Hmdb loader

Showing metabocard for Vinaginsenoside R1 (HMDB0034624)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 19:30:44 UTC
Update Date2022-03-07 02:54:10 UTC
HMDB IDHMDB0034624
Secondary Accession Numbers
  • HMDB34624
Metabolite Identification
Common NameVinaginsenoside R1
DescriptionVinaginsenoside R1 belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton. Based on a literature review a significant number of articles have been published on Vinaginsenoside R1.
Structure
Data?1563862593
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0034624 (Vinaginsenoside R1)


  Mrv0541 02241208102D          

 59 65  0  0  0  0            999 V2000
   -3.2098    1.1388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.0685   -0.0997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3557    0.3131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.3557    2.3718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.6163    1.9617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0034624 (Vinaginsenoside R1)

HMDB0034624
     RDKit          3D
Vinaginsenoside R1
133139  0  0  0  0  0  0  0  0999 V2000
   -4.6830   -0.4272   -6.3171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9300    0.0118   -5.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0361   -0.7219   -4.6591 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1975    1.1904   -4.4531 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5656    1.6947   -3.3152 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7487    0.7495   -2.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1137    1.3010   -1.0654 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0960    0.3848    0.0421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3425   -0.6786   -0.2306 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.0144   -0.2396   -0.4391 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822   -0.2834    0.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1420    0.5455    1.5720 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6529   -1.6658    0.7335 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8005   -2.2407   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0153   -1.3526    0.0033 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.5231    0.8493   -1.1000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.5044    1.3517    0.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7109   -0.3164   -1.5167 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0586    0.2195   -1.9867 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.6374   -1.7134   -1.2520 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.8064    0.0319   -3.0933 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6569    0.1237   -6.3831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1145   -0.2460   -7.2398 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.9998    2.6723   -3.0491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4748    1.8292   -3.5725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3120   -0.2427   -2.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7326    1.0608    0.8690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1713   -0.0689    1.2399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3158    0.8384   -0.5755 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0314   -0.6621   -1.4270 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0638   -0.1280    2.4648 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0480    1.1504    1.7777 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2948    1.2094    1.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1026   -1.6081    1.7742 H   0  0  0  0  0  0  0  0  0  0  0  0
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    3.1084   -3.2172    0.3763 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.1401    1.9163   -1.0631 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9051    0.8582    1.1367 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3112    2.4393    0.4472 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5871    1.2104    0.4746 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9481   -1.1131   -0.7800 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2437   -0.7725   -2.3901 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8598   -0.0478   -1.3000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2721   -0.0308   -3.0451 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3479    2.2018   -1.0973 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2685    1.4709   -2.9245 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0731    2.5651   -4.3620 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2263    3.2802   -2.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3868    4.2141   -4.0501 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.2479   -0.7644   -2.5483 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.9722   -0.6017   -2.4328 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1653    2.2203    0.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.5183   -4.2223   -0.3968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2467   -4.1952   -0.3923 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0207   -3.7808    1.9840 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9154   -3.9285    3.9872 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6760   -2.2368    3.5325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1720   -4.5394    2.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4233   -4.0984    5.0065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8564   -0.8785    3.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4250   -0.4571    2.7153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3955   -1.5979    4.0447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2794   -2.4952    0.9269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7093   -2.6857    2.7046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9895   -4.0597    1.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4338   -2.8520    0.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0065    1.1768    0.3067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7831    1.4875    1.7315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3238    2.1395    5.0005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2503    3.7249    2.4024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6880    3.1545    3.1327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8040    4.1676    4.0941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1241    2.7499    2.6557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8424    3.3734    5.2241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3244    0.3832    4.6378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3131    1.8269    3.3679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5474    0.0027    1.6735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6526   -1.2847    4.0486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2852   -0.6999   -0.5468 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.6624    1.4106   -1.5254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1201   -0.9085   -2.9045 H   0  0  0  0  0  0  0  0  0  0  0  0
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 59133  1  0
M  END
Download

3D SDF for HMDB0034624 (Vinaginsenoside R1)


