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Showing metabocard for Vinaginsenoside R13 (HMDB0040783)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 02:22:05 UTC
Update Date2022-03-07 02:56:44 UTC
HMDB IDHMDB0040783
Secondary Accession Numbers
  • HMDB40783
Metabolite Identification
Common NameVinaginsenoside R13
DescriptionVinaginsenoside R13 belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Vinaginsenoside R13 is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563863587
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040783 (Vinaginsenoside R13)


  Mrv0541 05061312072D          

 68 74  0  0  0  0            999 V2000
    3.4482   -1.5147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3876   -1.5087    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.6473    1.1787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0587    1.1927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8701   -0.0666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3523    1.9997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0602    1.1598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3503   -0.8877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0865    3.2611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1547    5.0068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 13 12  1  0  0  0  0
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 68 48  1  0  0  0  0
M  END
Download

3D MOL for HMDB0040783 (Vinaginsenoside R13)

HMDB0040783
     RDKit          3D
Vinaginsenoside R13
152158  0  0  0  0  0  0  0  0999 V2000
   -9.0932   -1.7887    4.6769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9618   -0.9205    4.0813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0977    0.4062    4.8142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8078   -1.5806    4.4098 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3009   -0.7919    2.6278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3895   -2.0690    2.1128 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7110    0.2672    1.8429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3526    0.5374    1.5109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5630   -0.3969    0.5568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4828   -1.7515    1.1120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3744   -0.3265   -0.5749 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1689   -1.0779   -1.6488 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1950   -2.0648   -1.7909 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1290   -1.7816   -2.7299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4167   -2.5403   -2.3971 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.5157   -0.3177   -2.7881 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.3350    0.4791   -3.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2651    1.7563   -2.7641 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0786   -0.2944   -2.9170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7272   -1.1630   -3.9625 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2401    0.2672    0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2786    1.5868   -0.3844 C   0  0  0  0  0  0  0  0  0  0  0  0
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    8.2829    3.8733   -2.3801 O   0  0  0  0  0  0  0  0  0  0  0  0
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   12.4893   -0.5274    2.0329 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1236   -2.3353    2.1587 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1648   -3.2699    1.8116 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6395   -1.2859    3.1120 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7817   -1.8675    4.0378 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052   -0.1669    2.4501 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5759    1.0532    2.6914 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1653   -0.0665    0.2950 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6758   -0.9795   -0.8501 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3938   -0.8893    1.5271 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7183    0.1449   -0.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9611   -1.1216   -0.2812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2010   -0.8017   -1.2090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8488    0.5234   -0.9862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5723    1.4854   -2.1556 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8057   -2.1392    5.6841 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0255   -1.1858    4.7249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3078   -2.6553    4.0283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1974    0.1655    5.8926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0161    0.8807    4.4775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1864    1.0220    4.7264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9296   -2.5340    4.1038 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.1833    1.2588    2.2674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3093    0.2614    0.8382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3297    1.5262    0.9304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6669    0.8022    2.3737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2986   -2.3630    0.6030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6559   -1.7859    2.1671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5664   -2.3282    0.7911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2057   -1.6524   -1.5238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8406   -2.1046   -3.7384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2486   -3.6371   -2.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1648   -2.2130   -3.1556 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0040783 (Vinaginsenoside R13)


  Mrv0541 05061312072D          

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M  END
> <DATABASE_ID>
HMDB0040783

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)(O)C(O)CCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C

> <INCHI_IDENTIFIER>
InChI=1S/C48H84O20/c1-43(2)26-10-15-46(6)27(45(26,5)13-12-29(43)66-42-39(36(59)33(56)25(20-51)65-42)67-40-37(60)34(57)31(54)23(18-49)63-40)17-22(52)30-21(9-14-47(30,46)7)48(8,16-11-28(53)44(3,4)62)68-41-38(61)35(58)32(55)24(19-50)64-41/h21-42,49-62H,9-20H2,1-8H3

> <INCHI_KEY>
IXHBKLVSPJTPAA-UHFFFAOYSA-N

> <FORMULA>
C48H84O20

> <MOLECULAR_WEIGHT>
981.1686

> <EXACT_MASS>
980.555595128

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
105.84842521420683

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
14

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[2-(5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-5,6-dihydroxy-6-methylheptan-2-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.16

> <JCHEM_LOGP>
-1.9210079426666686

> <ALOGPS_LOGS>
-2.86

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.313264759871124

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.847210195899308

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6483775957536517

> <JCHEM_POLAR_SURFACE_AREA>
338.6000000000001

> <JCHEM_REFRACTIVITY>
236.82340000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.34e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[2-(5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-5,6-dihydroxy-6-methylheptan-2-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0040783 (Vinaginsenoside R13)

