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Showing metabocard for Ginsenoside Rd (HMDB0035778)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 20:47:59 UTC
Update Date2022-03-07 02:54:37 UTC
HMDB IDHMDB0035778
Secondary Accession Numbers
  • HMDB35778
Metabolite Identification
Common NameGinsenoside Rd
DescriptionGinsenoside Rd, also known as gypenoside VIII, belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Ginsenoside Rd is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563862770
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035778 (Ginsenoside Rd)


  Mrv0541 02241215122D          

 66 72  0  0  0  0            999 V2000
    5.1432    3.2588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8875    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0818    2.3019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8260    1.5180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6112    1.2637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8717   -1.1675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7864   -0.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5702   -0.6009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0557    0.0674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5716    0.7343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7864    0.4785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0728    0.8910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3579    0.4771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3579   -0.3465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0714   -0.7590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0714    1.7146    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0714   -1.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3565   -1.9979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6428   -1.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6428   -0.7590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6428    0.0660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5018    2.8175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9505    3.4306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2048    4.2144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.9295   -2.8215    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.3582   -0.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.7868   -4.4730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3582   -1.9965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6030   -2.6276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0708   -1.9965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3118    3.9381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9250    4.4922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7545    5.2980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4719    2.2824    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0851    2.8353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9147    3.6411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5266    4.1938    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.4840   -1.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1 23  2  0  0  0  0
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  4 10  1  0  0  0  0
  4 54  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  1  0  0  0  0
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 63 64  1  0  0  0  0
M  END
Download

3D MOL for HMDB0035778 (Ginsenoside Rd)

HMDB0253000
     RDKit          3D
Gypenoside VIII
148154  0  0  0  0  0  0  0  0999 V2000
   -7.9623    1.9762    4.4063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6332    1.7718    3.1080 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1047    1.5393    3.0823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9478    1.7938    1.9636 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5125    2.0224    1.9803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5898    0.9928    1.4940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5998    0.4770    0.1232 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3978    1.5911   -0.9347 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7130   -0.1242   -0.2913 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4427   -1.1071    0.0322 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3368   -2.0886   -1.0126 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5569   -1.5916   -2.2555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7841   -2.8032   -3.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6924   -3.6404   -3.2078 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6532   -0.6152   -2.4377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6186   -1.1859   -3.2970 O   0  0  0  0  0  0  0  0  0  0  0  0
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  -10.7678   -0.3347   -1.3293 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.5303   -2.2387   -0.0548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4279   -0.4699   -0.1449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4597   -1.6893    0.7412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0779   -2.3021    0.4136 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1594    0.0137   -0.8236 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.6515    1.5341   -0.4201 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.6597    1.1994    1.0305 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5394    2.2616    1.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3036    2.0816    2.5006 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1987    3.1559    2.6947 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5197    2.3936    0.0859 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1570    3.6282    0.2084 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8849    2.3328   -1.2849 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1860    3.5056   -1.5744 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9078    1.1719   -1.2716 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6720    0.0376   -0.9655 O   0  0  0  0  0  0  0  0  0  0  0  0
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    7.0469   -2.0673   -1.4678 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8142   -2.8936   -0.7189 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.7327   -1.6304    1.3536 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3044   -2.8220   -0.9801 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9754   -1.9816   -0.1181 O   0  0  0  0  0  0  0  0  0  0  0  0
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    9.2878   -3.4287   -3.2362 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7980   -1.1254   -2.7448 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4639   -1.2531   -4.1140 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7338    1.2706    0.7211 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6458    0.8763    1.9098 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0070    2.4861    1.1980 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8941    0.0432    0.4668 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0561   -0.3639    1.6546 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1760   -1.4928    1.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8172   -1.2164    0.1584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8124   -2.5586   -0.6182 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7021    1.8382    5.2367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1943    1.1799    4.5626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4684    2.9630    4.4664 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5838    1.8113    4.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3674    0.4933    2.8811 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5885    2.1589    2.2869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4767    1.6617    1.0354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2501    3.0664    1.5804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2246    2.1771    3.0769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5488    1.3853    1.7308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6506    0.1612    2.2761 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.4143    2.5900   -0.5172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3125    1.6384   -1.6362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2462   -1.7438    0.9197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6099   -1.1304   -2.6719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7097   -3.3347   -2.8038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0202   -2.4410   -4.1935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1431   -3.3562   -4.0091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3087    0.2892   -3.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1631   -0.5114   -3.7383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1443    0.8841   -1.0468 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0591    0.5158   -1.7909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3417   -0.5361    0.9724 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0035778 (Ginsenoside Rd)


  Mrv0541 02241215122D          

 66 72  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0035778

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C48H82O18/c1-22(2)10-9-14-48(8,66-42-39(60)36(57)33(54)26(20-50)62-42)23-11-16-47(7)31(23)24(52)18-29-45(5)15-13-30(44(3,4)28(45)12-17-46(29,47)6)64-43-40(37(58)34(55)27(21-51)63-43)65-41-38(59)35(56)32(53)25(19-49)61-41/h10,23-43,49-60H,9,11-21H2,1-8H3

> <INCHI_KEY>
RLDVZILFNVRJTL-UHFFFAOYSA-N

> <FORMULA>
C48H82O18

> <MOLECULAR_WEIGHT>
947.1539

> <EXACT_MASS>
946.55011582

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
104.11205179369155

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.73

> <JCHEM_LOGP>
0.21943086799999983

> <ALOGPS_LOGS>
-3.39

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.31326468896987

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.847210111164957

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6483775957536517

> <JCHEM_POLAR_SURFACE_AREA>
298.14

> <JCHEM_REFRACTIVITY>
234.4758000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.90e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0035778 (Ginsenoside Rd)

HMDB0253000
     RDKit          3D
Gypenoside VIII
148154  0  0  0  0  0  0  0  0999 V2000
   -7.9623    1.9762    4.4063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6332    1.7718    3.1080 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1047    1.5393    3.0823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9478    1.7938    1.9636 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5125    2.0224    1.9803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5898    0.9928    1.4940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5998    0.4770    0.1232 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3978    1.5911   -0.9347 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7130   -0.1242   -0.2913 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4427   -1.1071    0.0322 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3368   -2.0886   -1.0126 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5569   -1.5916   -2.2555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7841   -2.8032   -3.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6924   -3.6404   -3.2078 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6532   -0.6152   -2.4377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6186   -1.1859   -3.2970 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3606   -0.2003   -1.1909 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7678   -0.3347   -1.3293 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9735   -0.9409    0.0399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5303   -2.2387   -0.0548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4279   -0.4699   -0.1449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4597   -1.6893    0.7412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0779   -2.3021    0.4136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2252   -1.0918    0.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3200   -0.8336    2.1258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0558   -0.0577   -0.1712 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3730    1.1458    0.1857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8556    2.3986   -0.0142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0116    1.1886   -0.5746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3528   -0.1117   -0.7332 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1594    0.0137   -0.8236 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6867   -1.1858   -1.6456 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5001    1.1941   -1.7108 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9812    1.4577   -1.7527 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6515    1.5341   -0.4201 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7833    0.7339   -0.2919 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9522    1.4208   -0.1275 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6597    1.1994    1.0305 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5394    2.2616    1.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3036    2.0816    2.5006 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1987    3.1559    2.6947 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5197    2.3936    0.0859 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1570    3.6282    0.2084 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8849    2.3328   -1.2849 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1860    3.5056   -1.5744 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9078    1.1719   -1.2716 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6720    0.0376   -0.9655 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5300   -0.9261   -1.9776 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0469   -2.0673   -1.4678 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8142   -2.8936   -0.7189 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5292   -2.8516    0.7758 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7327   -1.6304    1.3536 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3044   -2.8220   -0.9801 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9754   -1.9816   -0.1181 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.5809   -2.3425   -2.3934 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2878   -3.4287   -3.2362 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7980   -1.1254   -2.7448 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4639   -1.2531   -4.1140 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7338    1.2706    0.7211 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6458    0.8763    1.9098 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0070    2.4861    1.1980 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8941    0.0432    0.4668 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0561   -0.3639    1.6546 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1760   -1.4928    1.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8172   -1.2164    0.1584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8124   -2.5586   -0.6182 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7021    1.8382    5.2367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1943    1.1799    4.5626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4684    2.9630    4.4664 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5838    1.8113    4.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3674    0.4933    2.8811 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5885    2.1589    2.2869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4767    1.6617    1.0354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2501    3.0664    1.5804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2246    2.1771    3.0769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5488    1.3853    1.7308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6506    0.1612    2.2761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6103    1.3475   -1.6664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4143    2.5900   -0.5172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3125    1.6384   -1.6362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2462   -1.7438    0.9197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6099   -1.1304   -2.6719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7097   -3.3347   -2.8038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0202   -2.4410   -4.1935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1431   -3.3562   -4.0091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3087    0.2892   -3.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1631   -0.5114   -3.7383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1443    0.8841   -1.0468 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0591    0.5158   -1.7909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3417   -0.5361    0.9724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7984   -2.9261    0.0281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7359   -0.8922   -1.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6350   -1.5421    1.7867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1517   -2.4935    0.4039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1561   -2.6210   -0.6234 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9866   -3.1011    1.1731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2240   -0.3477    2.4818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4951   -0.3034    2.5877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3238   -1.8505    2.6400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6734   -0.3158   -1.2282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0052    1.1624    1.2671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4846    3.0788    0.5933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4467    2.0128   -0.1192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2807    1.5921   -1.6009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5906   -0.4824   -1.7873 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9238   -1.6058   -2.2968 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2281   -1.9001   -0.9897 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4996   -0.8619   -2.3638 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2173    0.8795   -2.7614 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9654    2.1100   -1.5335 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0707    2.4901   -2.2239 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5389    0.8252   -2.4753 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0618    2.5908   -0.2748 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7264    2.5363   -0.1431 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9546    3.2241    1.2265 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5868    2.1551    3.3465 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8924    1.1666    2.5040 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0765    2.9762    2.2783 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2788    1.5649    0.1473 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5413    3.8334   -0.6991 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7108    2.1506   -2.0127 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3248    3.8004   -2.5114 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3729    1.0503   -2.2382 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7859   -0.5361   -2.7303 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5266   -3.9496   -1.0169 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4675   -3.1758    0.9399 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.8888    3.2129    0.3571 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.8991   -2.3211    1.0024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3716   -3.2767    0.0427 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.2169   -3.0261   -0.5752 H   0  0  0  0  0  0  0  0  0  0  0  0
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 45122  1  0
 46123  1  0
 48124  1  0
 50125  1  0
 51126  1  0
 51127  1  0
 52128  1  0
 53129  1  0
 54130  1  0
 55131  1  0
 56132  1  0
 57133  1  0
 58134  1  0
 60135  1  0
 60136  1  0
 60137  1  0
 61138  1  0
 61139  1  0
 61140  1  0
 62141  1  0
 63142  1  0
 63143  1  0
 64144  1  0
 64145  1  0
 66146  1  0
 66147  1  0
 66148  1  0
M  END
Download

PDB for HMDB0035778 (Ginsenoside Rd)

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       9.601   6.083   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.123   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.619   4.297   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.142   2.834   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.608   2.359   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.361  -2.179   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.201  -0.649   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.664  -1.122   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.571   0.126   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.667   1.371   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.201   0.893   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.869   1.663   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.535   0.891   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.535  -0.647   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.867  -1.417   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.867   3.201   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       3.867  -2.957   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.532  -3.729   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.200  -2.959   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.200  -1.417   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.200   0.123   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      12.137   5.259   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.108   6.404   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.582   7.867   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.135  -0.647   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.469  -1.420   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.467  -2.957   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -2.801  -3.729   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -4.134  -2.959   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -4.134  -1.417   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -5.468  -0.647   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -5.468   0.891   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -6.803   1.661   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -5.468  -8.347   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -6.801  -7.577   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -8.135  -8.347   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -8.135  -9.890   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0     -12.137  -6.034   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0     -10.802  -5.267   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -9.467  -6.037   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      -8.138  -5.269   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      -6.803  -6.039   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      -5.468  -5.267   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      -5.468  -3.729   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      -6.803  -2.959   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -6.801  -1.420   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0      -8.135  -0.649   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0      -9.470  -7.577   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0     -10.802  -8.350   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      -8.135  -3.727   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      -1.126  -4.905   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -0.132  -3.727   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       0.853  -4.907   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0       5.676   3.311   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0       5.358   4.815   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0       6.500   5.847   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0       6.182   7.351   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       7.327   8.385   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0       7.008   9.890   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       2.748   4.260   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0       3.892   5.293   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       3.574   6.797   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       4.716   7.828   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0       4.395   9.335   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       2.109   7.274   0.000  0.00  0.00           O+0
HETATM   66  C   UNK     0       4.637  -2.752   0.000  0.00  0.00           C+0
CONECT    1    2   23                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10   54                                             
CONECT    5    4                                                            
CONECT    6    7                                                            
CONECT    7    6    8   11   15                                             
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    4    9   11                                                  
CONECT   11    7   10   12                                                  
CONECT   12   11   13   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   20                                                  
CONECT   15    7   14   17   66                                             
CONECT   16   12                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   52                                                  
CONECT   20   14   19   21   25                                             
CONECT   21   20                                                            
CONECT   22   23                                                            
CONECT   23    1   22   24                                                  
CONECT   24   23                                                            
CONECT   25   20   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   52                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   44                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32   46                                                  
CONECT   32   31   33                                                       
CONECT   33   32                                                            
CONECT   34   35                                                            
CONECT   35   34   36   42                                                  
CONECT   36   35   37   48                                                  
CONECT   37   36                                                            
CONECT   38   39                                                            
CONECT   39   38   40                                                       
CONECT   40   39   41   48                                                  
CONECT   41   40   42                                                       
CONECT   42   35   41   43                                                  
CONECT   43   42   44                                                       
CONECT   44   29   43   45                                                  
CONECT   45   44   46   50                                                  
CONECT   46   31   45   47                                                  
CONECT   47   46                                                            
CONECT   48   36   40   49                                                  
CONECT   49   48                                                            
CONECT   50   45                                                            
CONECT   51   52                                                            
CONECT   52   19   27   51   53                                             
CONECT   53   52                                                            
CONECT   54    4   55                                                       
CONECT   55   54   56   61                                                  
CONECT   56   55   57                                                       
CONECT   57   56   58   63                                                  
CONECT   58   57   59                                                       
CONECT   59   58                                                            
CONECT   60   61                                                            
CONECT   61   55   60   62                                                  
CONECT   62   61   63   65                                                  
CONECT   63   57   62   64                                                  
CONECT   64   63                                                            
CONECT   65   62                                                            
CONECT   66   15                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  144    0
END
Download

3D PDB for HMDB0035778 (Ginsenoside Rd)

COMPND    HMDB0253000
HETATM    1  C1  UNL     1      -7.962   1.976   4.406  1.00  0.00           C  
HETATM    2  C2  UNL     1      -8.633   1.772   3.108  1.00  0.00           C  
HETATM    3  C3  UNL     1     -10.105   1.539   3.082  1.00  0.00           C  
HETATM    4  C4  UNL     1      -7.948   1.794   1.964  1.00  0.00           C  
HETATM    5  C5  UNL     1      -6.512   2.022   1.980  1.00  0.00           C  
HETATM    6  C6  UNL     1      -5.590   0.993   1.494  1.00  0.00           C  
HETATM    7  C7  UNL     1      -5.600   0.477   0.123  1.00  0.00           C  
HETATM    8  C8  UNL     1      -5.398   1.591  -0.935  1.00  0.00           C  
HETATM    9  O1  UNL     1      -6.713  -0.124  -0.291  1.00  0.00           O  
HETATM   10  C9  UNL     1      -7.443  -1.107   0.032  1.00  0.00           C  
HETATM   11  O2  UNL     1      -7.337  -2.089  -1.013  1.00  0.00           O  
HETATM   12  C10 UNL     1      -7.557  -1.592  -2.255  1.00  0.00           C  
HETATM   13  C11 UNL     1      -7.784  -2.803  -3.177  1.00  0.00           C  
HETATM   14  O3  UNL     1      -6.692  -3.640  -3.208  1.00  0.00           O  
HETATM   15  C12 UNL     1      -8.653  -0.615  -2.438  1.00  0.00           C  
HETATM   16  O4  UNL     1      -9.619  -1.186  -3.297  1.00  0.00           O  
HETATM   17  C13 UNL     1      -9.361  -0.200  -1.191  1.00  0.00           C  
HETATM   18  O5  UNL     1     -10.768  -0.335  -1.329  1.00  0.00           O  
HETATM   19  C14 UNL     1      -8.974  -0.941   0.040  1.00  0.00           C  
HETATM   20  O6  UNL     1      -9.530  -2.239  -0.055  1.00  0.00           O  
HETATM   21  C15 UNL     1      -4.428  -0.470  -0.145  1.00  0.00           C  
HETATM   22  C16 UNL     1      -4.460  -1.689   0.741  1.00  0.00           C  
HETATM   23  C17 UNL     1      -3.078  -2.302   0.414  1.00  0.00           C  
HETATM   24  C18 UNL     1      -2.225  -1.092   0.650  1.00  0.00           C  
HETATM   25  C19 UNL     1      -2.320  -0.834   2.126  1.00  0.00           C  
HETATM   26  C20 UNL     1      -3.056  -0.058  -0.171  1.00  0.00           C  
HETATM   27  C21 UNL     1      -2.373   1.146   0.186  1.00  0.00           C  
HETATM   28  O7  UNL     1      -2.856   2.399  -0.014  1.00  0.00           O  
HETATM   29  C22 UNL     1      -1.012   1.189  -0.575  1.00  0.00           C  
HETATM   30  C23 UNL     1      -0.353  -0.112  -0.733  1.00  0.00           C  
HETATM   31  C24 UNL     1       1.159   0.014  -0.824  1.00  0.00           C  
HETATM   32  C25 UNL     1       1.687  -1.186  -1.646  1.00  0.00           C  
HETATM   33  C26 UNL     1       1.500   1.194  -1.711  1.00  0.00           C  
HETATM   34  C27 UNL     1       2.981   1.458  -1.753  1.00  0.00           C  
HETATM   35  C28 UNL     1       3.652   1.534  -0.420  1.00  0.00           C  
HETATM   36  O8  UNL     1       4.783   0.734  -0.292  1.00  0.00           O  
HETATM   37  C29 UNL     1       5.952   1.421  -0.127  1.00  0.00           C  
HETATM   38  O9  UNL     1       6.660   1.199   1.031  1.00  0.00           O  
HETATM   39  C30 UNL     1       7.539   2.262   1.210  1.00  0.00           C  
HETATM   40  C31 UNL     1       8.304   2.082   2.501  1.00  0.00           C  
HETATM   41  O10 UNL     1       9.199   3.156   2.695  1.00  0.00           O  
HETATM   42  C32 UNL     1       8.520   2.394   0.086  1.00  0.00           C  
HETATM   43  O11 UNL     1       9.157   3.628   0.208  1.00  0.00           O  
HETATM   44  C33 UNL     1       7.885   2.333  -1.285  1.00  0.00           C  
HETATM   45  O12 UNL     1       7.186   3.506  -1.574  1.00  0.00           O  
HETATM   46  C34 UNL     1       6.908   1.172  -1.272  1.00  0.00           C  
HETATM   47  O13 UNL     1       7.672   0.038  -0.965  1.00  0.00           O  
HETATM   48  C35 UNL     1       7.530  -0.926  -1.978  1.00  0.00           C  
HETATM   49  O14 UNL     1       7.047  -2.067  -1.468  1.00  0.00           O  
HETATM   50  C36 UNL     1       7.814  -2.894  -0.719  1.00  0.00           C  
HETATM   51  C37 UNL     1       7.529  -2.852   0.776  1.00  0.00           C  
HETATM   52  O15 UNL     1       7.733  -1.630   1.354  1.00  0.00           O  
HETATM   53  C38 UNL     1       9.304  -2.822  -0.980  1.00  0.00           C  
HETATM   54  O16 UNL     1       9.975  -1.982  -0.118  1.00  0.00           O  
HETATM   55  C39 UNL     1       9.581  -2.342  -2.393  1.00  0.00           C  
HETATM   56  O17 UNL     1       9.288  -3.429  -3.236  1.00  0.00           O  
HETATM   57  C40 UNL     1       8.798  -1.125  -2.745  1.00  0.00           C  
HETATM   58  O18 UNL     1       8.464  -1.253  -4.114  1.00  0.00           O  
HETATM   59  C41 UNL     1       2.734   1.271   0.721  1.00  0.00           C  
HETATM   60  C42 UNL     1       3.646   0.876   1.910  1.00  0.00           C  
HETATM   61  C43 UNL     1       2.007   2.486   1.198  1.00  0.00           C  
HETATM   62  C44 UNL     1       1.894   0.043   0.467  1.00  0.00           C  
HETATM   63  C45 UNL     1       1.056  -0.364   1.655  1.00  0.00           C  
HETATM   64  C46 UNL     1       0.176  -1.493   1.286  1.00  0.00           C  
HETATM   65  C47 UNL     1      -0.817  -1.216   0.158  1.00  0.00           C  
HETATM   66  C48 UNL     1      -0.812  -2.559  -0.618  1.00  0.00           C  
HETATM   67  H1  UNL     1      -8.702   1.838   5.237  1.00  0.00           H  
HETATM   68  H2  UNL     1      -7.194   1.180   4.563  1.00  0.00           H  
HETATM   69  H3  UNL     1      -7.468   2.963   4.466  1.00  0.00           H  
HETATM   70  H4  UNL     1     -10.584   1.811   4.041  1.00  0.00           H  
HETATM   71  H5  UNL     1     -10.367   0.493   2.881  1.00  0.00           H  
HETATM   72  H6  UNL     1     -10.588   2.159   2.287  1.00  0.00           H  
HETATM   73  H7  UNL     1      -8.477   1.662   1.035  1.00  0.00           H  
HETATM   74  H8  UNL     1      -6.250   3.066   1.580  1.00  0.00           H  
HETATM   75  H9  UNL     1      -6.225   2.177   3.077  1.00  0.00           H  
HETATM   76  H10 UNL     1      -4.549   1.385   1.731  1.00  0.00           H  
HETATM   77  H11 UNL     1      -5.651   0.161   2.276  1.00  0.00           H  
HETATM   78  H12 UNL     1      -4.610   1.347  -1.666  1.00  0.00           H  
HETATM   79  H13 UNL     1      -5.414   2.590  -0.517  1.00  0.00           H  
HETATM   80  H14 UNL     1      -6.313   1.638  -1.636  1.00  0.00           H  
HETATM   81  H15 UNL     1      -7.246  -1.744   0.920  1.00  0.00           H  
HETATM   82  H16 UNL     1      -6.610  -1.130  -2.672  1.00  0.00           H  
HETATM   83  H17 UNL     1      -8.710  -3.335  -2.804  1.00  0.00           H  
HETATM   84  H18 UNL     1      -8.020  -2.441  -4.193  1.00  0.00           H  
HETATM   85  H19 UNL     1      -6.143  -3.356  -4.009  1.00  0.00           H  
HETATM   86  H20 UNL     1      -8.309   0.289  -3.029  1.00  0.00           H  
HETATM   87  H21 UNL     1     -10.163  -0.511  -3.738  1.00  0.00           H  
HETATM   88  H22 UNL     1      -9.144   0.884  -1.047  1.00  0.00           H  
HETATM   89  H23 UNL     1     -11.059   0.516  -1.791  1.00  0.00           H  
HETATM   90  H24 UNL     1      -9.342  -0.536   0.972  1.00  0.00           H  
HETATM   91  H25 UNL     1      -8.798  -2.926   0.028  1.00  0.00           H  
HETATM   92  H26 UNL     1      -4.736  -0.892  -1.142  1.00  0.00           H  
HETATM   93  H27 UNL     1      -4.635  -1.542   1.787  1.00  0.00           H  
HETATM   94  H28 UNL     1      -5.152  -2.493   0.404  1.00  0.00           H  
HETATM   95  H29 UNL     1      -3.156  -2.621  -0.623  1.00  0.00           H  
HETATM   96  H30 UNL     1      -2.987  -3.101   1.173  1.00  0.00           H  
HETATM   97  H31 UNL     1      -3.224  -0.348   2.482  1.00  0.00           H  
HETATM   98  H32 UNL     1      -1.495  -0.303   2.588  1.00  0.00           H  
HETATM   99  H33 UNL     1      -2.324  -1.851   2.640  1.00  0.00           H  
HETATM  100  H34 UNL     1      -2.673  -0.316  -1.228  1.00  0.00           H  
HETATM  101  H35 UNL     1      -2.005   1.162   1.267  1.00  0.00           H  
HETATM  102  H36 UNL     1      -2.485   3.079   0.593  1.00  0.00           H  
HETATM  103  H37 UNL     1      -0.447   2.013  -0.119  1.00  0.00           H  
HETATM  104  H38 UNL     1      -1.281   1.592  -1.601  1.00  0.00           H  
HETATM  105  H39 UNL     1      -0.591  -0.482  -1.787  1.00  0.00           H  
HETATM  106  H40 UNL     1       0.924  -1.606  -2.297  1.00  0.00           H  
HETATM  107  H41 UNL     1       2.228  -1.900  -0.990  1.00  0.00           H  
HETATM  108  H42 UNL     1       2.500  -0.862  -2.364  1.00  0.00           H  
HETATM  109  H43 UNL     1       1.217   0.879  -2.761  1.00  0.00           H  
HETATM  110  H44 UNL     1       0.965   2.110  -1.534  1.00  0.00           H  
HETATM  111  H45 UNL     1       3.071   2.490  -2.224  1.00  0.00           H  
HETATM  112  H46 UNL     1       3.539   0.825  -2.475  1.00  0.00           H  
HETATM  113  H47 UNL     1       4.062   2.591  -0.275  1.00  0.00           H  
HETATM  114  H48 UNL     1       5.726   2.536  -0.143  1.00  0.00           H  
HETATM  115  H49 UNL     1       6.955   3.224   1.226  1.00  0.00           H  
HETATM  116  H50 UNL     1       7.587   2.155   3.347  1.00  0.00           H  
HETATM  117  H51 UNL     1       8.892   1.167   2.504  1.00  0.00           H  
HETATM  118  H52 UNL     1      10.076   2.976   2.278  1.00  0.00           H  
HETATM  119  H53 UNL     1       9.279   1.565   0.147  1.00  0.00           H  
HETATM  120  H54 UNL     1       9.541   3.833  -0.699  1.00  0.00           H  
HETATM  121  H55 UNL     1       8.711   2.151  -2.013  1.00  0.00           H  
HETATM  122  H56 UNL     1       7.325   3.800  -2.511  1.00  0.00           H  
HETATM  123  H57 UNL     1       6.373   1.050  -2.238  1.00  0.00           H  
HETATM  124  H58 UNL     1       6.786  -0.536  -2.730  1.00  0.00           H  
HETATM  125  H59 UNL     1       7.527  -3.950  -1.017  1.00  0.00           H  
HETATM  126  H60 UNL     1       6.468  -3.176   0.940  1.00  0.00           H  
HETATM  127  H61 UNL     1       8.170  -3.585   1.307  1.00  0.00           H  
HETATM  128  H62 UNL     1       8.545  -1.620   1.947  1.00  0.00           H  
HETATM  129  H63 UNL     1       9.767  -3.829  -0.897  1.00  0.00           H  
HETATM  130  H64 UNL     1      10.637  -1.383  -0.566  1.00  0.00           H  
HETATM  131  H65 UNL     1      10.675  -2.164  -2.464  1.00  0.00           H  
HETATM  132  H66 UNL     1       8.828  -4.152  -2.768  1.00  0.00           H  
HETATM  133  H67 UNL     1       9.439  -0.198  -2.715  1.00  0.00           H  
HETATM  134  H68 UNL     1       7.564  -1.652  -4.204  1.00  0.00           H  
HETATM  135  H69 UNL     1       2.987   0.715   2.782  1.00  0.00           H  
HETATM  136  H70 UNL     1       4.269   1.791   2.081  1.00  0.00           H  
HETATM  137  H71 UNL     1       4.268   0.046   1.605  1.00  0.00           H  
HETATM  138  H72 UNL     1       2.645   3.065   1.939  1.00  0.00           H  
HETATM  139  H73 UNL     1       1.054   2.350   1.682  1.00  0.00           H  
HETATM  140  H74 UNL     1       1.889   3.213   0.357  1.00  0.00           H  
HETATM  141  H75 UNL     1       2.700  -0.776   0.434  1.00  0.00           H  
HETATM  142  H76 UNL     1       0.631   0.486   2.191  1.00  0.00           H  
HETATM  143  H77 UNL     1       1.779  -0.810   2.415  1.00  0.00           H  
HETATM  144  H78 UNL     1      -0.355  -1.949   2.173  1.00  0.00           H  
HETATM  145  H79 UNL     1       0.899  -2.321   1.002  1.00  0.00           H  
HETATM  146  H80 UNL     1      -1.372  -3.277   0.043  1.00  0.00           H  
HETATM  147  H81 UNL     1      -1.216  -2.455  -1.620  1.00  0.00           H  
HETATM  148  H82 UNL     1       0.217  -3.026  -0.575  1.00  0.00           H  
CONECT    1    2   67   68   69
CONECT    2    3    4    4
CONECT    3   70   71   72
CONECT    4    5   73
CONECT    5    6   74   75
CONECT    6    7   76   77
CONECT    7    8    9   21
CONECT    8   78   79   80
CONECT    9   10
CONECT   10   11   19   81
CONECT   11   12
CONECT   12   13   15   82
CONECT   13   14   83   84
CONECT   14   85
CONECT   15   16   17   86
CONECT   16   87
CONECT   17   18   19   88
CONECT   18   89
CONECT   19   20   90
CONECT   20   91
CONECT   21   22   26   92
CONECT   22   23   93   94
CONECT   23   24   95   96
CONECT   24   25   26   65
CONECT   25   97   98   99
CONECT   26   27  100
CONECT   27   28   29  101
CONECT   28  102
CONECT   29   30  103  104
CONECT   30   31   65  105
CONECT   31   32   33   62
CONECT   32  106  107  108
CONECT   33   34  109  110
CONECT   34   35  111  112
CONECT   35   36   59  113
CONECT   36   37
CONECT   37   38   46  114
CONECT   38   39
CONECT   39   40   42  115
CONECT   40   41  116  117
CONECT   41  118
CONECT   42   43   44  119
CONECT   43  120
CONECT   44   45   46  121
CONECT   45  122
CONECT   46   47  123
CONECT   47   48
CONECT   48   49   57  124
CONECT   49   50
CONECT   50   51   53  125
CONECT   51   52  126  127
CONECT   52  128
CONECT   53   54   55  129
CONECT   54  130
CONECT   55   56   57  131
CONECT   56  132
CONECT   57   58  133
CONECT   58  134
CONECT   59   60   61   62
CONECT   60  135  136  137
CONECT   61  138  139  140
CONECT   62   63  141
CONECT   63   64  142  143
CONECT   64   65  144  145
CONECT   65   66
CONECT   66  146  147  148
END
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SMILES for HMDB0035778 (Ginsenoside Rd)

CC(C)=CCCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C
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INCHI for HMDB0035778 (Ginsenoside Rd)

InChI=1S/C48H82O18/c1-22(2)10-9-14-48(8,66-42-39(60)36(57)33(54)26(20-50)62-42)23-11-16-47(7)31(23)24(52)18-29-45(5)15-13-30(44(3,4)28(45)12-17-46(29,47)6)64-43-40(37(58)34(55)27(21-51)63-43)65-41-38(59)35(56)32(53)25(19-49)61-41/h10,23-43,49-60H,9,11-21H2,1-8H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Gypenoside VIIIHMDB
Chemical FormulaC48H82O18
Average Molecular Weight947.1539
Monoisotopic Molecular Weight946.55011582
IUPAC Name2-{[2-(5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-6-methylhept-5-en-2-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Name2-{[2-(5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-6-methylhept-5-en-2-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
CAS Registry Number52705-93-8
SMILES
CC(C)=CCCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C
InChI Identifier
InChI=1S/C48H82O18/c1-22(2)10-9-14-48(8,66-42-39(60)36(57)33(54)26(20-50)62-42)23-11-16-47(7)31(23)24(52)18-29-45(5)15-13-30(44(3,4)28(45)12-17-46(29,47)6)64-43-40(37(58)34(55)27(21-51)63-43)65-41-38(59)35(56)32(53)25(19-49)61-41/h10,23-43,49-60H,9,11-21H2,1-8H3
InChI KeyRLDVZILFNVRJTL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTriterpenoids
Direct ParentTriterpenoids
Alternative ParentsNot Available
SubstituentsNot Available
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point206 - 209 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.39 g/LALOGPS
logP0.73ALOGPS
logP0.22ChemAxon
logS-3.4ALOGPS
pKa (Strongest Acidic)11.85ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area298.14 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity234.48 m³·mol⁻¹ChemAxon
Polarizability104.11 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]-329.20830932474
DeepCCS[M+Na]+303.09730932474
AllCCS[M+H]+300.332859911
AllCCS[M+H-H2O]+300.432859911
AllCCS[M+NH4]+300.232859911
AllCCS[M+Na]+300.132859911
AllCCS[M-H]-255.432859911
AllCCS[M+Na-2H]-262.232859911
AllCCS[M+HCOO]-269.632859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 10V, Positive-QTOFsplash10-0ay0-0000206905-4aaf1df86aef01ba0a422015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 20V, Positive-QTOFsplash10-0avi-0100509600-b959734813f69da3296c2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 40V, Positive-QTOFsplash10-0ab9-1300709211-79d08bbb7bd3679dd4872015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 10V, Positive-QTOFsplash10-0ay0-0000206905-4aaf1df86aef01ba0a422015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 20V, Positive-QTOFsplash10-0avi-0100509600-b959734813f69da3296c2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 40V, Positive-QTOFsplash10-0ab9-1300709211-79d08bbb7bd3679dd4872015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 10V, Positive-QTOFsplash10-0ay0-0000206905-4aaf1df86aef01ba0a422015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 20V, Positive-QTOFsplash10-0avi-0100509600-b959734813f69da3296c2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 40V, Positive-QTOFsplash10-0ab9-1300709211-79d08bbb7bd3679dd4872015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 10V, Positive-QTOFsplash10-0ay0-0000206905-4aaf1df86aef01ba0a422015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 20V, Positive-QTOFsplash10-0avi-0100509600-b959734813f69da3296c2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 40V, Positive-QTOFsplash10-0ab9-1300709211-79d08bbb7bd3679dd4872015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 10V, Negative-QTOFsplash10-00pj-0200108819-0b59ec0a79dcda5969fb2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 20V, Negative-QTOFsplash10-0g30-1400309804-95031a2eef4e88c87e662015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 40V, Negative-QTOFsplash10-076r-2600409010-2d203d659fc1bbb9db3a2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 10V, Negative-QTOFsplash10-00pj-0200108819-0b59ec0a79dcda5969fb2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 20V, Negative-QTOFsplash10-0g30-1400309804-95031a2eef4e88c87e662015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 40V, Negative-QTOFsplash10-076r-2600409010-2d203d659fc1bbb9db3a2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 10V, Negative-QTOFsplash10-00pj-0200108819-0b59ec0a79dcda5969fb2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 20V, Negative-QTOFsplash10-0g30-1400309804-95031a2eef4e88c87e662015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 40V, Negative-QTOFsplash10-076r-2600409010-2d203d659fc1bbb9db3a2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 10V, Negative-QTOFsplash10-00pj-0200108819-0b59ec0a79dcda5969fb2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 20V, Negative-QTOFsplash10-0g30-1400309804-95031a2eef4e88c87e662015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 40V, Negative-QTOFsplash10-076r-2600409010-2d203d659fc1bbb9db3a2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rd 10V, Negative-QTOFsplash10-0002-0000000029-58b0661e192a312cf3322021-09-24Wishart 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 IDFDB014525
KNApSAcK IDC00030398
Chemspider ID382453
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound432448
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.