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Showing metabocard for Ginsenoside Rs1 (HMDB0039548)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:02:20 UTC
Update Date2022-03-07 02:56:15 UTC
HMDB IDHMDB0039548
Secondary Accession Numbers
  • HMDB39548
Metabolite Identification
Common NameGinsenoside Rs1
DescriptionGinsenoside Rs1 belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Ginsenoside Rs1 is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563863395
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039548 (Ginsenoside Rs1)


  Mrv0541 05061311132D          

 78 85  0  0  0  0            999 V2000
    4.2353    1.7538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6219    1.2021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7930    0.3950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5775    0.1397    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3620   -0.1157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6227   -2.5449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5369   -1.7244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3214   -1.9797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8067   -1.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3221   -0.6448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5374   -0.8994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8231   -0.4865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1084   -0.8986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1080   -1.7236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8223   -2.1365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8294   -1.3110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8216    0.3389    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8216   -2.9611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1080   -3.3736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3929   -2.9611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3929   -2.1361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3929   -1.3111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6776    3.1126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0642    2.5608    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2797    2.8162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6779   -1.7236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.7508   -3.3736    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    7.7647    3.0064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0201    3.7909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4684    4.4043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    6.1916    0.4819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    8.0611    1.6085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    8.8272    3.9620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3789    3.3486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
  1 24  2  0  0  0  0
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M  END
Download

3D MOL for HMDB0039548 (Ginsenoside Rs1)

HMDB0039548
     RDKit          3D
Ginsenoside Rs1
170177  0  0  0  0  0  0  0  0999 V2000
    9.4167   -1.7692   -1.2922 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5471   -1.8204    0.1920 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4602   -1.1531    0.7126 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7135   -2.5630    1.0035 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8005   -2.6336    2.4071 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5898   -1.3016    3.0086 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3188   -0.7871    2.6574 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4925    0.6165    2.7337 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5764    1.3118    1.9760 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0917    1.8426    0.8351 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2925    1.5219   -0.3847 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6434    0.3291   -0.4031 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3049    0.5068   -0.6269 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4657    0.2374    0.6208 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2439    1.0987    0.4025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5431    0.8393   -0.8749 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3488    2.2335   -1.5198 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2190   -0.0510   -1.8712 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4328   -1.2374   -2.3291 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4395   -1.8717   -1.4478 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0631   -1.0332   -0.2766 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5424   -1.5839    0.9263 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1202    0.3520   -0.7169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8235    1.3669   -0.1487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1990    1.0812   -0.7218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2110    1.8471   -1.9211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3674   -0.4087   -1.1075 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.6989   -1.0030   -2.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.4301   -5.1727   -6.3184 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.5609   -1.5995   -0.5697 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9141   -0.6923    0.4812 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1147   -0.0836    0.2933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2196    1.2185    1.0215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0765    1.1797    2.3780 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2359    2.4847    2.8670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0733    2.9917    3.4415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1083    2.9841    4.8253 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0349    4.0765    5.2740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2095    4.1243    6.6521 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3436    3.9168    4.5297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6352    4.9777    3.6980 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4192    2.6125    3.7845 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6299    2.5817    3.1027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2922   -1.0178    0.6161 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4124   -0.5252   -0.0110 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8447   -2.3663    0.0640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9242   -3.1839   -0.2304 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9051   -2.1933   -1.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3716   -1.5876   -2.1947 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6069   -2.2393   -0.1783 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0980   -2.5578   -0.1480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5837   -1.1877   -0.0711 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9439   -0.7128    1.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6890   -0.3048   -1.7113 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4857    0.1355   -2.9716 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0615   -1.7736   -1.6040 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1897    1.7125   -1.4762 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3211    3.0982   -1.6565 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0155    3.3839   -2.9357 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2824    2.8607   -3.0507 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8518    3.8220   -0.4662 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2039    3.4300   -0.3341 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1741    3.3880    0.8476 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8945    3.9269    0.8143 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5559    0.9899    4.1605 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7724    2.3494    4.3772 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0039548 (Ginsenoside Rs1)


  Mrv0541 05061311132D          

 78 85  0  0  0  0            999 V2000
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    7.7647    3.0064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0201    3.7909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4684    4.4043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7237    5.1888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    8.7861    6.1444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1425   -0.3321    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1916    0.4819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9987    0.6530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2540    1.4374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0611    1.6085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8896    4.9176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0825    4.7465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8272    3.9620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3789    3.3486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5504    0.0396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4668   -3.3736    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4668   -4.1986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1804   -4.6112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
HMDB0039548