HMDB0040783
     RDKit          3D
Vinaginsenoside R13
152158  0  0  0  0  0  0  0  0999 V2000
   -9.0932   -1.7887    4.6769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9618   -0.9205    4.0813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0977    0.4062    4.8142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8078   -1.5806    4.4098 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3009   -0.7919    2.6278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3895   -2.0690    2.1128 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7110    0.2672    1.8429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3526    0.5374    1.5109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5630   -0.3969    0.5568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4828   -1.7515    1.1120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3744   -0.3265   -0.5749 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1689   -1.0779   -1.6488 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1950   -2.0648   -1.7909 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1290   -1.7816   -2.7299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4167   -2.5403   -2.3971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8854   -2.1462   -1.1549 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5157   -0.3177   -2.7881 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5344   -0.2180   -3.7324 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3350    0.4791   -3.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2651    1.7563   -2.7641 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0786   -0.2944   -2.9170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7272   -1.1630   -3.9625 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2401    0.2672    0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2786    1.5868   -0.3844 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0653    1.6480   -1.2688 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3611    0.3247   -1.1291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4890   -0.3826   -2.4894 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0463   -0.4868   -0.0990 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1461   -0.6108    1.1295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0104   -0.7700    2.2518 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3945    0.6526    1.4413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5073    1.1398    0.3491 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9613    1.1360    0.6985 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1247    1.0104    2.2081 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6400    2.4657    0.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9966    2.4103   -0.1186 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8742    1.2607    0.2704 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9512    1.1708   -0.5509 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1917    1.3229   -0.0840 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6104    2.6180   -0.5261 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2727    2.6947   -1.8631 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8974    3.9460   -2.5012 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2829    3.8733   -2.3801 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6640    1.5291   -2.6960 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5678    0.7603   -3.1043 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6686    0.6651   -2.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9006    1.3254   -2.1019 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2846    0.4296   -0.5618 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3875    0.6811    0.2647 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8491   -0.4256    0.9572 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1572   -0.6220    0.5251 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7487   -1.7854    0.9236 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2348   -1.5190    1.0905 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4893   -0.5274    2.0329 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1236   -2.3353    2.1587 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1648   -3.2699    1.8116 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6395   -1.2859    3.1120 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7817   -1.8675    4.0378 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052   -0.1669    2.4501 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5759    1.0532    2.6914 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1653   -0.0665    0.2950 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6758   -0.9795   -0.8501 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3938   -0.8893    1.5271 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7183    0.1449   -0.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9611   -1.1216   -0.2812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2010   -0.8017   -1.2090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8488    0.5234   -0.9862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5723    1.4854   -2.1556 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8057   -2.1392    5.6841 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0255   -1.1858    4.7249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3078   -2.6553    4.0283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1974    0.1655    5.8926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0161    0.8807    4.4775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1864    1.0220    4.7264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9296   -2.5340    4.1038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4431   -0.4999    2.6853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1372   -2.1392    1.4795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1833    1.2588    2.2674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3093    0.2614    0.8382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3297    1.5262    0.9304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6669    0.8022    2.3737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2986   -2.3630    0.6030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6559   -1.7859    2.1671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5664   -2.3282    0.7911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2057   -1.6524   -1.5238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8406   -2.1046   -3.7384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2486   -3.6371   -2.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1648   -2.2130   -3.1556 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8400   -2.2812   -1.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8801    0.0688   -1.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6986    0.7305   -3.9676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3216    0.5691   -4.3850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1289    2.2282   -2.7632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2291    0.4121   -2.8330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9419   -0.8478   -4.4741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0161    0.6444    1.4420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2129    2.4784    0.3131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2102    1.7895   -0.9535 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4303    2.5111   -0.9932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3886    1.8370   -2.3111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9841    0.2759   -3.2509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1021   -1.2997   -2.4284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5238   -0.7005   -2.9057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1642   -1.5065   -0.4596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5604   -1.5357    1.1202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5278   -1.2686    2.9560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9173    0.4449    2.4153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1862    1.4209    1.7103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7439    2.2409    0.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4798    1.8225    2.6463 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0111    0.0306    2.6195 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1510    1.3789    2.5242 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6554    3.1098    1.3591 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9847    3.0137   -0.2889 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5166    3.3701    0.0806 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9030    2.3751   -1.2326 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2300    1.4446    1.3019 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2534    1.4867    1.0408 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1492    2.8113   -1.9921 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4959    4.8588   -2.0604 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6672    3.9316   -3.5845 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7744    4.2086   -3.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1160    1.8691   -3.6902 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8149   -0.1802   -3.2973 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6944   -0.2984   -2.5777 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2525    1.5789   -1.2109 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0659   -0.6500   -0.4470 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3118   -1.3533    0.7899 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6917   -2.5336    0.0776 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6474   -1.1843    0.1193 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7459   -2.4733    1.3470 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.4066    0.3592    1.5645 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9276   -2.9090    2.7044 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1681   -4.0765    2.3489 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.5234   -0.9146    3.6969 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4955   -2.7590    3.7686 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8740   -0.0207    2.8177 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3432    1.7187    1.9896 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7369   -0.7410   -1.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1210   -0.8323   -1.7745 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6153   -2.0506   -0.5628 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5191   -1.5576    1.7262 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2315   -1.6479    1.3756 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7512   -0.3371    2.4136 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8398    0.5566   -1.1294 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6961   -1.6572    0.6245 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6231   -1.8429   -0.8565 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2871   -0.7448   -2.2305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8683   -1.6620   -1.2198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6366    2.5385   -1.8299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3803    1.4201   -2.9501 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3261    1.2232   -2.7343 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
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 68152  1  0
M  END
Download

PDB for HMDB0040783 (Vinaginsenoside R13)

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       6.437  -2.827   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.457  -2.816   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.978   7.321   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      17.601   4.305   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.808   2.200   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.443   2.226   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.958  -0.124   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.724   3.733   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.179   2.165   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.121  -1.657   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.757   6.652   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.133   0.675   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.470   1.438   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.267   0.924   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.458  -0.895   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.249   6.340   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.146   2.963   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.161   6.087   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.755   9.346   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.549  -1.597   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.281   3.416   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.484   3.725   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.491   5.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.217   8.862   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.211  -0.835   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.791  -0.880   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.138   1.423   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      15.781   5.501   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.124  -0.865   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.814   2.948   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.829   6.073   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.367   9.886   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.202   0.705   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.158   5.295   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      11.829   9.402   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       0.136   1.467   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       4.150   3.755   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      12.141   7.894   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       1.465   0.690   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       2.812   2.993   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      10.991   6.870   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       1.457  -0.850   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       5.453  -1.642   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      17.289   5.813   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       6.800   0.660   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       9.467   0.645   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      10.805   1.408   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      12.765   4.878   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0       0.170   7.627   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0       7.444  10.854   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -2.557  -3.138   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       9.493   5.265   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      15.297   4.039   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       2.837   7.612   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      10.056  11.394   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      -2.532   1.482   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       5.496   6.058   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      12.980  10.426   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0       0.144   3.007   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       5.479   2.978   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      13.603   7.410   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      18.797   6.125   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0       1.482   3.770   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       9.529   7.354   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       0.119  -1.612   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       2.786  -1.627   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0       2.803   1.453   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      11.303   5.362   0.000  0.00  0.00           O+0
CONECT    1   43                                                            
CONECT    2   43                                                            
CONECT    3   44                                                            
CONECT    4   44                                                            
CONECT    5   45                                                            
CONECT    6   46                                                            
CONECT    7   47                                                            
CONECT    8   48                                                            
CONECT    9   14   21                                                       
CONECT   10   15   26                                                       
CONECT   11   16   28                                                       
CONECT   12   13   29                                                       
CONECT   13   12   45                                                       
CONECT   14    9   47                                                       
CONECT   15   10   46                                                       
CONECT   16   11   48                                                       
CONECT   17   22   27                                                       
CONECT   18   23   49                                                       
CONECT   19   24   50                                                       
CONECT   20   25   51                                                       
CONECT   21    9   30   48                                                  
CONECT   22   17   30   52                                                  
CONECT   23   18   31   63                                                  
CONECT   24   19   32   64                                                  
CONECT   25   20   33   65                                                  
CONECT   26   10   43   45                                                  
CONECT   27   17   45   46                                                  
CONECT   28   11   44   53                                                  
CONECT   29   12   43   66                                                  
CONECT   30   21   22   47                                                  
CONECT   31   23   34   54                                                  
CONECT   32   24   35   55                                                  
CONECT   33   25   36   56                                                  
CONECT   34   31   37   57                                                  
CONECT   35   32   38   58                                                  
CONECT   36   33   39   59                                                  
CONECT   37   34   40   60                                                  
CONECT   38   35   41   61                                                  
CONECT   39   36   42   67                                                  
CONECT   40   37   63   67                                                  
CONECT   41   38   64   68                                                  
CONECT   42   39   65   66                                                  
CONECT   43    1    2   26   29                                             
CONECT   44    3    4   28   62                                             
CONECT   45    5   13   26   27                                             
CONECT   46    6   15   27   47                                             
CONECT   47    7   14   30   46                                             
CONECT   48    8   16   21   68                                             
CONECT   49   18                                                            
CONECT   50   19                                                            
CONECT   51   20                                                            
CONECT   52   22                                                            
CONECT   53   28                                                            
CONECT   54   31                                                            
CONECT   55   32                                                            
CONECT   56   33                                                            
CONECT   57   34                                                            
CONECT   58   35                                                            
CONECT   59   36                                                            
CONECT   60   37                                                            
CONECT   61   38                                                            
CONECT   62   44                                                            
CONECT   63   23   40                                                       
CONECT   64   24   41                                                       
CONECT   65   25   42                                                       
CONECT   66   29   42                                                       
CONECT   67   39   40                                                       
CONECT   68   41   48                                                       
MASTER        0    0    0    0    0    0    0    0   68    0  148    0
END
Download

3D PDB for HMDB0040783 (Vinaginsenoside R13)

COMPND    HMDB0040783
HETATM    1  C1  UNL     1      -9.093  -1.789   4.677  1.00  0.00           C  
HETATM    2  C2  UNL     1      -7.962  -0.920   4.081  1.00  0.00           C  
HETATM    3  C3  UNL     1      -8.098   0.406   4.814  1.00  0.00           C  
HETATM    4  O1  UNL     1      -6.808  -1.581   4.410  1.00  0.00           O  
HETATM    5  C4  UNL     1      -8.301  -0.792   2.628  1.00  0.00           C  
HETATM    6  O2  UNL     1      -8.389  -2.069   2.113  1.00  0.00           O  
HETATM    7  C5  UNL     1      -7.711   0.267   1.843  1.00  0.00           C  
HETATM    8  C6  UNL     1      -6.353   0.537   1.511  1.00  0.00           C  
HETATM    9  C7  UNL     1      -5.563  -0.397   0.557  1.00  0.00           C  
HETATM   10  C8  UNL     1      -5.483  -1.752   1.112  1.00  0.00           C  
HETATM   11  O3  UNL     1      -6.374  -0.326  -0.575  1.00  0.00           O  
HETATM   12  C9  UNL     1      -6.169  -1.078  -1.649  1.00  0.00           C  
HETATM   13  O4  UNL     1      -7.195  -2.065  -1.791  1.00  0.00           O  
HETATM   14  C10 UNL     1      -8.129  -1.782  -2.730  1.00  0.00           C  
HETATM   15  C11 UNL     1      -9.417  -2.540  -2.397  1.00  0.00           C  
HETATM   16  O5  UNL     1      -9.885  -2.146  -1.155  1.00  0.00           O  
HETATM   17  C12 UNL     1      -8.516  -0.318  -2.788  1.00  0.00           C  
HETATM   18  O6  UNL     1      -9.534  -0.218  -3.732  1.00  0.00           O  
HETATM   19  C13 UNL     1      -7.335   0.479  -3.264  1.00  0.00           C  
HETATM   20  O7  UNL     1      -7.265   1.756  -2.764  1.00  0.00           O  
HETATM   21  C14 UNL     1      -6.079  -0.294  -2.917  1.00  0.00           C  
HETATM   22  O8  UNL     1      -5.727  -1.163  -3.963  1.00  0.00           O  
HETATM   23  C15 UNL     1      -4.240   0.267   0.311  1.00  0.00           C  
HETATM   24  C16 UNL     1      -4.279   1.587  -0.384  1.00  0.00           C  
HETATM   25  C17 UNL     1      -3.065   1.648  -1.269  1.00  0.00           C  
HETATM   26  C18 UNL     1      -2.361   0.325  -1.129  1.00  0.00           C  
HETATM   27  C19 UNL     1      -2.489  -0.383  -2.489  1.00  0.00           C  
HETATM   28  C20 UNL     1      -3.046  -0.487  -0.099  1.00  0.00           C  
HETATM   29  C21 UNL     1      -2.146  -0.611   1.130  1.00  0.00           C  
HETATM   30  O9  UNL     1      -3.010  -0.770   2.252  1.00  0.00           O  
HETATM   31  C22 UNL     1      -1.394   0.653   1.441  1.00  0.00           C  
HETATM   32  C23 UNL     1      -0.507   1.140   0.349  1.00  0.00           C  
HETATM   33  C24 UNL     1       0.961   1.136   0.698  1.00  0.00           C  
HETATM   34  C25 UNL     1       1.125   1.010   2.208  1.00  0.00           C  
HETATM   35  C26 UNL     1       1.640   2.466   0.437  1.00  0.00           C  
HETATM   36  C27 UNL     1       2.997   2.410  -0.119  1.00  0.00           C  
HETATM   37  C28 UNL     1       3.874   1.261   0.270  1.00  0.00           C  
HETATM   38  O10 UNL     1       4.951   1.171  -0.551  1.00  0.00           O  
HETATM   39  C29 UNL     1       6.192   1.323  -0.084  1.00  0.00           C  
HETATM   40  O11 UNL     1       6.610   2.618  -0.526  1.00  0.00           O  
HETATM   41  C30 UNL     1       6.273   2.695  -1.863  1.00  0.00           C  
HETATM   42  C31 UNL     1       6.897   3.946  -2.501  1.00  0.00           C  
HETATM   43  O12 UNL     1       8.283   3.873  -2.380  1.00  0.00           O  
HETATM   44  C32 UNL     1       6.664   1.529  -2.696  1.00  0.00           C  
HETATM   45  O13 UNL     1       5.568   0.760  -3.104  1.00  0.00           O  
HETATM   46  C33 UNL     1       7.669   0.665  -2.000  1.00  0.00           C  
HETATM   47  O14 UNL     1       8.901   1.325  -2.102  1.00  0.00           O  
HETATM   48  C34 UNL     1       7.285   0.430  -0.562  1.00  0.00           C  
HETATM   49  O15 UNL     1       8.387   0.681   0.265  1.00  0.00           O  
HETATM   50  C35 UNL     1       8.849  -0.426   0.957  1.00  0.00           C  
HETATM   51  O16 UNL     1      10.157  -0.622   0.525  1.00  0.00           O  
HETATM   52  C36 UNL     1      10.749  -1.785   0.924  1.00  0.00           C  
HETATM   53  C37 UNL     1      12.235  -1.519   1.090  1.00  0.00           C  
HETATM   54  O17 UNL     1      12.489  -0.527   2.033  1.00  0.00           O  
HETATM   55  C38 UNL     1      10.124  -2.335   2.159  1.00  0.00           C  
HETATM   56  O18 UNL     1       9.165  -3.270   1.812  1.00  0.00           O  
HETATM   57  C39 UNL     1       9.639  -1.286   3.112  1.00  0.00           C  
HETATM   58  O19 UNL     1       8.782  -1.867   4.038  1.00  0.00           O  
HETATM   59  C40 UNL     1       8.905  -0.167   2.450  1.00  0.00           C  
HETATM   60  O20 UNL     1       9.576   1.053   2.691  1.00  0.00           O  
HETATM   61  C41 UNL     1       3.165  -0.066   0.295  1.00  0.00           C  
HETATM   62  C42 UNL     1       3.676  -0.979  -0.850  1.00  0.00           C  
HETATM   63  C43 UNL     1       3.394  -0.889   1.527  1.00  0.00           C  
HETATM   64  C44 UNL     1       1.718   0.145  -0.079  1.00  0.00           C  
HETATM   65  C45 UNL     1       0.961  -1.122  -0.281  1.00  0.00           C  
HETATM   66  C46 UNL     1      -0.201  -0.802  -1.209  1.00  0.00           C  
HETATM   67  C47 UNL     1      -0.849   0.523  -0.986  1.00  0.00           C  
HETATM   68  C48 UNL     1      -0.572   1.485  -2.156  1.00  0.00           C  
HETATM   69  H1  UNL     1      -8.806  -2.139   5.684  1.00  0.00           H  
HETATM   70  H2  UNL     1     -10.026  -1.186   4.725  1.00  0.00           H  
HETATM   71  H3  UNL     1      -9.308  -2.655   4.028  1.00  0.00           H  
HETATM   72  H4  UNL     1      -8.197   0.165   5.893  1.00  0.00           H  
HETATM   73  H5  UNL     1      -9.016   0.881   4.477  1.00  0.00           H  
HETATM   74  H6  UNL     1      -7.186   1.022   4.726  1.00  0.00           H  
HETATM   75  H7  UNL     1      -6.930  -2.534   4.104  1.00  0.00           H  
HETATM   76  H8  UNL     1      -9.443  -0.500   2.685  1.00  0.00           H  
HETATM   77  H9  UNL     1      -9.137  -2.139   1.480  1.00  0.00           H  
HETATM   78  H10 UNL     1      -8.183   1.259   2.267  1.00  0.00           H  
HETATM   79  H11 UNL     1      -8.309   0.261   0.838  1.00  0.00           H  
HETATM   80  H12 UNL     1      -6.330   1.526   0.930  1.00  0.00           H  
HETATM   81  H13 UNL     1      -5.667   0.802   2.374  1.00  0.00           H  
HETATM   82  H14 UNL     1      -6.299  -2.363   0.603  1.00  0.00           H  
HETATM   83  H15 UNL     1      -5.656  -1.786   2.167  1.00  0.00           H  
HETATM   84  H16 UNL     1      -4.566  -2.328   0.791  1.00  0.00           H  
HETATM   85  H17 UNL     1      -5.206  -1.652  -1.524  1.00  0.00           H  
HETATM   86  H18 UNL     1      -7.841  -2.105  -3.738  1.00  0.00           H  
HETATM   87  H19 UNL     1      -9.249  -3.637  -2.444  1.00  0.00           H  
HETATM   88  H20 UNL     1     -10.165  -2.213  -3.156  1.00  0.00           H  
HETATM   89  H21 UNL     1     -10.840  -2.281  -1.012  1.00  0.00           H  
HETATM   90  H22 UNL     1      -8.880   0.069  -1.824  1.00  0.00           H  
HETATM   91  H23 UNL     1      -9.699   0.730  -3.968  1.00  0.00           H  
HETATM   92  H24 UNL     1      -7.322   0.569  -4.385  1.00  0.00           H  
HETATM   93  H25 UNL     1      -8.129   2.228  -2.763  1.00  0.00           H  
HETATM   94  H26 UNL     1      -5.229   0.412  -2.833  1.00  0.00           H  
HETATM   95  H27 UNL     1      -4.942  -0.848  -4.474  1.00  0.00           H  
HETATM   96  H28 UNL     1      -4.016   0.644   1.442  1.00  0.00           H  
HETATM   97  H29 UNL     1      -4.213   2.478   0.313  1.00  0.00           H  
HETATM   98  H30 UNL     1      -5.210   1.790  -0.954  1.00  0.00           H  
HETATM   99  H31 UNL     1      -2.430   2.511  -0.993  1.00  0.00           H  
HETATM  100  H32 UNL     1      -3.389   1.837  -2.311  1.00  0.00           H  
HETATM  101  H33 UNL     1      -2.984   0.276  -3.251  1.00  0.00           H  
HETATM  102  H34 UNL     1      -3.102  -1.300  -2.428  1.00  0.00           H  
HETATM  103  H35 UNL     1      -1.524  -0.701  -2.906  1.00  0.00           H  
HETATM  104  H36 UNL     1      -3.164  -1.506  -0.460  1.00  0.00           H  
HETATM  105  H37 UNL     1      -1.560  -1.536   1.120  1.00  0.00           H  
HETATM  106  H38 UNL     1      -2.528  -1.269   2.956  1.00  0.00           H  
HETATM  107  H39 UNL     1      -0.917   0.445   2.415  1.00  0.00           H  
HETATM  108  H40 UNL     1      -2.186   1.421   1.710  1.00  0.00           H  
HETATM  109  H41 UNL     1      -0.744   2.241   0.212  1.00  0.00           H  
HETATM  110  H42 UNL     1       0.480   1.822   2.646  1.00  0.00           H  
HETATM  111  H43 UNL     1       1.011   0.031   2.620  1.00  0.00           H  
HETATM  112  H44 UNL     1       2.151   1.379   2.524  1.00  0.00           H  
HETATM  113  H45 UNL     1       1.655   3.110   1.359  1.00  0.00           H  
HETATM  114  H46 UNL     1       0.985   3.014  -0.289  1.00  0.00           H  
HETATM  115  H47 UNL     1       3.517   3.370   0.081  1.00  0.00           H  
HETATM  116  H48 UNL     1       2.903   2.375  -1.233  1.00  0.00           H  
HETATM  117  H49 UNL     1       4.230   1.445   1.302  1.00  0.00           H  
HETATM  118  H50 UNL     1       6.253   1.487   1.041  1.00  0.00           H  
HETATM  119  H51 UNL     1       5.149   2.811  -1.992  1.00  0.00           H  
HETATM  120  H52 UNL     1       6.496   4.859  -2.060  1.00  0.00           H  
HETATM  121  H53 UNL     1       6.667   3.932  -3.585  1.00  0.00           H  
HETATM  122  H54 UNL     1       8.774   4.209  -3.159  1.00  0.00           H  
HETATM  123  H55 UNL     1       7.116   1.869  -3.690  1.00  0.00           H  
HETATM  124  H56 UNL     1       5.815  -0.180  -3.297  1.00  0.00           H  
HETATM  125  H57 UNL     1       7.694  -0.298  -2.578  1.00  0.00           H  
HETATM  126  H58 UNL     1       9.253   1.579  -1.211  1.00  0.00           H  
HETATM  127  H59 UNL     1       7.066  -0.650  -0.447  1.00  0.00           H  
HETATM  128  H60 UNL     1       8.312  -1.353   0.790  1.00  0.00           H  
HETATM  129  H61 UNL     1      10.692  -2.534   0.078  1.00  0.00           H  
HETATM  130  H62 UNL     1      12.647  -1.184   0.119  1.00  0.00           H  