  Mrv0541 02241208102D          

 59 65  0  0  0  0            999 V2000
   -3.2098    1.1388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2098    0.3131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4956   -0.0997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7828    0.3131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7828    1.1388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4956    1.5503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0685   -0.0997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3557    0.3131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3557    1.1388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0685    1.5503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3557    1.5503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3557    2.3718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3557    2.7818    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1360    1.2970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6163    1.9617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1360    2.6236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9254   -0.0997    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.7828    1.9617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2277    0.5553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5690    0.7521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3557    3.6076    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3919    3.4080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9755    2.8245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7103    3.1988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5809    4.0135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7636    4.1414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5939    3.6214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1645    4.5970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9625    4.3837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9511    5.3952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5773    5.3126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4850   -1.5089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6915   -2.3085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1025   -2.8864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6916   -2.6662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8965   -1.8694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3075   -1.2929    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4869   -2.5300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3089   -3.6860    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2805   -3.2442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6919   -1.6479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2810   -2.2259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8998   -3.2442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7254   -3.2442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1369   -3.9653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.9965   -0.9872    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4869   -5.3952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  2 18  1  0  0  0  0
  3  4  1  0  0  0  0
  3 19  1  0  0  0  0
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  4  5  1  0  0  0  0
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  5  6  1  0  0  0  0
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  5 22  1  0  0  0  0
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  9 11  1  0  0  0  0
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 10 14  1  0  0  0  0
 11 12  1  0  0  0  0
 11 15  1  0  0  0  0
 11 24  1  0  0  0  0
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 15 16  1  0  0  0  0
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 17 26  1  0  0  0  0
 21 36  1  0  0  0  0
 26 27  1  0  0  0  0
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 26 31  1  0  0  0  0
 27 28  1  0  0  0  0
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 29 32  1  0  0  0  0
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 32 34  1  0  0  0  0
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 36 37  1  0  0  0  0
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 37 38  1  0  0  0  0
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 38 39  1  0  0  0  0
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 39 40  1  0  0  0  0
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 42 47  1  0  0  0  0
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 46 56  1  0  0  0  0
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 49 50  1  0  0  0  0
 49 54  1  0  0  0  0
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 51 59  1  0  0  0  0
 56 57  1  0  0  0  0
 56 58  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034624

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1OC(OC2C(O)C(O)C(COC(C)=O)OC2OC2CC3(C)C(CC(O)C4C(CCC34C)C3(C)CCC(O3)C(C)(C)O)C3(C)CCC(O)C(C)(C)C23)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C44H74O15/c1-20-30(48)32(50)34(52)37(55-20)58-35-33(51)31(49)25(19-54-21(2)45)57-38(35)56-24-18-43(9)26(41(7)14-12-27(47)39(3,4)36(24)41)17-23(46)29-22(11-15-42(29,43)8)44(10)16-13-28(59-44)40(5,6)53/h20,22-38,46-53H,11-19H2,1-10H3

> <INCHI_KEY>
VTZDPCBUMTUOMY-UHFFFAOYSA-N

> <FORMULA>
C44H74O15

> <MOLECULAR_WEIGHT>
843.0494

> <EXACT_MASS>
842.502771698

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
91.5667893354655

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[6-({5,16-dihydroxy-14-[5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-8-yl}oxy)-3,4-dihydroxy-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]methyl acetate

> <ALOGPS_LOGP>
1.96

> <JCHEM_LOGP>
1.1908018553333326

> <ALOGPS_LOGS>
-4.02

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.710529535122344

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.097179382027743

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8389066824097524

> <JCHEM_POLAR_SURFACE_AREA>
234.28999999999996

> <JCHEM_REFRACTIVITY>
210.10030000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.09e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[6-({5,16-dihydroxy-14-[5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-8-yl}oxy)-3,4-dihydroxy-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]methyl acetate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0034624 (Vinaginsenoside R1)

HMDB0034624
     RDKit          3D
Vinaginsenoside R1
133139  0  0  0  0  0  0  0  0999 V2000
   -4.6830   -0.4272   -6.3171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9300    0.0118   -5.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0361   -0.7219   -4.6591 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1975    1.1904   -4.4531 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5656    1.6947   -3.3152 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7487    0.7495   -2.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1137    1.3010   -1.0654 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0960    0.3848    0.0421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3425   -0.6786   -0.2306 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1361   -0.8252    0.4477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0144   -0.2396   -0.4391 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822   -0.2834    0.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1420    0.5455    1.5720 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6529   -1.6658    0.7335 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8005   -2.2407   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0153   -1.3526    0.0033 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0034624 (Vinaginsenoside R1)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -5.992   2.126   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.992   0.584   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.659  -0.186   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.328   0.584   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.328   2.126   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.659   2.894   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.995  -0.186   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.664   0.584   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.664   2.126   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.995   2.894   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.664   2.894   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.664   4.427   0.000  0.00  0.00           C+0
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HETATM   15  C   UNK     0       2.121   2.421   0.000  0.00  0.00           C+0
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HETATM   22  C   UNK     0      -3.328   3.662   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.425   1.036   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.062   1.404   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -0.664   6.734   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       2.598   6.362   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.688   5.272   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.059   5.971   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.818   7.492   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       3.292   7.731   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.109   6.760   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.907   8.581   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       7.397   8.183   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       5.509  10.071   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       6.678   9.917   0.000  0.00  0.00           O+0
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HETATM   45  C   UNK     0       3.158  -3.076   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0       4.258  -4.155   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0      -3.546  -6.056   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -5.087  -6.056   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -5.856  -7.402   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -5.087  -8.735   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      -3.546  -8.735   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0      -2.776  -7.402   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      -5.856  -4.723   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      -7.397  -7.402   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      -5.856 -10.069   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0       5.593  -3.384   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       6.927  -4.155   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0       5.593  -1.843   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      -2.776 -10.071   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   18                                                  
CONECT    3    2    4   19   20                                             
CONECT    4    3    5    7                                                  
CONECT    5    4    6   10   22                                             
CONECT    6    1    5                                                       
CONECT    7    4    8   21                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11   23                                             
CONECT   10    5    9   14                                                  
CONECT   11    9   12   15   24                                             
CONECT   12   11   13   17                                                  
CONECT   13   12   14   25                                                  
CONECT   14   10   13                                                       
CONECT   15   11   16                                                       
CONECT   16   15   17                                                       
CONECT   17   12   16   26                                                  
CONECT   18    2                                                            
CONECT   19    3                                                            
CONECT   20    3                                                            
CONECT   21    7   36                                                       
CONECT   22    5                                                            
CONECT   23    9                                                            
CONECT   24   11                                                            
CONECT   25   13                                                            
CONECT   26   17   27   30   31                                             
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   32                                                  
CONECT   30   26   29                                                       
CONECT   31   26                                                            
CONECT   32   29   33   34   35                                             
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35   32                                                            
CONECT   36   21   37   41                                                  
CONECT   37   36   38   42                                                  
CONECT   38   37   39   43                                                  
CONECT   39   38   40   44                                                  
CONECT   40   39   41   45                                                  
CONECT   41   36   40                                                       
CONECT   42   37   47                                                       
CONECT   43   38                                                            
CONECT   44   39                                                            
CONECT   45   40   46                                                       
CONECT   46   45   56                                                       
CONECT   47   42   48   52                                                  
CONECT   48   47   49   53                                                  
CONECT   49   48   50   54                                                  
CONECT   50   49   51   55                                                  
CONECT   51   50   52   59                                                  
CONECT   52   47   51                                                       
CONECT   53   48                                                            
CONECT   54   49                                                            
CONECT   55   50                                                            
CONECT   56   46   57   58                                                  
CONECT   57   56                                                            
CONECT   58   56                                                            
CONECT   59   51                                                            
MASTER        0    0    0    0    0    0    0    0   59    0  130    0
END
Download

3D PDB for HMDB0034624 (Vinaginsenoside R1)

COMPND    HMDB0034624
HETATM    1  C1  UNL     1      -4.683  -0.427  -6.317  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.930   0.012  -5.096  1.00  0.00           C  
HETATM    3  O1  UNL     1      -3.036  -0.722  -4.659  1.00  0.00           O  
HETATM    4  O2  UNL     1      -4.197   1.190  -4.453  1.00  0.00           O  
HETATM    5  C3  UNL     1      -3.566   1.695  -3.315  1.00  0.00           C  
HETATM    6  C4  UNL     1      -3.749   0.749  -2.171  1.00  0.00           C  
HETATM    7  O3  UNL     1      -3.114   1.301  -1.065  1.00  0.00           O  
HETATM    8  C5  UNL     1      -3.096   0.385   0.042  1.00  0.00           C  
HETATM    9  O4  UNL     1      -2.342  -0.679  -0.231  1.00  0.00           O  
HETATM   10  C6  UNL     1      -1.136  -0.825   0.448  1.00  0.00           C  
HETATM   11  C7  UNL     1      -0.014  -0.240  -0.439  1.00  0.00           C  
HETATM   12  C8  UNL     1       1.282  -0.283   0.279  1.00  0.00           C  
HETATM   13  C9  UNL     1       1.142   0.546   1.572  1.00  0.00           C  
HETATM   14  C10 UNL     1       1.653  -1.666   0.734  1.00  0.00           C  
HETATM   15  C11 UNL     1       2.801  -2.241  -0.081  1.00  0.00           C  
HETATM   16  C12 UNL     1       4.015  -1.353   0.003  1.00  0.00           C  
HETATM   17  O5  UNL     1       4.612  -1.645   1.247  1.00  0.00           O  
HETATM   18  C13 UNL     1       3.747   0.097  -0.049  1.00  0.00           C  
HETATM   19  C14 UNL     1       4.523   0.849  -1.100  1.00  0.00           C  
HETATM   20  C15 UNL     1       5.983   0.852  -0.993  1.00  0.00           C  
HETATM   21  C16 UNL     1       6.504   1.352   0.339  1.00  0.00           C  
HETATM   22  C17 UNL     1       6.711  -0.316  -1.517  1.00  0.00           C  
HETATM   23  C18 UNL     1       8.059   0.220  -1.987  1.00  0.00           C  
HETATM   24  C19 UNL     1       7.814   1.710  -1.936  1.00  0.00           C  
HETATM   25  C20 UNL     1       8.306   2.427  -3.181  1.00  0.00           C  
HETATM   26  C21 UNL     1       9.807   2.402  -3.290  1.00  0.00           C  
HETATM   27  C22 UNL     1       7.784   3.860  -3.080  1.00  0.00           C  
HETATM   28  O6  UNL     1       7.708   1.844  -4.267  1.00  0.00           O  
HETATM   29  O7  UNL     1       6.435   1.871  -1.900  1.00  0.00           O  
HETATM   30  C23 UNL     1       3.913   0.271  -2.344  1.00  0.00           C  
HETATM   31  C24 UNL     1       2.416   0.256  -1.959  1.00  0.00           C  
HETATM   32  C25 UNL     1       2.321   0.450  -0.508  1.00  0.00           C  
HETATM   33  C26 UNL     1       2.175   1.940  -0.259  1.00  0.00           C  
HETATM   34  C27 UNL     1       0.549  -2.655   0.817  1.00  0.00           C  
HETATM   35  C28 UNL     1       0.668  -3.530  -0.450  1.00  0.00           C  
HETATM   36  C29 UNL     1       0.946  -3.681   1.889  1.00  0.00           C  
HETATM   37  C30 UNL     1       0.425  -3.256   3.249  1.00  0.00           C  
HETATM   38  C31 UNL     1      -1.050  -3.535   3.123  1.00  0.00           C  
HETATM   39  O8  UNL     1      -1.704  -3.427   4.343  1.00  0.00           O  
HETATM   40  C32 UNL     1      -1.576  -2.438   2.228  1.00  0.00           C  
HETATM   41  C33 UNL     1      -1.800  -1.262   3.135  1.00  0.00           C  
HETATM   42  C34 UNL     1      -3.012  -2.930   1.885  1.00  0.00           C  
HETATM   43  C35 UNL     1      -0.853  -2.176   0.963  1.00  0.00           C  
HETATM   44  C36 UNL     1      -4.533   0.119   0.328  1.00  0.00           C  
HETATM   45  O9  UNL     1      -4.853  -0.385   1.550  1.00  0.00           O  
HETATM   46  C37 UNL     1      -5.593   0.526   2.288  1.00  0.00           C  
HETATM   47  O10 UNL     1      -4.914   0.925   3.445  1.00  0.00           O  
HETATM   48  C38 UNL     1      -5.452   2.114   3.883  1.00  0.00           C  
HETATM   49  C39 UNL     1      -4.772   3.338   3.332  1.00  0.00           C  
HETATM   50  C40 UNL     1      -6.938   2.210   3.604  1.00  0.00           C  
HETATM   51  O11 UNL     1      -7.501   2.981   4.621  1.00  0.00           O  
HETATM   52  C41 UNL     1      -7.588   0.865   3.662  1.00  0.00           C  
HETATM   53  O12 UNL     1      -8.954   0.906   3.529  1.00  0.00           O  
HETATM   54  C42 UNL     1      -6.954  -0.034   2.607  1.00  0.00           C  
HETATM   55  O13 UNL     1      -6.873  -1.345   3.084  1.00  0.00           O  
HETATM   56  C43 UNL     1      -5.248  -0.561  -0.828  1.00  0.00           C  
HETATM   57  O14 UNL     1      -4.637  -1.713  -1.252  1.00  0.00           O  
HETATM   58  C44 UNL     1      -5.229   0.503  -1.948  1.00  0.00           C  
HETATM   59  O15 UNL     1      -5.806   0.032  -3.093  1.00  0.00           O  
HETATM   60  H1  UNL     1      -5.657   0.124  -6.383  1.00  0.00           H  
HETATM   61  H2  UNL     1      -4.115  -0.246  -7.240  1.00  0.00           H  
HETATM   62  H3  UNL     1      -4.935  -1.516  -6.248  1.00  0.00           H  
HETATM   63  H4  UNL     1      -4.000   2.672  -3.049  1.00  0.00           H  
HETATM   64  H5  UNL     1      -2.475   1.829  -3.573  1.00  0.00           H  
HETATM   65  H6  UNL     1      -3.312  -0.243  -2.402  1.00  0.00           H  
HETATM   66  H7  UNL     1      -2.733   1.061   0.869  1.00  0.00           H  
HETATM   67  H8  UNL     1      -1.171  -0.069   1.240  1.00  0.00           H  
HETATM   68  H9  UNL     1      -0.316   0.838  -0.575  1.00  0.00           H  
HETATM   69  H10 UNL     1       0.031  -0.662  -1.427  1.00  0.00           H  
HETATM   70  H11 UNL     1       1.064  -0.128   2.465  1.00  0.00           H  
HETATM   71  H12 UNL     1       2.048   1.150   1.778  1.00  0.00           H  
HETATM   72  H13 UNL     1       0.295   1.209   1.594  1.00  0.00           H  
HETATM   73  H14 UNL     1       2.103  -1.608   1.774  1.00  0.00           H  
HETATM   74  H15 UNL     1       2.517  -2.495  -1.110  1.00  0.00           H  
HETATM   75  H16 UNL     1       3.108  -3.217   0.376  1.00  0.00           H  
HETATM   76  H17 UNL     1       4.683  -1.715  -0.830  1.00  0.00           H  
HETATM   77  H18 UNL     1       5.067  -2.528   1.093  1.00  0.00           H  
HETATM   78  H19 UNL     1       3.900   0.606   0.933  1.00  0.00           H  
HETATM   79  H20 UNL     1       4.140   1.916  -1.063  1.00  0.00           H  
HETATM   80  H21 UNL     1       5.905   0.858   1.137  1.00  0.00           H  
HETATM   81  H22 UNL     1       6.311   2.439   0.447  1.00  0.00           H  
HETATM   82  H23 UNL     1       7.587   1.210   0.475  1.00  0.00           H  
HETATM   83  H24 UNL     1       6.948  -1.113  -0.780  1.00  0.00           H  
HETATM   84  H25 UNL     1       6.244  -0.772  -2.390  1.00  0.00           H  
HETATM   85  H26 UNL     1       8.860  -0.048  -1.300  1.00  0.00           H  
HETATM   86  H27 UNL     1       8.272  -0.031  -3.045  1.00  0.00           H  
HETATM   87  H28 UNL     1       8.348   2.202  -1.097  1.00  0.00           H  
HETATM   88  H29 UNL     1      10.268   1.471  -2.925  1.00  0.00           H  
HETATM   89  H30 UNL     1      10.073   2.565  -4.362  1.00  0.00           H  
HETATM   90  H31 UNL     1      10.226   3.280  -2.734  1.00  0.00           H  
HETATM   91  H32 UNL     1       7.387   4.214  -4.050  1.00  0.00           H  
HETATM   92  H33 UNL     1       6.957   3.931  -2.355  1.00  0.00           H  
HETATM   93  H34 UNL     1       8.587   4.547  -2.713  1.00  0.00           H  
HETATM   94  H35 UNL     1       7.122   2.443  -4.782  1.00  0.00           H  
HETATM   95  H36 UNL     1       4.248  -0.764  -2.548  1.00  0.00           H  
HETATM   96  H37 UNL     1       4.096   0.912  -3.230  1.00  0.00           H  
HETATM   97  H38 UNL     1       1.987   1.144  -2.520  1.00  0.00           H  
HETATM   98  H39 UNL     1       1.972  -0.602  -2.433  1.00  0.00           H  
HETATM   99  H40 UNL     1       1.165   2.220   0.103  1.00  0.00           H  
HETATM  100  H41 UNL     1       2.895   2.369   0.431  1.00  0.00           H  
HETATM  101  H42 UNL     1       2.243   2.532  -1.224  1.00  0.00           H  
HETATM  102  H43 UNL     1       1.518  -4.222  -0.397  1.00  0.00           H  
HETATM  103  H44 UNL     1      -0.247  -4.195  -0.392  1.00  0.00           H  
HETATM  104  H45 UNL     1       0.560  -2.979  -1.372  1.00  0.00           H  
HETATM  105  H46 UNL     1       0.516  -4.681   1.689  1.00  0.00           H  
HETATM  106  H47 UNL     1       2.021  -3.781   1.984  1.00  0.00           H  
HETATM  107  H48 UNL     1       0.915  -3.928   3.987  1.00  0.00           H  
HETATM  108  H49 UNL     1       0.676  -2.237   3.533  1.00  0.00           H  
HETATM  109  H50 UNL     1      -1.172  -4.539   2.667  1.00  0.00           H  
HETATM  110  H51 UNL     1      -1.423  -4.098   5.006  1.00  0.00           H  
HETATM  111  H52 UNL     1      -0.856  -0.878   3.612  1.00  0.00           H  
HETATM  112  H53 UNL     1      -2.425  -0.457   2.715  1.00  0.00           H  
HETATM  113  H54 UNL     1      -2.395  -1.598   4.045  1.00  0.00           H  
