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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:02:50 UTC

Update Date

2022-03-07 02:53:40 UTC

HMDB ID

HMDB0033332

Secondary Accession Numbers

HMDB33332

Metabolite Identification

Common Name

Garcinone D

Description

Garcinone D belongs to the class of organic compounds known as 8-prenylated xanthones. These are organic compounds containing a C5-isoprenoid group linked to a xanthone moiety at the 8-position. Xanthone is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring that carries a ketone group. Garcinone D has been detected, but not quantified in, fruits and purple mangosteens (Garcinia mangostana). This could make garcinone D a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Garcinone D.

Structure

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


  Mrv1652309272007472D          

 31 33  0  0  0  0            999 V2000
 9971.9405 9969.5265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9972.6520 9969.1140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9972.6520 9968.2890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9971.9322 9967.8889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9973.0667 9967.5753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9973.4770 9968.2890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9970.5090 9969.5265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9969.0799 9969.5265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9967.6489 9972.0016    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9967.6489 9970.3515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9966.9345 9970.7649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9966.2199 9970.3515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9965.5055 9970.7649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9966.2199 9969.5265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9973.3678 9970.3515    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9974.0814 9970.7649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9973.3678 9972.0016    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9972.6507 9970.7659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9971.9385 9970.3546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9971.9384 9971.9996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9972.6507 9971.5884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9969.0786 9970.3546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9968.3662 9970.7659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9968.3661 9971.5884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9969.0785 9971.9996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9970.5086 9970.3544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9969.7963 9970.7657    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9969.7963 9971.5883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9970.5086 9971.9994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9971.2210 9971.5883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9971.2210 9970.7657    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 15 16  1  0  0  0  0
 18 19  2  0  0  0  0
 20 21  2  0  0  0  0
 21 18  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 24  9  1  0  0  0  0
 23 10  1  0  0  0  0
 22  8  1  0  0  0  0
 18 15  1  0  0  0  0
 21 17  1  0  0  0  0
  1 19  1  0  0  0  0
 26 27  1  0  0  0  0
 26 31  1  0  0  0  0
 27 28  1  0  0  0  0
 30 31  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 26  7  2  0  0  0  0
 19 31  1  0  0  0  0
 30 20  1  0  0  0  0
 27 22  2  0  0  0  0
 25 28  2  0  0  0  0
M  END

HMDB0033332
     RDKit          3D
Garcinone D
 59 61  0  0  0  0  0  0  0  0999 V2000
   -4.7055   -2.4862   -2.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8850   -2.8255   -1.3092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5720   -2.6211   -1.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6918   -3.5047   -1.6426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2293   -4.4818   -2.5235 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3668   -3.4194   -1.4065 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1173   -2.4618   -0.5453 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4281   -2.4051   -0.3216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9891   -1.5453    0.4863 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3599   -1.5138    0.6970 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9714   -0.6318    1.5326 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3655   -0.6267    1.7244 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1711    0.2930    2.2144 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8478    1.2114    3.1413 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6210    2.3125    2.5653 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8192    2.7347    1.3598 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690    2.1730    0.1198 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7231    3.9416    1.1683 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7893    0.2743    2.0121 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9679    1.1596    2.6562 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1988   -0.6390    1.1523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1874   -0.6787    0.9295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8386    0.1457    1.5534 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7521   -1.5820    0.0780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1453   -1.6214   -0.1360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9858   -0.6162    0.4859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2401    0.7028   -0.0500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8522    1.0250   -1.3580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1439    0.5622   -2.5817 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3207    0.6507   -1.3298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9091    2.4719   -1.3997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6867   -2.0030   -2.0565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2515   -1.9500   -3.2013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9975   -3.4971   -2.8382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5847   -5.1283   -2.9844 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3159   -4.0970   -1.8893 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9679   -2.2521    0.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7447    0.0539    2.3610 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4812    0.6231    3.8894 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0744    1.6801    3.8276 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1535    2.8940    3.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1886    2.9672   -0.6881 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2513    1.8236    0.2462 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8840    1.3596   -0.3206 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3596    3.7293    0.2856 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0474    4.8072    0.9760 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3104    4.1240    2.0816 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1664    1.8855    3.2928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9244   -0.6408    1.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0431   -1.1383    0.4408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9304    1.3077    0.6810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2655    1.3289   -0.0515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8257    0.3533   -3.4304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5196    1.4458   -2.9551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4427   -0.2299   -2.3925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9521    1.5056   -0.9760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4459   -0.1443   -0.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6845    0.3663   -2.3427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2039    2.8279   -1.9653 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  2  3
 16 17  1  0
 16 18  1  0
 13 19  1  0
 19 20  1  0
 19 21  2  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 28 30  1  0
 28 31  1  0
 25  3  1  0
 24  7  1  0
 21  9  1  0
  1 32  1  0
  1 33  1  0
  1 34  1  0
  5 35  1  0
  6 36  1  0
 10 37  1  0
 12 38  1  0
 14 39  1  0
 14 40  1  0
 15 41  1  0
 17 42  1  0
 17 43  1  0
 17 44  1  0
 18 45  1  0
 18 46  1  0
 18 47  1  0
 20 48  1  0
 26 49  1  0
 26 50  1  0
 27 51  1  0
 27 52  1  0
 29 53  1  0
 29 54  1  0
 29 55  1  0
 30 56  1  0
 30 57  1  0
 30 58  1  0
 31 59  1  0
M  END


