Hmdb loader

Showing metabocard for Goshonoside F3 (HMDB0038376)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 23:41:09 UTC
Update Date2022-03-07 02:55:44 UTC
HMDB IDHMDB0038376
Secondary Accession Numbers
  • HMDB38376
Metabolite Identification
Common NameGoshonoside F3
DescriptionGoshonoside F3 belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. Based on a literature review a small amount of articles have been published on Goshonoside F3.
Structure
Data?1563863187
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0038376 (Goshonoside F3)

  Mrv0541 05061310242D          

 45 48  0  0  0  0            999 V2000
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M  END
Download

3D MOL for HMDB0038376 (Goshonoside F3)

HMDB0038376
     RDKit          3D
Goshonoside F3
 97100  0  0  0  0  0  0  0  0999 V2000
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M  END
Download

3D SDF for HMDB0038376 (Goshonoside F3)

  Mrv0541 05061310242D          

 45 48  0  0  0  0            999 V2000
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6737    1.8695    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
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   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
    3.5724    1.2375    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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3990    5.4592    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
    4.2868    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
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1168    4.6840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    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
    0.3044    4.5407    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
    0.0222    3.7654    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
    0.5525    3.1335    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
    1.3650    3.2767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6131    1.8695    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
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8687    6.0912    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7903    3.6222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2703    2.3582    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8006    1.7262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 O   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
    1.6471    4.0520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8953    2.6447    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 11  5  1  0  0  0  0
 12  5  1  0  0  0  0
 13 10  1  0  0  0  0
 16  1  1  0  0  0  0
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 17  2  2  0  0  0  0
 17  7  1  0  0  0  0
 18  8  1  0  0  0  0
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 20 15  1  0  0  0  0
 21  9  1  0  0  0  0
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 23 20  1  0  0  0  0
 24 22  1  0  0  0  0
 25 23  1  0  0  0  0
 26 24  1  0  0  0  0
 27 25  1  0  0  0  0
 28 26  1  0  0  0  0
 29 27  1  0  0  0  0
 31  3  1  0  0  0  0
 31 11  1  0  0  0  0
 31 18  1  0  0  0  0
 31 21  1  0  0  0  0
 32  4  1  0  0  0  0
 32 12  1  0  0  0  0
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 35 22  1  0  0  0  0
 36 23  1  0  0  0  0
 37 24  1  0  0  0  0
 38 25  1  0  0  0  0
 39 26  1  0  0  0  0
 40 27  1  0  0  0  0
 41 30  2  0  0  0  0
 42 13  1  0  0  0  0
 42 28  1  0  0  0  0
 43 19  1  0  0  0  0
 43 28  1  0  0  0  0
 44 20  1  0  0  0  0
 44 29  1  0  0  0  0
 45 29  1  0  0  0  0
 45 30  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0038376

> <DATABASE_NAME>
hmdb

> <SMILES>
C\C(CCC1C(=C)CCC2C1(C)CCCC2(C)C(=O)OC1OC(CO)C(O)C(O)C1O)=C\COC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C32H52O13/c1-16(10-13-42-28-26(39)24(37)22(35)19(14-33)43-28)6-8-18-17(2)7-9-21-31(18,3)11-5-12-32(21,4)30(41)45-29-27(40)25(38)23(36)20(15-34)44-29/h10,18-29,33-40H,2,5-9,11-15H2,1,3-4H3/b16-10-

> <INCHI_KEY>
DQBCTTXPKJBNHF-YBEGLDIGSA-N

> <FORMULA>
C32H52O13

> <MOLECULAR_WEIGHT>
644.7475

> <EXACT_MASS>
644.34079175

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
68.96055615349668

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 1,4a-dimethyl-5-[(3Z)-3-methyl-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}pent-3-en-1-yl]-6-methylidene-decahydronaphthalene-1-carboxylate

> <ALOGPS_LOGP>
0.29

> <JCHEM_LOGP>
0.3120993063333334

> <ALOGPS_LOGS>
-3.11

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.424216907144888

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.902243706577739

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810835511357308

> <JCHEM_POLAR_SURFACE_AREA>
215.82999999999996

> <JCHEM_REFRACTIVITY>
158.61550000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.01e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 1,4a-dimethyl-5-[(3Z)-3-methyl-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}pent-3-en-1-yl]-6-methylidene-hexahydro-2H-naphthalene-1-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0038376 (Goshonoside F3)