HETATM  131  H63 UNL     1      12.746  -2.473   1.347  1.00  0.00           H  
HETATM  132  H64 UNL     1      12.407   0.359   1.565  1.00  0.00           H  
HETATM  133  H65 UNL     1      10.928  -2.909   2.704  1.00  0.00           H  
HETATM  134  H66 UNL     1       9.168  -4.076   2.349  1.00  0.00           H  
HETATM  135  H67 UNL     1      10.523  -0.915   3.697  1.00  0.00           H  
HETATM  136  H68 UNL     1       8.496  -2.759   3.769  1.00  0.00           H  
HETATM  137  H69 UNL     1       7.874  -0.021   2.818  1.00  0.00           H  
HETATM  138  H70 UNL     1       9.343   1.719   1.990  1.00  0.00           H  
HETATM  139  H71 UNL     1       4.737  -0.741  -1.013  1.00  0.00           H  
HETATM  140  H72 UNL     1       3.121  -0.832  -1.774  1.00  0.00           H  
HETATM  141  H73 UNL     1       3.615  -2.051  -0.563  1.00  0.00           H  
HETATM  142  H74 UNL     1       2.519  -1.558   1.726  1.00  0.00           H  
HETATM  143  H75 UNL     1       4.232  -1.648   1.376  1.00  0.00           H  
HETATM  144  H76 UNL     1       3.751  -0.337   2.414  1.00  0.00           H  
HETATM  145  H77 UNL     1       1.840   0.557  -1.129  1.00  0.00           H  
HETATM  146  H78 UNL     1       0.696  -1.657   0.624  1.00  0.00           H  
HETATM  147  H79 UNL     1       1.623  -1.843  -0.856  1.00  0.00           H  
HETATM  148  H80 UNL     1       0.287  -0.745  -2.230  1.00  0.00           H  
HETATM  149  H81 UNL     1      -0.868  -1.662  -1.220  1.00  0.00           H  
HETATM  150  H82 UNL     1      -0.637   2.539  -1.830  1.00  0.00           H  
HETATM  151  H83 UNL     1      -1.380   1.420  -2.950  1.00  0.00           H  
HETATM  152  H84 UNL     1       0.326   1.223  -2.734  1.00  0.00           H  
CONECT    1    2   69   70   71
CONECT    2    3    4    5
CONECT    3   72   73   74
CONECT    4   75
CONECT    5    6    7   76
CONECT    6   77
CONECT    7    8   78   79
CONECT    8    9   80   81
CONECT    9   10   11   23
CONECT   10   82   83   84
CONECT   11   12
CONECT   12   13   21   85
CONECT   13   14
CONECT   14   15   17   86
CONECT   15   16   87   88
CONECT   16   89
CONECT   17   18   19   90
CONECT   18   91
CONECT   19   20   21   92
CONECT   20   93
CONECT   21   22   94
CONECT   22   95
CONECT   23   24   28   96
CONECT   24   25   97   98
CONECT   25   26   99  100
CONECT   26   27   28   67
CONECT   27  101  102  103
CONECT   28   29  104
CONECT   29   30   31  105
CONECT   30  106
CONECT   31   32  107  108
CONECT   32   33   67  109
CONECT   33   34   35   64
CONECT   34  110  111  112
CONECT   35   36  113  114
CONECT   36   37  115  116
CONECT   37   38   61  117
CONECT   38   39
CONECT   39   40   48  118
CONECT   40   41
CONECT   41   42   44  119
CONECT   42   43  120  121
CONECT   43  122
CONECT   44   45   46  123
CONECT   45  124
CONECT   46   47   48  125
CONECT   47  126
CONECT   48   49  127
CONECT   49   50
CONECT   50   51   59  128
CONECT   51   52
CONECT   52   53   55  129
CONECT   53   54  130  131
CONECT   54  132
CONECT   55   56   57  133
CONECT   56  134
CONECT   57   58   59  135
CONECT   58  136
CONECT   59   60  137
CONECT   60  138
CONECT   61   62   63   64
CONECT   62  139  140  141
CONECT   63  142  143  144
CONECT   64   65  145
CONECT   65   66  146  147
CONECT   66   67  148  149
CONECT   67   68
CONECT   68  150  151  152
END
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SMILES for HMDB0040783 (Vinaginsenoside R13)

CC(C)(O)C(O)CCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C
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INCHI for HMDB0040783 (Vinaginsenoside R13)

InChI=1S/C48H84O20/c1-43(2)26-10-15-46(6)27(45(26,5)13-12-29(43)66-42-39(36(59)33(56)25(20-51)65-42)67-40-37(60)34(57)31(54)23(18-49)63-40)17-22(52)30-21(9-14-47(30,46)7)48(8,16-11-28(53)44(3,4)62)68-41-38(61)35(58)32(55)24(19-50)64-41/h21-42,49-62H,9-20H2,1-8H3
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC48H84O20
Average Molecular Weight981.1686
Monoisotopic Molecular Weight980.555595128
IUPAC Name2-{[2-(5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-5,6-dihydroxy-6-methylheptan-2-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Name2-{[2-(5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-5,6-dihydroxy-6-methylheptan-2-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
CAS Registry Number156398-72-0
SMILES
CC(C)(O)C(O)CCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C
InChI Identifier
InChI=1S/C48H84O20/c1-43(2)26-10-15-46(6)27(45(26,5)13-12-29(43)66-42-39(36(59)33(56)25(20-51)65-42)67-40-37(60)34(57)31(54)23(18-49)63-40)17-22(52)30-21(9-14-47(30,46)7)48(8,16-11-28(53)44(3,4)62)68-41-38(61)35(58)32(55)24(19-50)64-41/h21-42,49-62H,9-20H2,1-8H3
InChI KeyIXHBKLVSPJTPAA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTriterpenoids
Direct ParentTriterpenoids
Alternative ParentsNot Available
SubstituentsNot Available
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
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.34 g/LALOGPS
logP-0.16ALOGPS
logP-1.9ChemAxon
logS-2.9ALOGPS
pKa (Strongest Acidic)11.85ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area338.6 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity236.82 m³·mol⁻¹ChemAxon
Polarizability105.85 ųChemAxon
Number of Rings7ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-331.32730932474
DeepCCS[M+Na]+305.42930932474
AllCCS[M+H]+301.232859911
AllCCS[M+H-H2O]+301.432859911
AllCCS[M+NH4]+300.932859911
AllCCS[M+Na]+300.832859911
AllCCS[M-H]-287.832859911
AllCCS[M+Na-2H]-294.532859911
AllCCS[M+HCOO]-301.932859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 10V, Positive-QTOFsplash10-0w2i-0000108196-de934ccea37401e413502015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 20V, Positive-QTOFsplash10-0zg0-0100409061-15a16bfdd5426ad18d4d2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 40V, Positive-QTOFsplash10-0pbc-1300709031-f96d42d02829fc5da1182015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 10V, Negative-QTOFsplash10-02bk-0200005539-2aa2d17bcd89447f0f2b2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 20V, Negative-QTOFsplash10-06vs-0600209534-9894cd0f156ad9a66f3c2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 40V, Negative-QTOFsplash10-054o-3600409100-a75b4bab1e813829a9c82015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 10V, Positive-QTOFsplash10-0f89-0100201976-7cb6f4e25fff1f92ee9b2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 20V, Positive-QTOFsplash10-05aj-3401444459-fc5ff6777403a615179d2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 40V, Positive-QTOFsplash10-0a4m-9400000051-907885ef1063dc032a702021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 10V, Negative-QTOFsplash10-004i-0000000019-2727a5bd4660c752bea12021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 20V, Negative-QTOFsplash10-0a6r-5000001139-49e7482c751ddf8e0b282021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R13 40V, Negative-QTOFsplash10-0a4i-9100000361-4fc735fb7a10a17988252021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB020599
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound73092886
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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.