  Mrv1652309272007472D          

 31 33  0  0  0  0            999 V2000
 9971.9405 9969.5265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9972.6520 9969.1140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9972.6520 9968.2890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9971.9322 9967.8889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9973.0667 9967.5753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9973.4770 9968.2890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9970.5090 9969.5265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9969.0799 9969.5265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9967.6489 9972.0016    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9967.6489 9970.3515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9966.9345 9970.7649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9966.2199 9970.3515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9965.5055 9970.7649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9966.2199 9969.5265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9973.3678 9970.3515    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9974.0814 9970.7649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9973.3678 9972.0016    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9972.6507 9970.7659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9971.9385 9970.3546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9971.9384 9971.9996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9972.6507 9971.5884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9969.0786 9970.3546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9968.3662 9970.7659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9968.3661 9971.5884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9969.0785 9971.9996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9970.5086 9970.3544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9969.7963 9970.7657    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9969.7963 9971.5883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9970.5086 9971.9994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9971.2210 9971.5883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9971.2210 9970.7657    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 15 16  1  0  0  0  0
 18 19  2  0  0  0  0
 20 21  2  0  0  0  0
 21 18  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 24  9  1  0  0  0  0
 23 10  1  0  0  0  0
 22  8  1  0  0  0  0
 18 15  1  0  0  0  0
 21 17  1  0  0  0  0
  1 19  1  0  0  0  0
 26 27  1  0  0  0  0
 26 31  1  0  0  0  0
 27 28  1  0  0  0  0
 30 31  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 26  7  2  0  0  0  0
 19 31  1  0  0  0  0
 30 20  1  0  0  0  0
 27 22  2  0  0  0  0
 25 28  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033332

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(CCC(C)(C)O)C2=C(OC3=CC(O)=C(CC=C(C)C)C(O)=C3C2=O)C=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H28O7/c1-12(2)6-7-13-15(25)10-18-20(21(13)27)22(28)19-14(8-9-24(3,4)29)23(30-5)16(26)11-17(19)31-18/h6,10-11,25-27,29H,7-9H2,1-5H3

> <INCHI_KEY>
TYALNCRUIKOKGP-UHFFFAOYSA-N

> <FORMULA>
C24H28O7

> <MOLECULAR_WEIGHT>
428.4749

> <EXACT_MASS>
428.18350325

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
46.87429488301001

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,3,6-trihydroxy-8-(3-hydroxy-3-methylbutyl)-7-methoxy-2-(3-methylbut-2-en-1-yl)-9H-xanthen-9-one

> <ALOGPS_LOGP>
3.77

> <JCHEM_LOGP>
4.9328717846666645

> <ALOGPS_LOGS>
-4.72

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.07230617444193

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.278594686131383

> <JCHEM_PKA_STRONGEST_BASIC>
-2.630420748619806

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
118.6939

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.23e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
garcinone D

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0033332
     RDKit          3D
Garcinone D
 59 61  0  0  0  0  0  0  0  0999 V2000
   -4.7055   -2.4862   -2.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8850   -2.8255   -1.3092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5720   -2.6211   -1.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6918   -3.5047   -1.6426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2293   -4.4818   -2.5235 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3668   -3.4194   -1.4065 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1173   -2.4618   -0.5453 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4281   -2.4051   -0.3216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9891   -1.5453    0.4863 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3599   -1.5138    0.6970 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9714   -0.6318    1.5326 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3655   -0.6267    1.7244 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1711    0.2930    2.2144 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8478    1.2114    3.1413 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6210    2.3125    2.5653 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8192    2.7347    1.3598 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690    2.1730    0.1198 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7231    3.9416    1.1683 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7893    0.2743    2.0121 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9679    1.1596    2.6562 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1988   -0.6390    1.1523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1874   -0.6787    0.9295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8386    0.1457    1.5534 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7521   -1.5820    0.0780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1453   -1.6214   -0.1360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9858   -0.6162    0.4859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2401    0.7028   -0.0500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8522    1.0250   -1.3580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1439    0.5622   -2.5817 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3207    0.6507   -1.3298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9091    2.4719   -1.3997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6867   -2.0030   -2.0565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2515   -1.9500   -3.2013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9975   -3.4971   -2.8382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5847   -5.1283   -2.9844 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3159   -4.0970   -1.8893 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9679   -2.2521    0.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7447    0.0539    2.3610 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4812    0.6231    3.8894 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0744    1.6801    3.8276 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1535    2.8940    3.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1886    2.9672   -0.6881 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2513    1.8236    0.2462 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8840    1.3596   -0.3206 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3596    3.7293    0.2856 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0474    4.8072    0.9760 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3104    4.1240    2.0816 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1664    1.8855    3.2928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9244   -0.6408    1.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0431   -1.1383    0.4408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9304    1.3077    0.6810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2655    1.3289   -0.0515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8257    0.3533   -3.4304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5196    1.4458   -2.9551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4427   -0.2299   -2.3925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9521    1.5056   -0.9760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4459   -0.1443   -0.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6845    0.3663   -2.3427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2039    2.8279   -1.9653 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  2  3
 16 17  1  0
 16 18  1  0
 13 19  1  0
 19 20  1  0
 19 21  2  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 28 30  1  0
 28 31  1  0
 25  3  1  0
 24  7  1  0
 21  9  1  0
  1 32  1  0
  1 33  1  0
  1 34  1  0
  5 35  1  0
  6 36  1  0
 10 37  1  0
 12 38  1  0
 14 39  1  0
 14 40  1  0
 15 41  1  0
 17 42  1  0
 17 43  1  0
 17 44  1  0
 18 45  1  0
 18 46  1  0
 18 47  1  0
 20 48  1  0
 26 49  1  0
 26 50  1  0
 27 51  1  0
 27 52  1  0
 29 53  1  0
 29 54  1  0
 29 55  1  0
 30 56  1  0
 30 57  1  0
 30 58  1  0
 31 59  1  0
M  END

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0    8614.2898609.783   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8615.6178609.013   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8615.6178607.473   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8614.2738606.726   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8616.3918606.141   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8617.1578607.473   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8611.6178609.783   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0    8608.9498609.783   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8606.2788614.403   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0    8606.2788611.323   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8604.9448612.094   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8603.6118611.323   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8602.2778612.094   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8603.6118609.783   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0    8616.9538611.323   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0    8618.2858612.094   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0    8616.9538614.403   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0    8615.6158612.096   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8614.2858611.329   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8614.2858614.399   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8615.6158613.632   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8608.9478611.329   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8607.6178612.096   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8607.6178613.632   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8608.9468614.399   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0    8611.6168611.328   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0    8610.2868612.096   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0    8610.2868613.631   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0    8611.6168614.399   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0    8612.9468613.631   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0    8612.9468612.096   0.000  0.00  0.00           C+0
CONECT    1    2   19                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3                                                            
CONECT    7   26                                                            
CONECT    8   22                                                            
CONECT    9   24                                                            
CONECT   10   11   23                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   16   18                                                       
CONECT   16   15                                                            
CONECT   17   21                                                            
CONECT   18   19   21   15                                                  
CONECT   19   18    1   31                                                  
CONECT   20   21   30                                                       
CONECT   21   20   18   17                                                  
CONECT   22   23    8   27                                                  
CONECT   23   22   24   10                                                  
CONECT   24   23   25    9                                                  
CONECT   25   24   28                                                       
CONECT   26   27   31    7                                                  
CONECT   27   26   28   22                                                  
CONECT   28   27   29   25                                                  
CONECT   29   28   30                                                       
CONECT   30   31   29   20                                                  
CONECT   31   26   30   19                                                  
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