HETATM  114  H55 UNL     1      -3.279  -2.495   0.927  1.00  0.00           H  
HETATM  115  H56 UNL     1      -3.709  -2.686   2.705  1.00  0.00           H  
HETATM  116  H57 UNL     1      -2.989  -4.060   1.837  1.00  0.00           H  
HETATM  117  H58 UNL     1      -1.434  -2.852   0.218  1.00  0.00           H  
HETATM  118  H59 UNL     1      -5.007   1.177   0.307  1.00  0.00           H  
HETATM  119  H60 UNL     1      -5.783   1.488   1.731  1.00  0.00           H  
HETATM  120  H61 UNL     1      -5.324   2.139   5.001  1.00  0.00           H  
HETATM  121  H62 UNL     1      -5.250   3.725   2.402  1.00  0.00           H  
HETATM  122  H63 UNL     1      -3.688   3.155   3.133  1.00  0.00           H  
HETATM  123  H64 UNL     1      -4.804   4.168   4.094  1.00  0.00           H  
HETATM  124  H65 UNL     1      -7.124   2.750   2.656  1.00  0.00           H  
HETATM  125  H66 UNL     1      -6.842   3.373   5.224  1.00  0.00           H  
HETATM  126  H67 UNL     1      -7.324   0.383   4.638  1.00  0.00           H  
HETATM  127  H68 UNL     1      -9.313   1.827   3.368  1.00  0.00           H  
HETATM  128  H69 UNL     1      -7.547   0.003   1.673  1.00  0.00           H  
HETATM  129  H70 UNL     1      -6.653  -1.285   4.049  1.00  0.00           H  
HETATM  130  H71 UNL     1      -6.285  -0.700  -0.547  1.00  0.00           H  
HETATM  131  H72 UNL     1      -5.085  -2.479  -0.847  1.00  0.00           H  
HETATM  132  H73 UNL     1      -5.662   1.411  -1.525  1.00  0.00           H  
HETATM  133  H74 UNL     1      -6.120  -0.908  -2.905  1.00  0.00           H  
CONECT    1    2   60   61   62
CONECT    2    3    3    4
CONECT    4    5
CONECT    5    6   63   64
CONECT    6    7   58   65
CONECT    7    8
CONECT    8    9   44   66
CONECT    9   10
CONECT   10   11   43   67
CONECT   11   12   68   69
CONECT   12   13   14   32
CONECT   13   70   71   72
CONECT   14   15   34   73
CONECT   15   16   74   75
CONECT   16   17   18   76
CONECT   17   77
CONECT   18   19   32   78
CONECT   19   20   30   79
CONECT   20   21   22   29
CONECT   21   80   81   82
CONECT   22   23   83   84
CONECT   23   24   85   86
CONECT   24   25   29   87
CONECT   25   26   27   28
CONECT   26   88   89   90
CONECT   27   91   92   93
CONECT   28   94
CONECT   30   31   95   96
CONECT   31   32   97   98
CONECT   32   33
CONECT   33   99  100  101
CONECT   34   35   36   43
CONECT   35  102  103  104
CONECT   36   37  105  106
CONECT   37   38  107  108
CONECT   38   39   40  109
CONECT   39  110
CONECT   40   41   42   43
CONECT   41  111  112  113
CONECT   42  114  115  116
CONECT   43  117
CONECT   44   45   56  118
CONECT   45   46
CONECT   46   47   54  119
CONECT   47   48
CONECT   48   49   50  120
CONECT   49  121  122  123
CONECT   50   51   52  124
CONECT   51  125
CONECT   52   53   54  126
CONECT   53  127
CONECT   54   55  128
CONECT   55  129
CONECT   56   57   58  130
CONECT   57  131
CONECT   58   59  132
CONECT   59  133
END
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SMILES for HMDB0034624 (Vinaginsenoside R1)