HMDB0038376
     RDKit          3D
Goshonoside F3
 97100  0  0  0  0  0  0  0  0999 V2000
   -0.1040   -1.5621   -2.7129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3676   -0.7944   -1.6912 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3518   -1.2167   -0.6231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4916   -0.2379   -0.8042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1242    1.1979   -0.7653 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3322    2.0242   -1.0634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3844    3.2197   -0.0888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5663    1.2526   -0.7958 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2998    0.9121   -1.7579 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0055    0.8554    0.4614 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2215    0.1054    0.6116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9372   -1.1277    1.1434 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0655   -1.8820    1.3384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9066   -3.2977    0.8158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0677   -4.0312    1.0290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3076   -1.2738    0.7445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4071   -2.0556    1.1374 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5381    0.1124    1.3271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3828    0.8429    0.5153 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1997    0.7961    1.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7786    0.5597    2.8432 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4138    2.5418   -2.4710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5483    1.8153   -3.4423 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1336    1.8928   -2.9934 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9062    1.6098   -1.5372 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3542    2.8798   -0.9291 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2069    0.5705   -1.4427 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8783    0.5782   -0.1328 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0340   -0.3447    0.0983 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2406   -0.1206   -0.6915 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3201   -0.2234   -2.1813 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3966    0.1911   -0.0649 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5767    0.3367    1.3868 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5204   -0.5881    1.8223 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7754   -0.4352    1.2740 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1327   -1.5056    0.4632 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4632   -1.6089    0.1721 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9470   -0.4610   -0.7239 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3074   -0.6129   -0.9923 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3361   -1.7385    1.3961 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8595   -3.0021    1.4650 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5846   -1.3316    2.6497 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7132   -2.3685    2.9670 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7481   -0.1064    2.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0312    0.1594    3.5310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6302   -2.5288   -2.7582 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5631   -1.3388   -3.5113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7549   -2.2305   -0.8691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9343   -1.1787    0.3901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1675   -0.4312    0.0795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0215   -0.5558   -1.7257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8646    1.4071    0.3197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2174    4.1824   -0.6434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4052    3.3406    0.3398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7199    3.0799    0.7691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6803   -0.0680   -0.4068 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2373   -1.9711    2.4348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6606   -3.3341   -0.2609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0987   -3.8386    1.3803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3843   -3.9942    1.9508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3197   -1.2741   -0.3599 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2298   -1.7136    0.6628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0401   -0.0357    2.3048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1083    1.8012    0.4874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2485    1.8807    1.3072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9172    1.3381    3.4304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4484    2.5559   -2.8745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0841    3.6097   -2.4619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8986    0.7948   -3.6975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6108    2.3799   -4.4133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5565    1.1701   -3.6485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7291    2.8882   -3.3083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9640    3.7339   -1.2926 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6784    3.0962   -1.2957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4154    2.8975    0.1738 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9407    0.7454   -2.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1712    0.3944    0.7363 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2766    1.6029    0.1464 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2143   -0.4984    1.1871 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7047   -1.4194   -0.2088 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2496    0.7862   -2.6484 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3737   -0.5736   -2.4358 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6771   -0.9846   -2.6073 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2686    0.3488   -0.7278 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0578    1.3717    1.5309 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6897    0.3803    2.0039 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7577    0.4565    0.5766 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6002   -2.5233   -0.4374 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8353    0.5219   -0.2208 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4195   -0.5154   -1.6880 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4355   -1.3582   -1.6426 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1730   -1.0189    1.2829 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3907   -3.5971    2.0993 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2617   -1.1691    3.5022 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0774   -2.9457    3.6938 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3809    0.7780    2.1199 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2738    1.0275    3.9241 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