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCCC(C)(OC1OC(COC2OCC(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(COC(C)=O)C(O)C(O)C4O)C(C)(C)C3CCC21C

> <INCHI_IDENTIFIER>
InChI=1S/C55H92O23/c1-24(2)11-10-15-55(9,78-49-45(69)41(65)39(63)31(75-49)23-72-47-43(67)36(60)28(59)21-71-47)26-12-17-54(8)35(26)27(58)19-33-52(6)16-14-34(51(4,5)32(52)13-18-53(33,54)7)76-50-46(42(66)37(61)29(20-56)73-50)77-48-44(68)40(64)38(62)30(74-48)22-70-25(3)57/h11,26-50,56,58-69H,10,12-23H2,1-9H3

> <INCHI_KEY>
HAJTYGKLQDXTPO-UHFFFAOYSA-N

> <FORMULA>
C55H92O23

> <MOLECULAR_WEIGHT>
1121.3052

> <EXACT_MASS>
1120.60293925

> <JCHEM_ACCEPTOR_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
120.22565434752337

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
13

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[6-({4,5-dihydroxy-2-[(16-hydroxy-2,6,6,10,11-pentamethyl-14-{6-methyl-2-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]hept-5-en-2-yl}tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-5-yl)oxy]-6-(hydroxymethyl)oxan-3-yl}oxy)-3,4,5-trihydroxyoxan-2-yl]methyl acetate

> <ALOGPS_LOGP>
-0.04

> <JCHEM_LOGP>
-0.47994442533333437

> <ALOGPS_LOGS>
-3.37

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.18895427267292

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.752675288492249

> <JCHEM_PKA_STRONGEST_BASIC>
-3.649085064414308

> <JCHEM_POLAR_SURFACE_AREA>
363.13

> <JCHEM_REFRACTIVITY>
270.07810000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
17

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.84e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[6-({4,5-dihydroxy-2-[(16-hydroxy-2,6,6,10,11-pentamethyl-14-{6-methyl-2-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]hept-5-en-2-yl}tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-5-yl)oxy]-6-(hydroxymethyl)oxan-3-yl}oxy)-3,4,5-trihydroxyoxan-2-yl]methyl acetate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0039548 (Ginsenoside Rs1)