CC1OC(OC2C(O)C(O)C(COC(C)=O)OC2OC2CC3(C)C(CC(O)C4C(CCC34C)C3(C)CCC(O3)C(C)(C)O)C3(C)CCC(O)C(C)(C)C23)C(O)C(O)C1O
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INCHI for HMDB0034624 (Vinaginsenoside R1)

InChI=1S/C44H74O15/c1-20-30(48)32(50)34(52)37(55-20)58-35-33(51)31(49)25(19-54-21(2)45)57-38(35)56-24-18-43(9)26(41(7)14-12-27(47)39(3,4)36(24)41)17-23(46)29-22(11-15-42(29,43)8)44(10)16-13-28(59-44)40(5,6)53/h20,22-38,46-53H,11-19H2,1-10H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[6-({5,16-dihydroxy-14-[5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-8-yl}oxy)-3,4-dihydroxy-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]methyl acetic acidHMDB
Chemical FormulaC44H74O15
Average Molecular Weight843.0494
Monoisotopic Molecular Weight842.502771698
IUPAC Name[6-({5,16-dihydroxy-14-[5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-8-yl}oxy)-3,4-dihydroxy-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]methyl acetate
Traditional Name[6-({5,16-dihydroxy-14-[5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-8-yl}oxy)-3,4-dihydroxy-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]methyl acetate
CAS Registry Number156980-41-5
SMILES
CC1OC(OC2C(O)C(O)C(COC(C)=O)OC2OC2CC3(C)C(CC(O)C4C(CCC34C)C3(C)CCC(O3)C(C)(C)O)C3(C)CCC(O)C(C)(C)C23)C(O)C(O)C1O
InChI Identifier
InChI=1S/C44H74O15/c1-20-30(48)32(50)34(52)37(55-20)58-35-33(51)31(49)25(19-54-21(2)45)57-38(35)56-24-18-43(9)26(41(7)14-12-27(47)39(3,4)36(24)41)17-23(46)29-22(11-15-42(29,43)8)44(10)16-13-28(59-44)40(5,6)53/h20,22-38,46-53H,11-19H2,1-10H3
InChI KeyVTZDPCBUMTUOMY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene glycosides
Direct ParentTriterpene saponins
Alternative Parents
Substituents
  • Triterpene saponin
  • Triterpenoid
  • 3-hydroxysteroid
  • 12-hydroxysteroid
  • Hydroxysteroid
  • Steroid
  • Disaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • Oxane
  • Cyclic alcohol
  • Tetrahydrofuran
  • Tertiary alcohol
  • Secondary alcohol
  • Carboxylic acid ester
  • Polyol
  • Carboxylic acid derivative
  • Acetal
  • Dialkyl ether
  • Ether
  • Oxacycle
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Organic oxide
  • Carbonyl group
  • Hydrocarbon derivative
  • Organooxygen compound
  • Alcohol
  • Organic oxygen compound
  • 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
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 Solubility0.081 g/LALOGPS
logP1.96ALOGPS
logP1.19ChemAxon
logS-4ALOGPS
pKa (Strongest Acidic)12.1ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area234.29 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity210.1 m³·mol⁻¹ChemAxon
Polarizability91.57 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]-312.89930932474
DeepCCS[M+Na]+286.93730932474
AllCCS[M+H]+277.532859911
AllCCS[M+H-H2O]+277.432859911
AllCCS[M+NH4]+277.532859911
AllCCS[M+Na]+277.532859911
AllCCS[M-H]-247.332859911
AllCCS[M+Na-2H]-253.532859911
AllCCS[M+HCOO]-260.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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, 2022.7.21 minutes32390414
Predicted by Siyang on May 30, 202214.5161 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.85 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid130.8 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3685.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid134.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid219.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid170.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid180.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid639.6 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid760.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)232.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1051.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid622.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1769.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid456.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid450.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate186.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA203.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water11.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Vinaginsenoside R1CC1OC(OC2C(O)C(O)C(COC(C)=O)OC2OC2CC3(C)C(CC(O)C4C(CCC34C)C3(C)CCC(O3)C(C)(C)O)C3(C)CCC(O)C(C)(C)C23)C(O)C(O)C1O4150.8Standard polar33892256
Vinaginsenoside R1CC1OC(OC2C(O)C(O)C(COC(C)=O)OC2OC2CC3(C)C(CC(O)C4C(CCC34C)C3(C)CCC(O3)C(C)(C)O)C3(C)CCC(O)C(C)(C)C23)C(O)C(O)C1O4655.7Standard non polar33892256
Vinaginsenoside R1CC1OC(OC2C(O)C(O)C(COC(C)=O)OC2OC2CC3(C)C(CC(O)C4C(CCC34C)C3(C)CCC(O3)C(C)(C)O)C3(C)CCC(O)C(C)(C)C23)C(O)C(O)C1O5931.9Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 10V, Positive-QTOFsplash10-004i-0100907270-ce1429fa03ddb815dca72015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 20V, Positive-QTOFsplash10-004i-0000905010-1940164793bbe33ee2712015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 40V, Positive-QTOFsplash10-004l-2110902010-b40433dad8bad81e748b2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 10V, Negative-QTOFsplash10-0596-9200404140-b1901269fa153eadf0df2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 20V, Negative-QTOFsplash10-0abc-9400603000-29b160738773936df69d2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 40V, Negative-QTOFsplash10-052f-9300600000-5ccc3648283eaaa5a5352015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 10V, Negative-QTOFsplash10-0006-1000002490-63f82947d88d0212f7e42021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 20V, Negative-QTOFsplash10-0a4m-9200004740-8ff4a9c881e5c45f90932021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 40V, Negative-QTOFsplash10-0a4l-9000006000-66f109197c3450e313422021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 10V, Positive-QTOFsplash10-002f-0000001290-ee714559a911080d4b312021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 20V, Positive-QTOFsplash10-004i-0200219220-599038997b79e8ed334c2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinaginsenoside R1 40V, Positive-QTOFsplash10-00kb-9300013200-bf93c46c6c4541e7a0262021-09-25Wishart LabView Spectrum
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 IDFDB013143
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound74933433
PDB IDNot Available
ChEBI ID185753
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.