  6 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 25 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 30 32  2  0
 32 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  1  0
 37 38  1  0
 38 39  1  0
 37 40  1  0
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 44 45  1  0
 27  2  1  0
 44 35  1  0
 25  5  1  0
 20 11  1  0
  1 46  1  0
  1 47  1  0
  3 48  1  0
  3 49  1  0
  4 50  1  0
  4 51  1  0
  5 52  1  0
  7 53  1  0
  7 54  1  0
  7 55  1  0
 11 56  1  0
 13 57  1  0
 14 58  1  0
 14 59  1  0
 15 60  1  0
 16 61  1  0
 17 62  1  0
 18 63  1  0
 19 64  1  0
 20 65  1  0
 21 66  1  0
 22 67  1  0
 22 68  1  0
 23 69  1  0
 23 70  1  0
 24 71  1  0
 24 72  1  0
 26 73  1  0
 26 74  1  0
 26 75  1  0
 27 76  1  0
 28 77  1  0
 28 78  1  0
 29 79  1  0
 29 80  1  0
 31 81  1  0
 31 82  1  0
 31 83  1  0
 32 84  1  0
 33 85  1  0
 33 86  1  0
 35 87  1  0
 37 88  1  0
 38 89  1  0
 38 90  1  0
 39 91  1  0
 40 92  1  0
 41 93  1  0
 42 94  1  0
 43 95  1  0
 44 96  1  0
 45 97  1  0
M  END
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PDB for HMDB0038376 (Goshonoside F3)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335  -1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.991   3.490   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.611  10.191   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.085   8.743   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.568   8.476   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.041   7.029   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.031   5.849   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.548   6.117   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.011   3.490   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       1.622  11.370   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -0.422   9.656   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -1.475   6.761   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       0.505   4.402   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       1.494   3.222   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0       3.075   7.564   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0       3.538   4.937   0.000  0.00  0.00           O+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3   31                                                            
CONECT    4   32                                                            
CONECT    5   11   12                                                       
CONECT    6    8   16                                                       
CONECT    7    9   17                                                       
CONECT    8    6   18                                                       
CONECT    9    7   21                                                       
CONECT   10   13   16                                                       
CONECT   11    5   31                                                       
CONECT   12    5   32                                                       
CONECT   13   10   42                                                       
CONECT   14   19   33                                                       
CONECT   15   20   34                                                       
CONECT   16    1    6   10                                                  
CONECT   17    2    7   18                                                  
CONECT   18    8   17   31                                                  
CONECT   19   14   22   43                                                  
CONECT   20   15   23   44                                                  
CONECT   21    9   31   32                                                  
CONECT   22   19   24   35                                                  
CONECT   23   20   25   36                                                  
CONECT   24   22   26   37                                                  
CONECT   25   23   27   38                                                  
CONECT   26   24   28   39                                                  
CONECT   27   25   29   40                                                  
CONECT   28   26   42   43                                                  
CONECT   29   27   44   45                                                  
CONECT   30   32   41   45                                                  
CONECT   31    3   11   18   21                                             
CONECT   32    4   12   21   30                                             
CONECT   33   14                                                            
CONECT   34   15                                                            
CONECT   35   22                                                            
CONECT   36   23                                                            
CONECT   37   24                                                            
CONECT   38   25                                                            
CONECT   39   26                                                            
CONECT   40   27                                                            
CONECT   41   30                                                            
CONECT   42   13   28                                                       
CONECT   43   19   28                                                       
CONECT   44   20   29                                                       
CONECT   45   29   30                                                       
MASTER        0    0    0    0    0    0    0    0   45    0   96    0
END
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3D PDB for HMDB0038376 (Goshonoside F3)

COMPND    HMDB0038376
HETATM    1  C1  UNL     1      -0.104  -1.562  -2.713  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.368  -0.794  -1.691  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.352  -1.217  -0.623  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.492  -0.238  -0.804  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.124   1.198  -0.765  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.332   2.024  -1.063  1.00  0.00           C  
HETATM    7  C7  UNL     1      -3.384   3.220  -0.089  1.00  0.00           C  
HETATM    8  C8  UNL     1      -4.566   1.253  -0.796  1.00  0.00           C  
HETATM    9  O1  UNL     1      -5.300   0.912  -1.758  1.00  0.00           O  
HETATM   10  O2  UNL     1      -5.005   0.855   0.461  1.00  0.00           O  
HETATM   11  C9  UNL     1      -6.222   0.105   0.612  1.00  0.00           C  
HETATM   12  O3  UNL     1      -5.937  -1.128   1.143  1.00  0.00           O  
HETATM   13  C10 UNL     1      -7.065  -1.882   1.338  1.00  0.00           C  
HETATM   14  C11 UNL     1      -6.907  -3.298   0.816  1.00  0.00           C  
HETATM   15  O4  UNL     1      -8.068  -4.031   1.029  1.00  0.00           O  
HETATM   16  C12 UNL     1      -8.308  -1.274   0.745  1.00  0.00           C  
HETATM   17  O5  UNL     1      -9.407  -2.056   1.137  1.00  0.00           O  
HETATM   18  C13 UNL     1      -8.538   0.112   1.327  1.00  0.00           C  
HETATM   19  O6  UNL     1      -9.383   0.843   0.515  1.00  0.00           O  
HETATM   20  C14 UNL     1      -7.200   0.796   1.529  1.00  0.00           C  
HETATM   21  O7  UNL     1      -6.779   0.560   2.843  1.00  0.00           O  
HETATM   22  C15 UNL     1      -3.414   2.542  -2.471  1.00  0.00           C  
HETATM   23  C16 UNL     1      -2.548   1.815  -3.442  1.00  0.00           C  
HETATM   24  C17 UNL     1      -1.134   1.893  -2.993  1.00  0.00           C  
HETATM   25  C18 UNL     1      -0.906   1.610  -1.537  1.00  0.00           C  
HETATM   26  C19 UNL     1      -0.354   2.880  -0.929  1.00  0.00           C  
HETATM   27  C20 UNL     1       0.207   0.571  -1.443  1.00  0.00           C  
HETATM   28  C21 UNL     1       0.878   0.578  -0.133  1.00  0.00           C  
HETATM   29  C22 UNL     1       2.034  -0.345   0.098  1.00  0.00           C  
HETATM   30  C23 UNL     1       3.241  -0.121  -0.692  1.00  0.00           C  
HETATM   31  C24 UNL     1       3.320  -0.223  -2.181  1.00  0.00           C  
HETATM   32  C25 UNL     1       4.397   0.191  -0.065  1.00  0.00           C  
HETATM   33  C26 UNL     1       4.577   0.337   1.387  1.00  0.00           C  
HETATM   34  O8  UNL     1       5.520  -0.588   1.822  1.00  0.00           O  
HETATM   35  C27 UNL     1       6.775  -0.435   1.274  1.00  0.00           C  
HETATM   36  O9  UNL     1       7.133  -1.506   0.463  1.00  0.00           O  
HETATM   37  C28 UNL     1       8.463  -1.609   0.172  1.00  0.00           C  
HETATM   38  C29 UNL     1       8.947  -0.461  -0.724  1.00  0.00           C  
HETATM   39  O10 UNL     1      10.307  -0.613  -0.992  1.00  0.00           O  
HETATM   40  C30 UNL     1       9.336  -1.738   1.396  1.00  0.00           C  
HETATM   41  O11 UNL     1       9.859  -3.002   1.465  1.00  0.00           O  
HETATM   42  C31 UNL     1       8.585  -1.332   2.650  1.00  0.00           C  
HETATM   43  O12 UNL     1       7.713  -2.369   2.967  1.00  0.00           O  
HETATM   44  C32 UNL     1       7.748  -0.106   2.355  1.00  0.00           C  
HETATM   45  O13 UNL     1       7.031   0.159   3.531  1.00  0.00           O  
HETATM   46  H1  UNL     1      -0.630  -2.529  -2.758  1.00  0.00           H  
HETATM   47  H2  UNL     1       0.563  -1.339  -3.511  1.00  0.00           H  
HETATM   48  H3  UNL     1      -1.755  -2.230  -0.869  1.00  0.00           H  
HETATM   49  H4  UNL     1      -0.934  -1.179   0.390  1.00  0.00           H  
HETATM   50  H5  UNL     1      -3.167  -0.431   0.079  1.00  0.00           H  
HETATM   51  H6  UNL     1      -3.022  -0.556  -1.726  1.00  0.00           H  
HETATM   52  H7  UNL     1      -1.865   1.407   0.320  1.00  0.00           H  
HETATM   53  H8  UNL     1      -3.217   4.182  -0.643  1.00  0.00           H  
HETATM   54  H9  UNL     1      -4.405   3.341   0.340  1.00  0.00           H  
HETATM   55  H10 UNL     1      -2.720   3.080   0.769  1.00  0.00           H  
HETATM   56  H11 UNL     1      -6.680  -0.068  -0.407  1.00  0.00           H  
HETATM   57  H12 UNL     1      -7.237  -1.971   2.435  1.00  0.00           H  
HETATM   58  H13 UNL     1      -6.661  -3.334  -0.261  1.00  0.00           H  
HETATM   59  H14 UNL     1      -6.099  -3.839   1.380  1.00  0.00           H  
HETATM   60  H15 UNL     1      -8.384  -3.994   1.951  1.00  0.00           H  
HETATM   61  H16 UNL     1      -8.320  -1.274  -0.360  1.00  0.00           H  
HETATM   62  H17 UNL     1     -10.230  -1.714   0.663  1.00  0.00           H  
HETATM   63  H18 UNL     1      -9.040  -0.036   2.305  1.00  0.00           H  
HETATM   64  H19 UNL     1      -9.108   1.801   0.487  1.00  0.00           H  
HETATM   65  H20 UNL     1      -7.249   1.881   1.307  1.00  0.00           H  
HETATM   66  H21 UNL     1      -6.917   1.338   3.430  1.00  0.00           H  
HETATM   67  H22 UNL     1      -4.448   2.556  -2.875  1.00  0.00           H  
HETATM   68  H23 UNL     1      -3.084   3.610  -2.462  1.00  0.00           H  
HETATM   69  H24 UNL     1      -2.899   0.795  -3.697  1.00  0.00           H  
HETATM   70  H25 UNL     1      -2.611   2.380  -4.413  1.00  0.00           H  
HETATM   71  H26 UNL     1      -0.557   1.170  -3.648  1.00  0.00           H  
HETATM   72  H27 UNL     1      -0.729   2.888  -3.308  1.00  0.00           H  
HETATM   73  H28 UNL     1      -0.964   3.734  -1.293  1.00  0.00           H  
HETATM   74  H29 UNL     1       0.678   3.096  -1.296  1.00  0.00           H  
HETATM   75  H30 UNL     1      -0.415   2.897   0.174  1.00  0.00           H  
HETATM   76  H31 UNL     1       0.941   0.745  -2.243  1.00  0.00           H  
HETATM   77  H32 UNL     1       0.171   0.394   0.736  1.00  0.00           H  
HETATM   78  H33 UNL     1       1.277   1.603   0.146  1.00  0.00           H  
HETATM   79  H34 UNL     1       2.214  -0.498   1.187  1.00  0.00           H  
HETATM   80  H35 UNL     1       1.705  -1.419  -0.209  1.00  0.00           H  
HETATM   81  H36 UNL     1       3.250   0.786  -2.648  1.00  0.00           H  
HETATM   82  H37 UNL     1       4.374  -0.574  -2.436  1.00  0.00           H  
HETATM   83  H38 UNL     1       2.677  -0.985  -2.607  1.00  0.00           H  
HETATM   84  H39 UNL     1       5.269   0.349  -0.728  1.00  0.00           H  
HETATM   85  H40 UNL     1       5.058   1.372   1.531  1.00  0.00           H  
HETATM   86  H41 UNL     1       3.690   0.380   2.004  1.00  0.00           H  
HETATM   87  H42 UNL     1       6.758   0.456   0.577  1.00  0.00           H  
HETATM   88  H43 UNL     1       8.600  -2.523  -0.437  1.00  0.00           H  
HETATM   89  H44 UNL     1       8.835   0.522  -0.221  1.00  0.00           H  
HETATM   90  H45 UNL     1       8.420  -0.515  -1.688  1.00  0.00           H  
HETATM   91  H46 UNL     1      10.436  -1.358  -1.643  1.00  0.00           H  
HETATM   92  H47 UNL     1      10.173  -1.019   1.283  1.00  0.00           H  
HETATM   93  H48 UNL     1       9.391  -3.597   2.099  1.00  0.00           H  
HETATM   94  H49 UNL     1       9.262  -1.169   3.502  1.00  0.00           H  
HETATM   95  H50 UNL     1       8.077  -2.946   3.694  1.00  0.00           H  
HETATM   96  H51 UNL     1       8.381   0.778   2.120  1.00  0.00           H  
HETATM   97  H52 UNL     1       7.274   1.027   3.924  1.00  0.00           H  
CONECT    1    2    2   46   47
CONECT    2    3   27
CONECT    3    4   48   49
CONECT    4    5   50   51
CONECT    5    6   25   52
CONECT    6    7    8   22
CONECT    7   53   54   55
CONECT    8    9    9   10
CONECT   10   11
CONECT   11   12   20   56
CONECT   12   13
CONECT   13   14   16   57
CONECT   14   15   58   59
CONECT   15   60
CONECT   16   17   18   61
CONECT   17   62
CONECT   18   19   20   63
CONECT   19   64
CONECT   20   21   65
CONECT   21   66
CONECT   22   23   67   68
CONECT   23   24   69   70
CONECT   24   25   71   72
CONECT   25   26   27
CONECT   26   73   74   75
CONECT   27   28   76
CONECT   28   29   77   78
CONECT   29   30   79   80
CONECT   30   31   32   32
CONECT   31   81   82   83
CONECT   32   33   84
CONECT   33   34   85   86
CONECT   34   35
CONECT   35   36   44   87
CONECT   36   37
CONECT   37   38   40   88
CONECT   38   39   89   90
CONECT   39   91
CONECT   40   41   42   92
CONECT   41   93
CONECT   42   43   44   94
CONECT   43   95
CONECT   44   45   96
CONECT   45   97
END
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SMILES for HMDB0038376 (Goshonoside F3)

C\C(CCC1C(=C)CCC2C1(C)CCCC2(C)C(=O)OC1OC(CO)C(O)C(O)C1O)=C\COC1OC(CO)C(O)C(O)C1O
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INCHI for HMDB0038376 (Goshonoside F3)

InChI=1S/C32H52O13/c1-16(10-13-42-28-26(39)24(37)22(35)19(14-33)43-28)6-8-18-17(2)7-9-21-31(18,3)11-5-12-32(21,4)30(41)45-29-27(40)25(38)23(36)20(15-34)44-29/h10,18-29,33-40H,2,5-9,11-15H2,1,3-4H3/b16-10-
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3,4,5-Trihydroxy-6-(hydroxymethyl)oxan-2-yl 1,4a-dimethyl-5-[(3Z)-3-methyl-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}pent-3-en-1-yl]-6-methylidene-decahydronaphthalene-1-carboxylic acidHMDB
Chemical FormulaC32H52O13
Average Molecular Weight644.7475
Monoisotopic Molecular Weight644.34079175
IUPAC Name3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 1,4a-dimethyl-5-[(3Z)-3-methyl-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}pent-3-en-1-yl]-6-methylidene-decahydronaphthalene-1-carboxylate
Traditional Name3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 1,4a-dimethyl-5-[(3Z)-3-methyl-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}pent-3-en-1-yl]-6-methylidene-hexahydro-2H-naphthalene-1-carboxylate
CAS Registry Number90851-26-6
SMILES
C\C(CCC1C(=C)CCC2C1(C)CCCC2(C)C(=O)OC1OC(CO)C(O)C(O)C1O)=C\COC1OC(CO)C(O)C(O)C1O
InChI Identifier
InChI=1S/C32H52O13/c1-16(10-13-42-28-26(39)24(37)22(35)19(14-33)43-28)6-8-18-17(2)7-9-21-31(18,3)11-5-12-32(21,4)30(41)45-29-27(40)25(38)23(36)20(15-34)44-29/h10,18-29,33-40H,2,5-9,11-15H2,1,3-4H3/b16-10-
InChI KeyDQBCTTXPKJBNHF-YBEGLDIGSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene glycosides
Direct ParentDiterpene glycosides
Alternative Parents
Substituents
  • Diterpene glycoside
  • Labdane diterpenoid
  • Diterpenoid
  • Fatty acyl glycoside
  • Fatty acyl glycoside of mono- or disaccharide
  • Alkyl glycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Fatty acyl
  • Oxane
  • Monosaccharide
  • Carboxylic acid ester
  • Secondary alcohol
  • Acetal
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Monocarboxylic acid or derivatives
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Primary alcohol
  • Carbonyl group
  • Organooxygen compound
  • Alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility15.56 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB017719
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131752349
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1867811
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.