COMPND    HMDB0033332
HETATM    1  C1  UNL     1      -4.705  -2.486  -2.345  1.00  0.00           C  
HETATM    2  O1  UNL     1      -3.885  -2.825  -1.309  1.00  0.00           O  
HETATM    3  C2  UNL     1      -2.572  -2.621  -1.015  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.692  -3.505  -1.643  1.00  0.00           C  
HETATM    5  O2  UNL     1      -2.229  -4.482  -2.524  1.00  0.00           O  
HETATM    6  C4  UNL     1      -0.367  -3.419  -1.406  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.117  -2.462  -0.545  1.00  0.00           C  
HETATM    8  O3  UNL     1       1.428  -2.405  -0.322  1.00  0.00           O  
HETATM    9  C6  UNL     1       1.989  -1.545   0.486  1.00  0.00           C  
HETATM   10  C7  UNL     1       3.360  -1.514   0.697  1.00  0.00           C  
HETATM   11  C8  UNL     1       3.971  -0.632   1.533  1.00  0.00           C  
HETATM   12  O4  UNL     1       5.366  -0.627   1.724  1.00  0.00           O  
HETATM   13  C9  UNL     1       3.171   0.293   2.214  1.00  0.00           C  
HETATM   14  C10 UNL     1       3.848   1.211   3.141  1.00  0.00           C  
HETATM   15  C11 UNL     1       4.621   2.313   2.565  1.00  0.00           C  
HETATM   16  C12 UNL     1       4.819   2.735   1.360  1.00  0.00           C  
HETATM   17  C13 UNL     1       4.269   2.173   0.120  1.00  0.00           C  
HETATM   18  C14 UNL     1       5.723   3.942   1.168  1.00  0.00           C  
HETATM   19  C15 UNL     1       1.789   0.274   2.012  1.00  0.00           C  
HETATM   20  O5  UNL     1       0.968   1.160   2.656  1.00  0.00           O  
HETATM   21  C16 UNL     1       1.199  -0.639   1.152  1.00  0.00           C  
HETATM   22  C17 UNL     1      -0.187  -0.679   0.929  1.00  0.00           C  
HETATM   23  O6  UNL     1      -0.839   0.146   1.553  1.00  0.00           O  
HETATM   24  C18 UNL     1      -0.752  -1.582   0.078  1.00  0.00           C  
HETATM   25  C19 UNL     1      -2.145  -1.621  -0.136  1.00  0.00           C  
HETATM   26  C20 UNL     1      -2.986  -0.616   0.486  1.00  0.00           C  
HETATM   27  C21 UNL     1      -3.240   0.703  -0.050  1.00  0.00           C  
HETATM   28  C22 UNL     1      -3.852   1.025  -1.358  1.00  0.00           C  
HETATM   29  C23 UNL     1      -3.144   0.562  -2.582  1.00  0.00           C  
HETATM   30  C24 UNL     1      -5.321   0.651  -1.330  1.00  0.00           C  
HETATM   31  O7  UNL     1      -3.909   2.472  -1.400  1.00  0.00           O  
HETATM   32  H1  UNL     1      -5.687  -2.003  -2.057  1.00  0.00           H  
HETATM   33  H2  UNL     1      -4.251  -1.950  -3.201  1.00  0.00           H  
HETATM   34  H3  UNL     1      -4.998  -3.497  -2.838  1.00  0.00           H  
HETATM   35  H4  UNL     1      -1.585  -5.128  -2.984  1.00  0.00           H  
HETATM   36  H5  UNL     1       0.316  -4.097  -1.889  1.00  0.00           H  
HETATM   37  H6  UNL     1       3.968  -2.252   0.149  1.00  0.00           H  
HETATM   38  H7  UNL     1       5.745   0.054   2.361  1.00  0.00           H  
HETATM   39  H8  UNL     1       4.481   0.623   3.889  1.00  0.00           H  
HETATM   40  H9  UNL     1       3.074   1.680   3.828  1.00  0.00           H  
HETATM   41  H10 UNL     1       5.153   2.894   3.402  1.00  0.00           H  
HETATM   42  H11 UNL     1       4.189   2.967  -0.688  1.00  0.00           H  
HETATM   43  H12 UNL     1       3.251   1.824   0.246  1.00  0.00           H  
HETATM   44  H13 UNL     1       4.884   1.360  -0.321  1.00  0.00           H  
HETATM   45  H14 UNL     1       6.360   3.729   0.286  1.00  0.00           H  
HETATM   46  H15 UNL     1       5.047   4.807   0.976  1.00  0.00           H  
HETATM   47  H16 UNL     1       6.310   4.124   2.082  1.00  0.00           H  
HETATM   48  H17 UNL     1       1.166   1.885   3.293  1.00  0.00           H  
HETATM   49  H18 UNL     1      -2.924  -0.641   1.625  1.00  0.00           H  
HETATM   50  H19 UNL     1      -4.043  -1.138   0.441  1.00  0.00           H  
HETATM   51  H20 UNL     1      -3.930   1.308   0.681  1.00  0.00           H  
HETATM   52  H21 UNL     1      -2.266   1.329  -0.052  1.00  0.00           H  
HETATM   53  H22 UNL     1      -3.826   0.353  -3.430  1.00  0.00           H  
HETATM   54  H23 UNL     1      -2.520   1.446  -2.955  1.00  0.00           H  
HETATM   55  H24 UNL     1      -2.443  -0.230  -2.393  1.00  0.00           H  
HETATM   56  H25 UNL     1      -5.952   1.506  -0.976  1.00  0.00           H  
HETATM   57  H26 UNL     1      -5.446  -0.144  -0.578  1.00  0.00           H  
HETATM   58  H27 UNL     1      -5.685   0.366  -2.343  1.00  0.00           H  
HETATM   59  H28 UNL     1      -3.204   2.828  -1.965  1.00  0.00           H  
CONECT    1    2   32   33   34
CONECT    2    3
CONECT    3    4    4   25
CONECT    4    5    6
CONECT    5   35
CONECT    6    7    7   36
CONECT    7    8   24
CONECT    8    9
CONECT    9   10   10   21
CONECT   10   11   37
CONECT   11   12   13   13
CONECT   12   38
CONECT   13   14   19
CONECT   14   15   39   40
CONECT   15   16   16   41
CONECT   16   17   18
CONECT   17   42   43   44
CONECT   18   45   46   47
CONECT   19   20   21   21
CONECT   20   48
CONECT   21   22
CONECT   22   23   23   24
CONECT   24   25   25
CONECT   25   26
CONECT   26   27   49   50
CONECT   27   28   51   52
CONECT   28   29   30   31
CONECT   29   53   54   55
CONECT   30   56   57   58
CONECT   31   59
END

HMDB0033332
     RDKit          3D
Garcinone D
 59 61  0  0  0  0  0  0  0  0999 V2000
   -4.7055   -2.4862   -2.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8850   -2.8255   -1.3092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5720   -2.6211   -1.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6918   -3.5047   -1.6426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2293   -4.4818   -2.5235 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3668   -3.4194   -1.4065 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1173   -2.4618   -0.5453 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4281   -2.4051   -0.3216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9891   -1.5453    0.4863 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3599   -1.5138    0.6970 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9714   -0.6318    1.5326 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3655   -0.6267    1.7244 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1711    0.2930    2.2144 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8478    1.2114    3.1413 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6210    2.3125    2.5653 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8192    2.7347    1.3598 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690    2.1730    0.1198 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7231    3.9416    1.1683 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7893    0.2743    2.0121 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9679    1.1596    2.6562 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1988   -0.6390    1.1523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1874   -0.6787    0.9295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8386    0.1457    1.5534 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7521   -1.5820    0.0780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1453   -1.6214   -0.1360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9858   -0.6162    0.4859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2401    0.7028   -0.0500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8522    1.0250   -1.3580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1439    0.5622   -2.5817 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3207    0.6507   -1.3298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9091    2.4719   -1.3997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6867   -2.0030   -2.0565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2515   -1.9500   -3.2013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9975   -3.4971   -2.8382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5847   -5.1283   -2.9844 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3159   -4.0970   -1.8893 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9679   -2.2521    0.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7447    0.0539    2.3610 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4812    0.6231    3.8894 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0744    1.6801    3.8276 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1535    2.8940    3.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1886    2.9672   -0.6881 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2513    1.8236    0.2462 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8840    1.3596   -0.3206 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3596    3.7293    0.2856 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0474    4.8072    0.9760 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3104    4.1240    2.0816 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1664    1.8855    3.2928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9244   -0.6408    1.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0431   -1.1383    0.4408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9304    1.3077    0.6810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2655    1.3289   -0.0515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8257    0.3533   -3.4304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5196    1.4458   -2.9551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4427   -0.2299   -2.3925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9521    1.5056   -0.9760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4459   -0.1443   -0.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6845    0.3663   -2.3427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2039    2.8279   -1.9653 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  2  3
 16 17  1  0
 16 18  1  0
 13 19  1  0
 19 20  1  0
 19 21  2  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 28 30  1  0
 28 31  1  0
 25  3  1  0
 24  7  1  0
 21  9  1  0
  1 32  1  0
  1 33  1  0
  1 34  1  0
  5 35  1  0
  6 36  1  0
 10 37  1  0
 12 38  1  0
 14 39  1  0
 14 40  1  0
 15 41  1  0
 17 42  1  0
 17 43  1  0
 17 44  1  0
 18 45  1  0
 18 46  1  0
 18 47  1  0
 20 48  1  0
 26 49  1  0
 26 50  1  0
 27 51  1  0
 27 52  1  0
 29 53  1  0
 29 54  1  0
 29 55  1  0
 30 56  1  0
 30 57  1  0
 30 58  1  0
 31 59  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Garcinone D	MeSH

Chemical Formula

C₂₄H₂₈O₇

Average Molecular Weight

428.4749

Monoisotopic Molecular Weight

428.18350325

IUPAC Name

1,3,6-trihydroxy-8-(3-hydroxy-3-methylbutyl)-7-methoxy-2-(3-methylbut-2-en-1-yl)-9H-xanthen-9-one

Traditional Name

garcinone D

CAS Registry Number

107390-08-9

SMILES

COC1=C(O)C=C2OC3=C(C(O)=C(CC=C(C)C)C(O)=C3)C(=O)C2=C1CCC(C)(C)O

InChI Identifier

InChI=1S/C24H28O7/c1-12(2)6-7-13-15(25)10-18-20(21(13)27)22(28)19-14(8-9-24(3,4)29)23(30-5)16(26)11-17(19)31-18/h6,10-11,25-27,29H,7-9H2,1-5H3

InChI Key

TYALNCRUIKOKGP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 8-prenylated xanthones. These are organic compounds containing a C5-isoprenoid group linked to a xanthone moiety at the 8-position. Xanthone is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring that carries a ketone group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

8-prenylated xanthones

Alternative Parents

Substituents

2-prenylated xanthone
8-prenylated xanthone
Chromone
Anisole
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Tertiary alcohol
Vinylogous acid
Polyol
Ether
Oxacycle
Alcohol
Organooxygen compound
Hydrocarbon derivative
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: HMDB0033332)
Cell membrane (HMDB: HMDB0033332)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033332)

Source

Exogenous

Exogenous (HMDB: HMDB0033332)

Food

Food (HMDB: HMDB0033332)

Fruit

Tropical fruit

Purple mangosteen (FooDB: FOOD00406)

Fruits (FooDB: FOOD00871)

Endogenous

Plant

Plant (HMDB: HMDB0033332)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0033332)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	202 - 204 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.0082 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0082 g/L	ALOGPS
logP	3.77	ALOGPS
logP	4.93	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	7.28	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	118.69 m³·mol⁻¹	ChemAxon
Polarizability	46.87 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	207.431	30932474
DeepCCS	[M-H]-	205.073	30932474
DeepCCS	[M-2H]-	238.226	30932474
DeepCCS	[M+Na]+	213.564	30932474
AllCCS	[M+H]+	203.3	32859911
AllCCS	[M+H-H2O]+	200.8	32859911
AllCCS	[M+NH4]+	205.6	32859911
AllCCS	[M+Na]+	206.2	32859911
AllCCS	[M-H]-	207.0	32859911
AllCCS	[M+Na-2H]-	207.5	32859911
AllCCS	[M+HCOO]-	208.2	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	7.86 minutes	32390414
Predicted by Siyang on May 30, 2022	15.7093 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.6 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	3204.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	283.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	208.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	156.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	186.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	834.3 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	940.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	80.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1322.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	629.9 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	1722.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	491.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	480.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	252.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	256.7 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	8.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Garcinone D	COC1=C(O)C=C2OC3=C(C(O)=C(CC=C(C)C)C(O)=C3)C(=O)C2=C1CCC(C)(C)O	5296.9	Standard polar	33892256
Garcinone D	COC1=C(O)C=C2OC3=C(C(O)=C(CC=C(C)C)C(O)=C3)C(=O)C2=C1CCC(C)(C)O	3456.8	Standard non polar	33892256
Garcinone D	COC1=C(O)C=C2OC3=C(C(O)=C(CC=C(C)C)C(O)=C3)C(=O)C2=C1CCC(C)(C)O	3741.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Garcinone D,1TMS,isomer #1	COC1=C(O[Si](C)(C)C)C=C2OC3=CC(O)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O	3435.7	Semi standard non polar	33892256
Garcinone D,1TMS,isomer #2	COC1=C(O)C=C2OC3=CC(O)=C(CC=C(C)C)C(O[Si](C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O	3380.2	Semi standard non polar	33892256
Garcinone D,1TMS,isomer #3	COC1=C(O)C=C2OC3=CC(O[Si](C)(C)C)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O	3416.2	Semi standard non polar	33892256
Garcinone D,1TMS,isomer #4	COC1=C(O)C=C2OC3=CC(O)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C	3543.1	Semi standard non polar	33892256
Garcinone D,2TMS,isomer #1	COC1=C(O[Si](C)(C)C)C=C2OC3=CC(O[Si](C)(C)C)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O	3359.4	Semi standard non polar	33892256
Garcinone D,2TMS,isomer #2	COC1=C(O[Si](C)(C)C)C=C2OC3=CC(O)=C(CC=C(C)C)C(O[Si](C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O	3320.1	Semi standard non polar	33892256
Garcinone D,2TMS,isomer #3	COC1=C(O[Si](C)(C)C)C=C2OC3=CC(O)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C	3476.4	Semi standard non polar	33892256
Garcinone D,2TMS,isomer #4	COC1=C(O)C=C2OC3=CC(O[Si](C)(C)C)=C(CC=C(C)C)C(O[Si](C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O	3355.7	Semi standard non polar	33892256
Garcinone D,2TMS,isomer #5	COC1=C(O)C=C2OC3=CC(O)=C(CC=C(C)C)C(O[Si](C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C	3417.0	Semi standard non polar	33892256
Garcinone D,2TMS,isomer #6	COC1=C(O)C=C2OC3=CC(O[Si](C)(C)C)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C	3462.9	Semi standard non polar	33892256
Garcinone D,3TMS,isomer #1	COC1=C(O[Si](C)(C)C)C=C2OC3=CC(O[Si](C)(C)C)=C(CC=C(C)C)C(O[Si](C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O	3327.4	Semi standard non polar	33892256
Garcinone D,3TMS,isomer #2	COC1=C(O[Si](C)(C)C)C=C2OC3=CC(O[Si](C)(C)C)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C	3425.6	Semi standard non polar	33892256
Garcinone D,3TMS,isomer #3	COC1=C(O[Si](C)(C)C)C=C2OC3=CC(O)=C(CC=C(C)C)C(O[Si](C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C	3387.9	Semi standard non polar	33892256
Garcinone D,3TMS,isomer #4	COC1=C(O)C=C2OC3=CC(O[Si](C)(C)C)=C(CC=C(C)C)C(O[Si](C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C	3440.3	Semi standard non polar	33892256
Garcinone D,4TMS,isomer #1	COC1=C(O[Si](C)(C)C)C=C2OC3=CC(O[Si](C)(C)C)=C(CC=C(C)C)C(O[Si](C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C	3449.6	Semi standard non polar	33892256
Garcinone D,1TBDMS,isomer #1	COC1=C(O[Si](C)(C)C(C)(C)C)C=C2OC3=CC(O)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O	3660.1	Semi standard non polar	33892256
Garcinone D,1TBDMS,isomer #2	COC1=C(O)C=C2OC3=CC(O)=C(CC=C(C)C)C(O[Si](C)(C)C(C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O	3602.5	Semi standard non polar	33892256
Garcinone D,1TBDMS,isomer #3	COC1=C(O)C=C2OC3=CC(O[Si](C)(C)C(C)(C)C)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O	3637.4	Semi standard non polar	33892256
Garcinone D,1TBDMS,isomer #4	COC1=C(O)C=C2OC3=CC(O)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C(C)(C)C	3773.6	Semi standard non polar	33892256
Garcinone D,2TBDMS,isomer #1	COC1=C(O[Si](C)(C)C(C)(C)C)C=C2OC3=CC(O[Si](C)(C)C(C)(C)C)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O	3808.4	Semi standard non polar	33892256
Garcinone D,2TBDMS,isomer #2	COC1=C(O[Si](C)(C)C(C)(C)C)C=C2OC3=CC(O)=C(CC=C(C)C)C(O[Si](C)(C)C(C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O	3755.2	Semi standard non polar	33892256
Garcinone D,2TBDMS,isomer #3	COC1=C(O[Si](C)(C)C(C)(C)C)C=C2OC3=CC(O)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C(C)(C)C	3943.5	Semi standard non polar	33892256
Garcinone D,2TBDMS,isomer #4	COC1=C(O)C=C2OC3=CC(O[Si](C)(C)C(C)(C)C)=C(CC=C(C)C)C(O[Si](C)(C)C(C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O	3769.0	Semi standard non polar	33892256
Garcinone D,2TBDMS,isomer #5	COC1=C(O)C=C2OC3=CC(O)=C(CC=C(C)C)C(O[Si](C)(C)C(C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C(C)(C)C	3870.7	Semi standard non polar	33892256
Garcinone D,2TBDMS,isomer #6	COC1=C(O)C=C2OC3=CC(O[Si](C)(C)C(C)(C)C)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C(C)(C)C	3920.1	Semi standard non polar	33892256
Garcinone D,3TBDMS,isomer #1	COC1=C(O[Si](C)(C)C(C)(C)C)C=C2OC3=CC(O[Si](C)(C)C(C)(C)C)=C(CC=C(C)C)C(O[Si](C)(C)C(C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O	3923.0	Semi standard non polar	33892256
Garcinone D,3TBDMS,isomer #2	COC1=C(O[Si](C)(C)C(C)(C)C)C=C2OC3=CC(O[Si](C)(C)C(C)(C)C)=C(CC=C(C)C)C(O)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C(C)(C)C	4092.8	Semi standard non polar	33892256
Garcinone D,3TBDMS,isomer #3	COC1=C(O[Si](C)(C)C(C)(C)C)C=C2OC3=CC(O)=C(CC=C(C)C)C(O[Si](C)(C)C(C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C(C)(C)C	4016.7	Semi standard non polar	33892256
Garcinone D,3TBDMS,isomer #4	COC1=C(O)C=C2OC3=CC(O[Si](C)(C)C(C)(C)C)=C(CC=C(C)C)C(O[Si](C)(C)C(C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C(C)(C)C	4067.8	Semi standard non polar	33892256
Garcinone D,4TBDMS,isomer #1	COC1=C(O[Si](C)(C)C(C)(C)C)C=C2OC3=CC(O[Si](C)(C)C(C)(C)C)=C(CC=C(C)C)C(O[Si](C)(C)C(C)(C)C)=C3C(=O)C2=C1CCC(C)(C)O[Si](C)(C)C(C)(C)C	4216.7	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 - Garcinone D GC-MS (Non-derivatized) - 70eV, Positive	splash10-0bt9-9116700000-0a1e38dddb4e84786b90	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Garcinone D GC-MS (3 TMS) - 70eV, Positive	splash10-05e9-4000039000-c84eee9da2d54152b52a	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Garcinone D 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 - Garcinone D 10V, Positive-QTOF	splash10-03di-0005900000-710f50d70e9073781363	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 20V, Positive-QTOF	splash10-0cdi-2009300000-9dfa6f8a922faada1eff	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 40V, Positive-QTOF	splash10-06dl-3119000000-7f35cf9953b55d6c5e61	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 10V, Negative-QTOF	splash10-004i-0001900000-737e6f11b27509029ab5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 20V, Negative-QTOF	splash10-056r-0004900000-803dbe575d48b122b76b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 40V, Negative-QTOF	splash10-002f-3937100000-9ab33927327a1a799186	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 10V, Positive-QTOF	splash10-0bt9-0019500000-4b1681c98cc9e8d51a77	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 20V, Positive-QTOF	splash10-0ab9-0019000000-25ec3849710884bed669	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 40V, Positive-QTOF	splash10-000i-0095000000-95500c23f11e955ec708	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 10V, Negative-QTOF	splash10-004i-0000900000-3f017d04e9063a16e11f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 20V, Negative-QTOF	splash10-004i-0004900000-0bdce2b37deb90ed359f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Garcinone D 40V, Negative-QTOF	splash10-004i-1029800000-5b6a3fa10a74994d4b8d	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB011359

KNApSAcK ID

C00030358

Chemspider ID

4593094

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5495926

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1834881

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Garcinone D (HMDB0033332)

MOL for HMDB0033332 (Garcinone D)

3D MOL for HMDB0033332 (Garcinone D)

3D SDF for HMDB0033332 (Garcinone D)

3D-SDF for HMDB0033332 (Garcinone D)

PDB for HMDB0033332 (Garcinone D)

3D PDB for HMDB0033332 (Garcinone D)

SMILES for HMDB0033332 (Garcinone D)

INCHI for HMDB0033332 (Garcinone D)

Structure for HMDB0033332 (Garcinone D)

3D Structure for HMDB0033332 (Garcinone D)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra