 11  1  0
 11 12  1  1
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 18 20  1  0
 11 21  1  0
 21 22  1  0
  8  2  1  0
 22  6  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  9 28  1  0
  9 29  1  0
  9 30  1  0
 12 31  1  0
 12 32  1  0
 12 33  1  0
 13 34  1  0
 13 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
 16 40  1  6
 17 41  1  0
 17 42  1  0
 17 43  1  0
 20 44  1  0
 21 45  1  0
 21 46  1  0
 22 47  1  0
 22 48  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(2S)-5-[(2R)-6-Hydroxy-2,7,8-trimethyl-3,4-dihydro-2H-1-benzopyran-2-yl]-2-methylpentanoate	HMDB
Γ-CMBHC	HMDB
gamma-CMBHC	HMDB
γ-Carboxymethylbutyl hydroxychroman	HMDB
γ-Carboxymethylbutylhydroxychroman	HMDB
gamma-Carboxymethylbutyl hydroxychroman	HMDB
gamma-Carboxymethylbutylhydroxychroman	HMDB

Chemical Formula

C₁₈H₂₆O₄

Average Molecular Weight

306.402

Monoisotopic Molecular Weight

306.183109317

IUPAC Name

(2S)-5-[(2R)-6-hydroxy-2,7,8-trimethyl-3,4-dihydro-2H-1-benzopyran-2-yl]-2-methylpentanoic acid

Traditional Name

(2S)-5-[(2R)-6-hydroxy-2,7,8-trimethyl-3,4-dihydro-1-benzopyran-2-yl]-2-methylpentanoic acid

CAS Registry Number

1221262-11-8

SMILES

C[C@@H](CCC[C@]1(C)CCC2=CC(O)=C(C)C(C)=C2O1)C(O)=O

InChI Identifier

InChI=1S/C18H26O4/c1-11(17(20)21)6-5-8-18(4)9-7-14-10-15(19)12(2)13(3)16(14)22-18/h10-11,19H,5-9H2,1-4H3,(H,20,21)/t11-,18+/m0/s1

InChI Key

CNGKBUHOCIWLHJ-BBATYDOGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1-benzopyrans. These are organic aromatic compounds that 1-benzopyran, a bicyclic compound made up of a benzene ring fused to a pyran, so that the oxygen atom is at the 1-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

1-benzopyrans

Alternative Parents

Substituents

1-benzopyran
Medium-chain fatty acid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Branched fatty acid
Heterocyclic fatty acid
Hydroxy fatty acid
Methyl-branched fatty acid
Fatty acyl
Fatty acid
Benzenoid
Monocarboxylic acid or derivatives
Oxacycle
Ether
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Hydrocarbon derivative
Carbonyl group
Organic oxygen compound
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0012799)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

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
Water Solubility	0.033 g/L	ALOGPS
logP	3.92	ALOGPS
logP	4.8	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	4.27	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	86.12 m³·mol⁻¹	ChemAxon
Polarizability	35.02 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	177.198	30932474
DeepCCS	[M-H]-	174.84	30932474
DeepCCS	[M-2H]-	208.635	30932474
DeepCCS	[M+Na]+	183.907	30932474
AllCCS	[M+H]+	175.9	32859911
AllCCS	[M+H-H2O]+	172.6	32859911
AllCCS	[M+NH4]+	178.9	32859911
AllCCS	[M+Na]+	179.7	32859911
AllCCS	[M-H]-	181.3	32859911
AllCCS	[M+Na-2H]-	181.7	32859911
AllCCS	[M+HCOO]-	182.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5'-Carboxy-gamma-chromanol	C[C@@H](CCC[C@]1(C)CCC2=CC(O)=C(C)C(C)=C2O1)C(O)=O	3743.7	Standard polar	33892256
5'-Carboxy-gamma-chromanol	C[C@@H](CCC[C@]1(C)CCC2=CC(O)=C(C)C(C)=C2O1)C(O)=O	2492.2	Standard non polar	33892256
5'-Carboxy-gamma-chromanol	C[C@@H](CCC[C@]1(C)CCC2=CC(O)=C(C)C(C)=C2O1)C(O)=O	2584.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5'-Carboxy-gamma-chromanol,1TMS,isomer #1	CC1=C(O[Si](C)(C)C)C=C2CC[C@@](C)(CCC[C@H](C)C(=O)O)OC2=C1C	2528.6	Semi standard non polar	33892256
5'-Carboxy-gamma-chromanol,1TMS,isomer #2	CC1=C(O)C=C2CC[C@@](C)(CCC[C@H](C)C(=O)O[Si](C)(C)C)OC2=C1C	2453.6	Semi standard non polar	33892256
5'-Carboxy-gamma-chromanol,2TMS,isomer #1	CC1=C(O[Si](C)(C)C)C=C2CC[C@@](C)(CCC[C@H](C)C(=O)O[Si](C)(C)C)OC2=C1C	2498.8	Semi standard non polar	33892256
5'-Carboxy-gamma-chromanol,1TBDMS,isomer #1	CC1=C(O[Si](C)(C)C(C)(C)C)C=C2CC[C@@](C)(CCC[C@H](C)C(=O)O)OC2=C1C	2787.9	Semi standard non polar	33892256
5'-Carboxy-gamma-chromanol,1TBDMS,isomer #2	CC1=C(O)C=C2CC[C@@](C)(CCC[C@H](C)C(=O)O[Si](C)(C)C(C)(C)C)OC2=C1C	2725.8	Semi standard non polar	33892256
5'-Carboxy-gamma-chromanol,2TBDMS,isomer #1	CC1=C(O[Si](C)(C)C(C)(C)C)C=C2CC[C@@](C)(CCC[C@H](C)C(=O)O[Si](C)(C)C(C)(C)C)OC2=C1C	2985.2	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5'-Carboxy-gamma-chromanol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 10V, Positive-QTOF	splash10-0pbi-0795000000-2a760615a1137de9e063	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 20V, Positive-QTOF	splash10-0udi-1920000000-0b6e86db1ccc007ae9ae	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 40V, Positive-QTOF	splash10-0pb9-5900000000-a1641967f03e449c84ae	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 10V, Negative-QTOF	splash10-0a4i-0129000000-ca2b2a47f99db6cbbdcf	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 20V, Negative-QTOF	splash10-0bta-1895000000-31aed0c986eda055c878	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 40V, Negative-QTOF	splash10-0002-7970000000-84306781d9a92ffbebff	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 10V, Negative-QTOF	splash10-0a4i-0009000000-f8a5e82e8af4d5edf5e8	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 20V, Negative-QTOF	splash10-0lxt-1974000000-2e3c70bb39be5f027e99	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 40V, Negative-QTOF	splash10-006w-0940000000-16b1c3ee83486876f9af	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 10V, Positive-QTOF	splash10-08g0-0192000000-c340a46203f3dd7a4c1b	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 20V, Positive-QTOF	splash10-06xx-2290000000-f0e4037b879a4f1c1eb1	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5'-Carboxy-gamma-chromanol 40V, Positive-QTOF	splash10-0pvu-6900000000-6fcdce7d23a6a930918a	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

74854293

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

134159052

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

CE5723

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Birringer M, Pfluger P, Kluth D, Landes N, Brigelius-Flohe R: Identities and differences in the metabolism of tocotrienols and tocopherols in HepG2 cells. J Nutr. 2002 Oct;132(10):3113-8. [PubMed:12368403 ]
Zhao Y, Lee MJ, Cheung C, Ju JH, Chen YK, Liu B, Hu LQ, Yang CS: Analysis of multiple metabolites of tocopherols and tocotrienols in mice and humans. J Agric Food Chem. 2010 Apr 28;58(8):4844-52. doi: 10.1021/jf904464u. [PubMed:20222730 ]

Showing metabocard for 5'-Carboxy-gamma-chromanol (HMDB0012799)

MOL for HMDB0012799 (5'-Carboxy-gamma-chromanol)

3D MOL for HMDB0012799 (5'-Carboxy-gamma-chromanol)

3D SDF for HMDB0012799 (5'-Carboxy-gamma-chromanol)

3D-SDF for HMDB0012799 (5'-Carboxy-gamma-chromanol)

PDB for HMDB0012799 (5'-Carboxy-gamma-chromanol)

3D PDB for HMDB0012799 (5'-Carboxy-gamma-chromanol)

SMILES for HMDB0012799 (5'-Carboxy-gamma-chromanol)

INCHI for HMDB0012799 (5'-Carboxy-gamma-chromanol)

Structure for HMDB0012799 (5'-Carboxy-gamma-chromanol)

3D Structure for HMDB0012799 (5'-Carboxy-gamma-chromanol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra