Hmdb loader

Showing metabocard for Arvensoside D (HMDB0039406)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 00:51:08 UTC
Update Date2022-03-07 02:56:11 UTC
HMDB IDHMDB0039406
Secondary Accession Numbers
  • HMDB39406
Metabolite Identification
Common NameArvensoside D
DescriptionArvensoside D 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 Arvensoside D.
Structure
Data?1563863369
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039406 (Arvensoside D)


  Mrv0541 05061311062D          

 66 73  0  0  0  0            999 V2000
   11.7469    3.8956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8075    3.8956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5206   -1.4933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4600   -1.4933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7048    1.2012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8483   -0.0363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1450    1.1227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1338    2.0262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4193    1.6137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4193   -0.8613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2759    0.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9904    0.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1338   -0.4488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9917    2.8512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5627    0.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9917    2.0261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2772    0.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5627    2.8512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2746    1.6136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9904   -1.6863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1325    1.6137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8483    1.6137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5627    2.0262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.2759   -2.0988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.2759   -0.4488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5601    0.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2759   -2.9238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4180    0.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5601   -0.4488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5614   -3.3363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2746   -0.8613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.1325   -0.8613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9891   -0.4488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.8470   -0.4488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9917    1.2012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2772    3.2637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9904   -0.8614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7049    0.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8483    0.7886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1338    0.3761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2772    1.6136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5601    2.0262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7049   -2.0988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8470    2.0262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8457    0.7886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9904   -3.3363    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    6.5615   -4.1613    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2746   -1.6864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1325   -3.3363    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9917    0.3762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.7061    1.6137    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9891    0.3762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5615   -1.6864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8470    0.3761    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.1325   -1.6863    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 12 11  1  0  0  0  0
 13 10  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  1  0  0  0  0
 22  8  2  0  0  0  0
 23 18  1  0  0  0  0
 23 22  1  0  0  0  0
 24 19  1  0  0  0  0
 25 20  1  0  0  0  0
 26 21  1  0  0  0  0
 27 10  1  0  0  0  0
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 44  3  1  0  0  0  0
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 65 39  1  0  0  0  0
 66 38  1  0  0  0  0
 66 40  1  0  0  0  0
M  END
Download

3D MOL for HMDB0039406 (Arvensoside D)

HMDB0039406
     RDKit          3D
Arvensoside D
144151  0  0  0  0  0  0  0  0999 V2000
   10.3537   -0.4278   -3.5009 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3854   -0.8029   -2.3576 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2121   -2.2903   -2.5282 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1311   -0.4230   -1.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3074   -0.7314    0.0874 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9863    0.0038    0.1276 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2295    1.1265    1.0879 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5930    1.2682    2.1516 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2118    2.0445    0.7682 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0127   -0.8872    0.7960 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5774   -0.4096    0.6675 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2956   -0.3343   -0.8164 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6837   -1.6506   -1.4077 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1272    0.8398   -1.2021 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5544    2.0004   -1.4507 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0910    2.2909   -1.3821 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4379    1.1861   -0.6112 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0280    1.2789   -0.2133 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8746    0.4873    1.1151 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4838    2.6342    0.0813 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1330    2.5415    0.7689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6582    1.3533    0.3521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0267    1.6923    0.4866 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7121    0.7683    1.2037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8415    1.1187    2.5902 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0064   -0.0798    3.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8626   -0.2600    4.2238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6214   -0.3095    3.6273 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3151   -1.2779    2.4476 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.9276   -1.8679    0.7023 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9845   -2.5786    1.1938 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6600   -3.9397    1.1563 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.3569   -6.7005    0.7511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9525   -4.3947    1.4653 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6258   -3.5214    2.3300 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592   -3.7814    0.0688 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1421   -3.5385   -0.3777 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1536   -2.4291    0.2208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7835   -1.9971   -1.0238 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1157    0.4236    0.8126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9012    1.5031    1.3055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6077    2.1262    0.2999 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1891    3.4498    0.2213 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0396    4.2701   -0.4721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1627    3.9443   -1.9454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9308    4.0542   -2.5908 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4066    4.4357    0.1648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4187    4.2872   -0.7883 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6130    3.3538    1.1911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9765    3.6505    2.3954 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0843    2.0437    0.6350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3067    1.1088    1.6720 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3396    0.9002   -1.0436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8411    2.0303   -1.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1993   -0.2928   -1.3888 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1265    0.6169   -1.2319 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5160   -0.8120   -1.3335 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9174   -1.1682   -1.0302 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9067   -0.0653   -1.2660 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0224    0.0477   -2.8023 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6129    0.6136   -1.1894 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1398    0.0037   -2.4371 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3556   -0.8079   -3.1507 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0906   -1.0391   -4.3851 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3507    0.6515   -3.6989 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3117   -2.4759   -3.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0239   -2.8491   -1.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0577   -2.7878   -3.0475 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3526    0.6765   -1.2075 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0908   -1.0099   -0.9954 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1486   -1.8277    0.1345 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9555   -0.5070    0.9881 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9802    2.2510    1.4252 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1370   -1.9699    0.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2010   -0.8066    1.9240 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6525    0.6021    1.1527 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8736   -1.0669    1.1922 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4104   -1.8174   -2.4584 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0470   -2.4067   -0.8481 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6923   -1.9943   -1.2700 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1983    2.8282   -1.7286 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6333    2.5533   -2.3404 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0108    3.2274   -0.7521 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9952    1.2348    0.3932 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4680    1.1093    1.9223 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4538   -0.4985    0.9736 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0039406 (Arvensoside D)


  Mrv0541 05061311062D          

 66 73  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0039406

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(OC6OC(CO)C(O)C(OC7OC(CO)C(O)C(O)C7O)C6OC6OC(CO)C(O)C(O)C6O)C(C)(C)C5CCC34C)C2C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C48H78O18/c1-43(2)14-16-48(42(59)60)17-15-46(6)22(23(48)18-43)8-9-28-45(5)12-11-29(44(3,4)27(45)10-13-47(28,46)7)64-41-38(66-40-36(58)34(56)31(53)25(20-50)62-40)37(32(54)26(21-51)63-41)65-39-35(57)33(55)30(52)24(19-49)61-39/h8,23-41,49-58H,9-21H2,1-7H3,(H,59,60)

> <INCHI_KEY>
OGKRHYLZKFTGGO-UHFFFAOYSA-N

> <FORMULA>
C48H78O18

> <MOLECULAR_WEIGHT>
943.1221

> <EXACT_MASS>
942.518815692

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
100.54882598348377

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
10-{[5-hydroxy-6-(hydroxymethyl)-3,4-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})oxan-2-yl]oxy}-2,2,6a,6b,9,9,12a-heptamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid

> <ALOGPS_LOGP>
1.86

> <JCHEM_LOGP>
1.2823264963333365

> <ALOGPS_LOGS>
-3.53

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.880022374468783

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.744259160809896

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6483775752817795

> <JCHEM_POLAR_SURFACE_AREA>
294.98

> <JCHEM_REFRACTIVITY>
230.86440000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.77e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
10-{[5-hydroxy-6-(hydroxymethyl)-3,4-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})oxan-2-yl]oxy}-2,2,6a,6b,9,9,12a-heptamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0039406 (Arvensoside D)

HMDB0039406
     RDKit          3D
Arvensoside D
144151  0  0  0  0  0  0  0  0999 V2000
   10.3537   -0.4278   -3.5009 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3854   -0.8029   -2.3576 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2121   -2.2903   -2.5282 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1311   -0.4230   -1.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3074   -0.7314    0.0874 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9863    0.0038    0.1276 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2295    1.1265    1.0879 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5930    1.2682    2.1516 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2118    2.0445    0.7682 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0127   -0.8872    0.7960 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5774   -0.4096    0.6675 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2956   -0.3343   -0.8164 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6837   -1.6506   -1.4077 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1272    0.8398   -1.2021 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5544    2.0004   -1.4507 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0910    2.2909   -1.3821 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4379    1.1861   -0.6112 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0280    1.2789   -0.2133 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8746    0.4873    1.1151 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4838    2.6342    0.0813 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1330    2.5415    0.7689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6582    1.3533    0.3521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0267    1.6923    0.4866 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7121    0.7683    1.2037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8415    1.1187    2.5902 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0064   -0.0798    3.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8626   -0.2600    4.2238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6214   -0.3095    3.6273 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3151   -1.2779    2.4476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8635   -2.2289    3.3707 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4497   -0.8641    1.5083 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9276   -1.8679    0.7023 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9845   -2.5786    1.1938 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6600   -3.9397    1.1563 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5504   -4.6129    1.9678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2699   -6.1041    2.0079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3569   -6.7005    0.7511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9525   -4.3947    1.4653 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6258   -3.5214    2.3300 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592   -3.7814    0.0688 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1421   -3.5385   -0.3777 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1536   -2.4291    0.2208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7835   -1.9971   -1.0238 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1157    0.4236    0.8126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9012    1.5031    1.3055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6077    2.1262    0.2999 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1891    3.4498    0.2213 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0396    4.2701   -0.4721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1627    3.9443   -1.9454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9308    4.0542   -2.5908 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4066    4.4357    0.1648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4187    4.2872   -0.7883 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6130    3.3538    1.1911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9765    3.6505    2.3954 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0843    2.0437    0.6350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3067    1.1088    1.6720 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3396    0.9002   -1.0436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8411    2.0303   -1.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1993   -0.2928   -1.3888 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1265    0.6169   -1.2319 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5160   -0.8120   -1.3335 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9174   -1.1682   -1.0302 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9067   -0.0653   -1.2660 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0224    0.0477   -2.8023 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6129    0.6136   -1.1894 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1398    0.0037   -2.4371 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3556   -0.8079   -3.1507 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0906   -1.0391   -4.3851 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3507    0.6515   -3.6989 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3117   -2.4759   -3.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0239   -2.8491   -1.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0577   -2.7878   -3.0475 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3526    0.6765   -1.2075 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0908   -1.0099   -0.9954 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1486   -1.8277    0.1345 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9555   -0.5070    0.9881 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9802    2.2510    1.4252 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1370   -1.9699    0.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2010   -0.8066    1.9240 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6525    0.6021    1.1527 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8736   -1.0669    1.1922 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4104   -1.8174   -2.4584 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0470   -2.4067   -0.8481 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6923   -1.9943   -1.2700 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1983    2.8282   -1.7286 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6333    2.5533   -2.3404 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0108    3.2274   -0.7521 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9952    1.2348    0.3932 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4680    1.1093    1.9223 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4538   -0.4985    0.9736 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9279    0.2779    1.5046 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4326    3.2185   -0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1718    3.1979    0.7749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1826    2.6381    1.8697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4052    3.4892    0.4595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754    0.4536    0.9970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0201   -0.1053    1.3086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9346    0.0971    3.9135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8229    0.6124    4.9413 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0039406 (Arvensoside D)

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      21.928   7.272   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      23.907   7.272   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.905  -2.787   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.925  -2.787   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.249   2.242   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      20.250  -0.068   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.937   2.096   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.916   3.782   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      17.583   3.012   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      17.583  -1.608   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.582   0.702   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.915   1.472   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      18.916  -0.838   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      24.251   5.322   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      21.584   0.702   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      24.251   3.782   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      22.917   1.472   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      21.584   5.322   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.246   3.012   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      14.915  -3.148   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.581   3.012   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      20.250   3.012   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      21.584   3.782   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.246   1.472   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      13.582  -3.918   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.581   1.472   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      16.249  -0.838   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      17.583   1.472   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      13.582  -0.838   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.912   0.702   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      13.582  -5.458   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.247   0.702   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.912  -0.838   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      12.248  -6.228   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.246  -1.608   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      10.914  -5.458   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       8.247  -0.838   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       9.581  -1.608   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       5.580  -0.838   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      10.914  -3.918   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      10.914  -0.838   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      24.251   2.242   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      22.917   6.092   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      14.915  -1.608   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      16.249   0.702   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      20.250   1.472   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      18.916   0.702   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      22.917   3.012   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0       2.912   3.782   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      16.249  -3.918   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      10.914   3.782   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       1.579   1.472   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      14.915  -6.228   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       6.913   1.472   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       1.579  -1.608   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      12.248  -7.768   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       4.246  -3.148   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0       9.581  -6.228   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      24.251   0.702   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      25.585   3.012   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0       5.580   0.702   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      12.248  -3.148   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      10.914   0.702   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      12.248  -1.608   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       6.913  -1.608   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       9.581  -3.148   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    9   22                                                       
CONECT    9    8   28                                                       
CONECT   10   13   27                                                       
CONECT   11   12   29                                                       
CONECT   12   11   45                                                       
CONECT   13   10   47                                                       
CONECT   14   16   43                                                       
CONECT   15   17   46                                                       
CONECT   16   14   48                                                       
CONECT   17   15   48                                                       
CONECT   18   23   43                                                       
CONECT   19   24   49                                                       
CONECT   20   25   50                                                       
CONECT   21   26   51                                                       
CONECT   22    8   23   46                                                  
CONECT   23   18   22   48                                                  
CONECT   24   19   30   61                                                  
CONECT   25   20   31   62                                                  
CONECT   26   21   32   63                                                  
CONECT   27   10   44   45                                                  
CONECT   28    9   45   47                                                  
CONECT   29   11   44   64                                                  
CONECT   30   24   33   52                                                  
CONECT   31   25   34   53                                                  
CONECT   32   26   37   54                                                  
CONECT   33   30   35   55                                                  
CONECT   34   31   36   56                                                  
CONECT   35   33   39   57                                                  
CONECT   36   34   40   58                                                  
CONECT   37   32   38   65                                                  
CONECT   38   37   41   66                                                  
CONECT   39   35   61   65                                                  
CONECT   40   36   62   66                                                  
CONECT   41   38   63   64                                                  
CONECT   42   48   59   60                                                  
CONECT   43    1    2   14   18                                             
CONECT   44    3    4   27   29                                             
CONECT   45    5   12   27   28                                             
CONECT   46    6   15   22   47                                             
CONECT   47    7   13   28   46                                             
CONECT   48   16   17   23   42                                             
CONECT   49   19                                                            
CONECT   50   20                                                            
CONECT   51   21                                                            
CONECT   52   30                                                            
CONECT   53   31                                                            
CONECT   54   32                                                            
CONECT   55   33                                                            
CONECT   56   34                                                            
CONECT   57   35                                                            
CONECT   58   36                                                            
CONECT   59   42                                                            
CONECT   60   42                                                            
CONECT   61   24   39                                                       
CONECT   62   25   40                                                       
CONECT   63   26   41                                                       
CONECT   64   29   41                                                       
CONECT   65   37   39                                                       
CONECT   66   38   40                                                       
MASTER        0    0    0    0    0    0    0    0   66    0  146    0
END
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3D PDB for HMDB0039406 (Arvensoside D)

COMPND    HMDB0039406
HETATM    1  C1  UNL     1      10.354  -0.428  -3.501  1.00  0.00           C  
HETATM    2  C2  UNL     1       9.385  -0.803  -2.358  1.00  0.00           C  
HETATM    3  C3  UNL     1       9.212  -2.290  -2.528  1.00  0.00           C  
HETATM    4  C4  UNL     1      10.131  -0.423  -1.108  1.00  0.00           C  
HETATM    5  C5  UNL     1       9.307  -0.731   0.087  1.00  0.00           C  
HETATM    6  C6  UNL     1       7.986   0.004   0.128  1.00  0.00           C  
HETATM    7  C7  UNL     1       8.229   1.127   1.088  1.00  0.00           C  
HETATM    8  O1  UNL     1       7.593   1.268   2.152  1.00  0.00           O  
HETATM    9  O2  UNL     1       9.212   2.045   0.768  1.00  0.00           O  
HETATM   10  C8  UNL     1       7.013  -0.887   0.796  1.00  0.00           C  
HETATM   11  C9  UNL     1       5.577  -0.410   0.668  1.00  0.00           C  
HETATM   12  C10 UNL     1       5.296  -0.334  -0.816  1.00  0.00           C  
HETATM   13  C11 UNL     1       5.684  -1.651  -1.408  1.00  0.00           C  
HETATM   14  C12 UNL     1       6.127   0.840  -1.202  1.00  0.00           C  
HETATM   15  C13 UNL     1       5.554   2.000  -1.451  1.00  0.00           C  
HETATM   16  C14 UNL     1       4.091   2.291  -1.382  1.00  0.00           C  
HETATM   17  C15 UNL     1       3.438   1.186  -0.611  1.00  0.00           C  
HETATM   18  C16 UNL     1       2.028   1.279  -0.213  1.00  0.00           C  
HETATM   19  C17 UNL     1       1.875   0.487   1.115  1.00  0.00           C  
HETATM   20  C18 UNL     1       1.484   2.634   0.081  1.00  0.00           C  
HETATM   21  C19 UNL     1       0.133   2.541   0.769  1.00  0.00           C  
HETATM   22  C20 UNL     1      -0.658   1.353   0.352  1.00  0.00           C  
HETATM   23  O3  UNL     1      -2.027   1.692   0.487  1.00  0.00           O  
HETATM   24  C21 UNL     1      -2.712   0.768   1.204  1.00  0.00           C  
HETATM   25  O4  UNL     1      -2.841   1.119   2.590  1.00  0.00           O  
HETATM   26  C22 UNL     1      -3.006  -0.080   3.287  1.00  0.00           C  
HETATM   27  C23 UNL     1      -1.863  -0.260   4.224  1.00  0.00           C  
HETATM   28  O5  UNL     1      -0.621  -0.309   3.627  1.00  0.00           O  
HETATM   29  C24 UNL     1      -3.315  -1.278   2.448  1.00  0.00           C  
HETATM   30  O6  UNL     1      -3.863  -2.229   3.371  1.00  0.00           O  
HETATM   31  C25 UNL     1      -4.450  -0.864   1.508  1.00  0.00           C  
HETATM   32  O7  UNL     1      -4.928  -1.868   0.702  1.00  0.00           O  
HETATM   33  C26 UNL     1      -5.984  -2.579   1.194  1.00  0.00           C  
HETATM   34  O8  UNL     1      -5.660  -3.940   1.156  1.00  0.00           O  
HETATM   35  C27 UNL     1      -6.550  -4.613   1.968  1.00  0.00           C  
HETATM   36  C28 UNL     1      -6.270  -6.104   2.008  1.00  0.00           C  
HETATM   37  O9  UNL     1      -6.357  -6.701   0.751  1.00  0.00           O  
HETATM   38  C29 UNL     1      -7.952  -4.395   1.465  1.00  0.00           C  
HETATM   39  O10 UNL     1      -8.626  -3.521   2.330  1.00  0.00           O  
HETATM   40  C30 UNL     1      -7.859  -3.781   0.069  1.00  0.00           C  
HETATM   41  O11 UNL     1      -9.142  -3.538  -0.378  1.00  0.00           O  
HETATM   42  C31 UNL     1      -7.154  -2.429   0.221  1.00  0.00           C  
HETATM   43  O12 UNL     1      -6.783  -1.997  -1.024  1.00  0.00           O  
HETATM   44  C32 UNL     1      -4.116   0.424   0.813  1.00  0.00           C  
HETATM   45  O13 UNL     1      -4.901   1.503   1.305  1.00  0.00           O  
HETATM   46  C33 UNL     1      -5.608   2.126   0.300  1.00  0.00           C  
HETATM   47  O14 UNL     1      -5.189   3.450   0.221  1.00  0.00           O  
HETATM   48  C34 UNL     1      -6.040   4.270  -0.472  1.00  0.00           C  
HETATM   49  C35 UNL     1      -6.163   3.944  -1.945  1.00  0.00           C  
HETATM   50  O15 UNL     1      -4.931   4.054  -2.591  1.00  0.00           O  
HETATM   51  C36 UNL     1      -7.407   4.436   0.165  1.00  0.00           C  
HETATM   52  O16 UNL     1      -8.419   4.287  -0.788  1.00  0.00           O  
HETATM   53  C37 UNL     1      -7.613   3.354   1.191  1.00  0.00           C  
HETATM   54  O17 UNL     1      -6.976   3.650   2.395  1.00  0.00           O  
HETATM   55  C38 UNL     1      -7.084   2.044   0.635  1.00  0.00           C  
HETATM   56  O18 UNL     1      -7.307   1.109   1.672  1.00  0.00           O  
HETATM   57  C39 UNL     1      -0.340   0.900  -1.044  1.00  0.00           C  
HETATM   58  C40 UNL     1      -0.841   2.030  -1.951  1.00  0.00           C  
HETATM   59  C41 UNL     1      -1.199  -0.293  -1.389  1.00  0.00           C  
HETATM   60  C42 UNL     1       1.127   0.617  -1.232  1.00  0.00           C  
HETATM   61  C43 UNL     1       1.516  -0.812  -1.333  1.00  0.00           C  
HETATM   62  C44 UNL     1       2.917  -1.168  -1.030  1.00  0.00           C  
HETATM   63  C45 UNL     1       3.907  -0.065  -1.266  1.00  0.00           C  
HETATM   64  C46 UNL     1       4.022   0.048  -2.802  1.00  0.00           C  
HETATM   65  C47 UNL     1       7.613   0.614  -1.189  1.00  0.00           C  
HETATM   66  C48 UNL     1       8.140   0.004  -2.437  1.00  0.00           C  
HETATM   67  H1  UNL     1      11.356  -0.808  -3.151  1.00  0.00           H  
HETATM   68  H2  UNL     1      10.091  -1.039  -4.385  1.00  0.00           H  
HETATM   69  H3  UNL     1      10.351   0.651  -3.699  1.00  0.00           H  
HETATM   70  H4  UNL     1       8.312  -2.476  -3.185  1.00  0.00           H  
HETATM   71  H5  UNL     1       9.024  -2.849  -1.612  1.00  0.00           H  
HETATM   72  H6  UNL     1      10.058  -2.788  -3.047  1.00  0.00           H  
HETATM   73  H7  UNL     1      10.353   0.676  -1.207  1.00  0.00           H  
HETATM   74  H8  UNL     1      11.091  -1.010  -0.995  1.00  0.00           H  
HETATM   75  H9  UNL     1       9.149  -1.828   0.135  1.00  0.00           H  
HETATM   76  H10 UNL     1       9.955  -0.507   0.988  1.00  0.00           H  
HETATM   77  H11 UNL     1       9.980   2.251   1.425  1.00  0.00           H  
HETATM   78  H12 UNL     1       7.137  -1.970   0.639  1.00  0.00           H  
HETATM   79  H13 UNL     1       7.201  -0.807   1.924  1.00  0.00           H  
HETATM   80  H14 UNL     1       5.652   0.602   1.153  1.00  0.00           H  
HETATM   81  H15 UNL     1       4.874  -1.067   1.192  1.00  0.00           H  
HETATM   82  H16 UNL     1       5.410  -1.817  -2.458  1.00  0.00           H  
HETATM   83  H17 UNL     1       5.047  -2.407  -0.848  1.00  0.00           H  
HETATM   84  H18 UNL     1       6.692  -1.994  -1.270  1.00  0.00           H  
HETATM   85  H19 UNL     1       6.198   2.828  -1.729  1.00  0.00           H  
HETATM   86  H20 UNL     1       3.633   2.553  -2.340  1.00  0.00           H  
HETATM   87  H21 UNL     1       4.011   3.227  -0.752  1.00  0.00           H  
HETATM   88  H22 UNL     1       3.995   1.235   0.393  1.00  0.00           H  
HETATM   89  H23 UNL     1       1.468   1.109   1.922  1.00  0.00           H  
HETATM   90  H24 UNL     1       1.454  -0.499   0.974  1.00  0.00           H  
HETATM   91  H25 UNL     1       2.928   0.278   1.505  1.00  0.00           H  
HETATM   92  H26 UNL     1       1.433   3.219  -0.849  1.00  0.00           H  
HETATM   93  H27 UNL     1       2.172   3.198   0.775  1.00  0.00           H  
HETATM   94  H28 UNL     1       0.183   2.638   1.870  1.00  0.00           H  
HETATM   95  H29 UNL     1      -0.405   3.489   0.460  1.00  0.00           H  
HETATM   96  H30 UNL     1      -0.575   0.454   0.997  1.00  0.00           H  
HETATM   97  H31 UNL     1      -2.020  -0.105   1.309  1.00  0.00           H  
HETATM   98  H32 UNL     1      -3.935   0.097   3.913  1.00  0.00           H  
HETATM   99  H33 UNL     1      -1.823   0.612   4.941  1.00  0.00           H  
HETATM  100  H34 UNL     1      -2.060  -1.131   4.893  1.00  0.00           H  
HETATM  101  H35 UNL     1      -0.629  -1.061   2.968  1.00  0.00           H  
HETATM  102  H36 UNL     1      -2.485  -1.780   2.017  1.00  0.00           H  
HETATM  103  H37 UNL     1      -4.665  -1.861   3.822  1.00  0.00           H  
HETATM  104  H38 UNL     1      -5.256  -0.688   2.260  1.00  0.00           H  
HETATM  105  H39 UNL     1      -6.364  -2.343   2.168  1.00  0.00           H  
HETATM  106  H40 UNL     1      -6.491  -4.264   3.025  1.00  0.00           H  
HETATM  107  H41 UNL     1      -5.267  -6.266   2.451  1.00  0.00           H  
HETATM  108  H42 UNL     1      -7.033  -6.559   2.665  1.00  0.00           H  
HETATM  109  H43 UNL     1      -5.847  -6.140   0.128  1.00  0.00           H  
HETATM  110  H44 UNL     1      -8.498  -5.372   1.396  1.00  0.00           H  
HETATM  111  H45 UNL     1      -9.521  -3.918   2.549  1.00  0.00           H  
HETATM  112  H46 UNL     1      -7.347  -4.447  -0.616  1.00  0.00           H  
HETATM  113  H47 UNL     1      -9.424  -2.619  -0.197  1.00  0.00           H  
HETATM  114  H48 UNL     1      -7.935  -1.750   0.644  1.00  0.00           H  
HETATM  115  H49 UNL     1      -7.164  -1.112  -1.270  1.00  0.00           H  
HETATM  116  H50 UNL     1      -4.268   0.357  -0.291  1.00  0.00           H  
HETATM  117  H51 UNL     1      -5.442   1.688  -0.695  1.00  0.00           H  
HETATM  118  H52 UNL     1      -5.561   5.291  -0.445  1.00  0.00           H  
HETATM  119  H53 UNL     1      -6.851   4.659  -2.436  1.00  0.00           H  
HETATM  120  H54 UNL     1      -6.480   2.892  -2.028  1.00  0.00           H  
HETATM  121  H55 UNL     1      -4.835   3.305  -3.239  1.00  0.00           H  
HETATM  122  H56 UNL     1      -7.492   5.398   0.683  1.00  0.00           H  
HETATM  123  H57 UNL     1      -8.928   5.148  -0.799  1.00  0.00           H  
HETATM  124  H58 UNL     1      -8.685   3.190   1.421  1.00  0.00           H  
HETATM  125  H59 UNL     1      -6.391   4.463   2.258  1.00  0.00           H  
HETATM  126  H60 UNL     1      -7.690   1.727  -0.219  1.00  0.00           H  
HETATM  127  H61 UNL     1      -6.621   1.264   2.390  1.00  0.00           H  
HETATM  128  H62 UNL     1      -1.888   1.832  -2.305  1.00  0.00           H  
HETATM  129  H63 UNL     1      -0.885   3.002  -1.426  1.00  0.00           H  
HETATM  130  H64 UNL     1      -0.212   2.113  -2.855  1.00  0.00           H  
HETATM  131  H65 UNL     1      -1.091  -1.061  -0.620  1.00  0.00           H  
HETATM  132  H66 UNL     1      -2.272   0.012  -1.541  1.00  0.00           H  
HETATM  133  H67 UNL     1      -0.929  -0.694  -2.414  1.00  0.00           H  
HETATM  134  H68 UNL     1       1.358   1.116  -2.207  1.00  0.00           H  
HETATM  135  H69 UNL     1       1.279  -1.132  -2.397  1.00  0.00           H  
HETATM  136  H70 UNL     1       0.875  -1.492  -0.692  1.00  0.00           H  
HETATM  137  H71 UNL     1       3.199  -2.001  -1.773  1.00  0.00           H  
HETATM  138  H72 UNL     1       3.114  -1.672  -0.063  1.00  0.00           H  
HETATM  139  H73 UNL     1       3.416   0.821  -3.250  1.00  0.00           H  
HETATM  140  H74 UNL     1       3.799  -0.972  -3.256  1.00  0.00           H  
HETATM  141  H75 UNL     1       5.069   0.256  -3.122  1.00  0.00           H  
HETATM  142  H76 UNL     1       8.049   1.656  -1.173  1.00  0.00           H  
HETATM  143  H77 UNL     1       7.330  -0.535  -3.026  1.00  0.00           H  
HETATM  144  H78 UNL     1       8.379   0.818  -3.209  1.00  0.00           H  
CONECT    1    2   67   68   69
CONECT    2    3    4   66
CONECT    3   70   71   72
CONECT    4    5   73   74
CONECT    5    6   75   76
CONECT    6    7   10   65
CONECT    7    8    8    9
CONECT    9   77
CONECT   10   11   78   79
CONECT   11   12   80   81
CONECT   12   13   14   63
CONECT   13   82   83   84
CONECT   14   15   15   65
CONECT   15   16   85
CONECT   16   17   86   87
CONECT   17   18   63   88
CONECT   18   19   20   60
CONECT   19   89   90   91
CONECT   20   21   92   93
CONECT   21   22   94   95
CONECT   22   23   57   96
CONECT   23   24
CONECT   24   25   44   97
CONECT   25   26
CONECT   26   27   29   98
CONECT   27   28   99  100
CONECT   28  101
CONECT   29   30   31  102
CONECT   30  103
CONECT   31   32   44  104
CONECT   32   33
CONECT   33   34   42  105
CONECT   34   35
CONECT   35   36   38  106
CONECT   36   37  107  108
CONECT   37  109
CONECT   38   39   40  110
CONECT   39  111
CONECT   40   41   42  112
CONECT   41  113
CONECT   42   43  114
CONECT   43  115
CONECT   44   45  116
CONECT   45   46
CONECT   46   47   55  117
CONECT   47   48
CONECT   48   49   51  118
CONECT   49   50  119  120
CONECT   50  121
CONECT   51   52   53  122
CONECT   52  123
CONECT   53   54   55  124
CONECT   54  125
CONECT   55   56  126
CONECT   56  127
CONECT   57   58   59   60
CONECT   58  128  129  130
CONECT   59  131  132  133
CONECT   60   61  134
CONECT   61   62  135  136
CONECT   62   63  137  138
CONECT   63   64
CONECT   64  139  140  141
CONECT   65   66  142
CONECT   66  143  144
END
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SMILES for HMDB0039406 (Arvensoside D)

CC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(OC6OC(CO)C(O)C(OC7OC(CO)C(O)C(O)C7O)C6OC6OC(CO)C(O)C(O)C6O)C(C)(C)C5CCC34C)C2C1)C(O)=O
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INCHI for HMDB0039406 (Arvensoside D)

InChI=1S/C48H78O18/c1-43(2)14-16-48(42(59)60)17-15-46(6)22(23(48)18-43)8-9-28-45(5)12-11-29(44(3,4)27(45)10-13-47(28,46)7)64-41-38(66-40-36(58)34(56)31(53)25(20-50)62-40)37(32(54)26(21-51)63-41)65-39-35(57)33(55)30(52)24(19-49)61-39/h8,23-41,49-58H,9-21H2,1-7H3,(H,59,60)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Arvensoside aHMDB
Calenduloside CHMDB
10-{[5-hydroxy-6-(hydroxymethyl)-3,4-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})oxan-2-yl]oxy}-2,2,6a,6b,9,9,12a-heptamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylateGenerator
Chemical FormulaC48H78O18
Average Molecular Weight943.1221
Monoisotopic Molecular Weight942.518815692
IUPAC Name10-{[5-hydroxy-6-(hydroxymethyl)-3,4-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})oxan-2-yl]oxy}-2,2,6a,6b,9,9,12a-heptamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid
Traditional Name10-{[5-hydroxy-6-(hydroxymethyl)-3,4-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})oxan-2-yl]oxy}-2,2,6a,6b,9,9,12a-heptamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid
CAS Registry Number58231-97-3
SMILES
CC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(OC6OC(CO)C(O)C(OC7OC(CO)C(O)C(O)C7O)C6OC6OC(CO)C(O)C(O)C6O)C(C)(C)C5CCC34C)C2C1)C(O)=O
InChI Identifier
InChI=1S/C48H78O18/c1-43(2)14-16-48(42(59)60)17-15-46(6)22(23(48)18-43)8-9-28-45(5)12-11-29(44(3,4)27(45)10-13-47(28,46)7)64-41-38(66-40-36(58)34(56)31(53)25(20-50)62-40)37(32(54)26(21-51)63-41)65-39-35(57)33(55)30(52)24(19-49)61-39/h8,23-41,49-58H,9-21H2,1-7H3,(H,59,60)
InChI KeyOGKRHYLZKFTGGO-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
  • Oligosaccharide
  • Fatty acyl glycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Oxane
  • Fatty acyl
  • Secondary alcohol
  • Polyol
  • Acetal
  • Oxacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Primary alcohol
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point226 - 228 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.022 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.28 g/LALOGPS
logP1.86ALOGPS
logP1.28ChemAxon
logS-3.5ALOGPS
pKa (Strongest Acidic)4.74ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area294.98 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity230.86 m³·mol⁻¹ChemAxon
Polarizability100.55 ųChemAxon
Number of Rings8ChemAxon
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]-333.09230932474
DeepCCS[M+Na]+306.8730932474
AllCCS[M+H]+299.932859911
AllCCS[M+H-H2O]+300.132859911
AllCCS[M+NH4]+299.732859911
AllCCS[M+Na]+299.732859911
AllCCS[M-H]-249.032859911
AllCCS[M+Na-2H]-255.232859911
AllCCS[M+HCOO]-262.132859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 10V, Positive-QTOFsplash10-08j0-0000601904-826f1bab8f384aef60fd2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 20V, Positive-QTOFsplash10-0cdr-0001904700-dbaf22189bddb26ad8e12015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 40V, Positive-QTOFsplash10-0cdi-0104907500-85e9d2d258712169190c2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 10V, Negative-QTOFsplash10-072l-0300903838-e4b256536c866b81392f2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 20V, Negative-QTOFsplash10-0bvi-0301912612-cfe7cdc6a0db4236a2d52015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 40V, Negative-QTOFsplash10-0a6r-1500903000-7107bd97e9c6a401915b2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 10V, Positive-QTOFsplash10-002f-0001100219-1bd255802fcfa88802a72021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 20V, Positive-QTOFsplash10-0006-0428303519-eed925ddac1f9d5e6b242021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 40V, Positive-QTOFsplash10-007c-5831003952-c06b855f974ce3b35b5e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 10V, Negative-QTOFsplash10-0006-0000000019-c639e953f3c0cabe9e5e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 20V, Negative-QTOFsplash10-05mo-6200100193-b5f1d0af72bea77a21422021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Arvensoside D 40V, Negative-QTOFsplash10-0aor-9100017230-780c4eb6b2f4037687b32021-09-24Wishart 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 IDFDB018981
KNApSAcK IDC00055340
Chemspider ID383918
KEGG Compound IDC08923
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound434120
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1876961
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.