HMDB0039548
     RDKit          3D
Ginsenoside Rs1
170177  0  0  0  0  0  0  0  0999 V2000
    9.4167   -1.7692   -1.2922 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5471   -1.8204    0.1920 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4602   -1.1531    0.7126 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7135   -2.5630    1.0035 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8005   -2.6336    2.4071 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5898   -1.3016    3.0086 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3188   -0.7871    2.6574 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4925    0.6165    2.7337 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5764    1.3118    1.9760 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0917    1.8426    0.8351 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2925    1.5219   -0.3847 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6434    0.3291   -0.4031 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3049    0.5068   -0.6269 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4657    0.2374    0.6208 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2439    1.0987    0.4025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5431    0.8393   -0.8749 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3488    2.2335   -1.5198 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2190   -0.0510   -1.8712 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4328   -1.2374   -2.3291 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4395   -1.8717   -1.4478 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0631   -1.0332   -0.2766 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5424   -1.5839    0.9263 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1202    0.3520   -0.7169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8235    1.3669   -0.1487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1990    1.0812   -0.7218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2110    1.8471   -1.9211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3674   -0.4087   -1.1075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7600   -0.8933   -0.8776 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6989   -1.0030   -2.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7794    0.3676   -2.7826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5651   -2.0871   -2.9911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3621   -2.3111   -3.7812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2427   -3.3559   -4.7703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0141   -4.2503   -5.2411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4301   -5.1727   -6.3184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4151   -4.4973   -4.8740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9696   -0.9014   -1.4663 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5609   -1.5995   -0.5697 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9141   -0.6923    0.4812 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1147   -0.0836    0.2933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2196    1.2185    1.0215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0765    1.1797    2.3780 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2359    2.4847    2.8670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0733    2.9917    3.4415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1083    2.9841    4.8253 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0349    4.0765    5.2740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2095    4.1243    6.6521 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3436    3.9168    4.5297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6352    4.9777    3.6980 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4192    2.6125    3.7845 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6299    2.5817    3.1027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2922   -1.0178    0.6161 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4124   -0.5252   -0.0110 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8447   -2.3663    0.0640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9242   -3.1839   -0.2304 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9051   -2.1933   -1.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3716   -1.5876   -2.1947 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6069   -2.2393   -0.1783 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0980   -2.5578   -0.1480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5837   -1.1877   -0.0711 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9439   -0.7128    1.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6890   -0.3048   -1.7113 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4857    0.1355   -2.9716 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0615   -1.7736   -1.6040 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1897    1.7125   -1.4762 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3211    3.0982   -1.6565 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0155    3.3839   -2.9357 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2824    2.8607   -3.0507 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8518    3.8220   -0.4662 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2039    3.4300   -0.3341 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1741    3.3880    0.8476 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8945    3.9269    0.8143 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5559    0.9899    4.1605 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7724    2.3494    4.3772 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6669    0.2542    4.8596 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5379    0.3388    6.2562 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7246   -1.2283    4.5114 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9841   -1.6925    4.8612 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.3114   -2.1866   -1.7662 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2897   -0.6898   -1.6011 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4677   -2.2690   -1.6422 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0707   -3.3795    2.7835 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8194   -3.0475    2.6221 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3773   -0.5883    2.6273 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4888    0.7690    2.2422 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1538    1.5260    0.7450 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5046    2.3432   -0.4998 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1092    1.5971   -0.8423 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0297    0.6375    1.4752 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3086   -0.8129    0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5655    1.1886    1.2590 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7290    2.1406    0.4001 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2777    2.3374   -2.1665 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4237    3.0464   -0.8094 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5263    2.2548   -2.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2285    0.5875   -2.8323 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2145   -2.0402   -2.5348 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0221   -1.0916   -3.3851 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6961   -2.9102   -1.1236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4909   -2.0238   -2.0738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1375   -2.3589    1.4076 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4373   -2.2392    0.6679 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8901   -0.9696    1.7345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2051    0.3519   -1.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4472    2.3785   -0.5076 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.0317    1.4636   -0.1388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8433    1.2836   -2.6347 H   0  0  0  0  0  0  0  0  0  0  0  0
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    7.9394   -1.8011    4.9976 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6831   -1.0160    4.6853 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0039548 (Ginsenoside Rs1)

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       7.906   3.274   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.761   2.244   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.080   0.737   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.545   0.261   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.009  -0.216   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.762  -4.750   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.602  -3.219   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.067  -3.695   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.973  -2.450   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.068  -1.204   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.603  -1.679   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.270  -0.908   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.936  -1.677   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.935  -3.217   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.268  -3.988   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.282  -2.447   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.267   0.633   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       5.267  -5.527   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.935  -6.297   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.600  -5.527   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.600  -3.987   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.600  -2.447   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.732   5.810   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.587   4.780   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.122   5.257   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.265  -3.217   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.067  -3.987   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.067  -5.527   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -1.401  -6.297   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -2.734  -5.527   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -2.734  -3.987   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -4.068  -3.217   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.068  -1.677   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -5.403  -0.907   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -4.068 -10.918   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -5.403 -10.148   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -6.735 -10.918   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -6.735 -12.458   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0     -10.737  -8.608   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -9.404  -7.837   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -8.070  -8.608   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      -6.735  -7.837   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -5.403  -8.608   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      -4.068  -7.837   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -4.068  -6.297   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -5.403  -5.527   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -5.403  -3.987   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0      -6.735  -3.217   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0      -8.070 -10.148   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0      -9.404 -10.918   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -6.735  -6.297   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0       0.277  -7.476   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       1.265  -6.297   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       2.256  -7.476   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0       9.021   1.725   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0      10.528   2.044   0.000  0.00  0.00           C+0
HETATM   57  O   UNK     0      11.005   3.509   0.000  0.00  0.00           O+0
HETATM   58  C   UNK     0      12.511   3.828   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      12.988   5.293   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0      14.494   5.612   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0      14.971   7.076   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0      13.941   8.221   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0      14.418   9.686   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      15.924  10.005   0.000  0.00  0.00           C+0
HETATM   65  O   UNK     0      16.401  11.470   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      11.466  -0.620   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0      11.558   0.900   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      13.064   1.219   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      13.541   2.683   0.000  0.00  0.00           C+0
HETATM   70  O   UNK     0      15.047   3.003   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0      18.461   9.180   0.000  0.00  0.00           O+0
HETATM   72  C   UNK     0      16.954   8.860   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0      16.477   7.396   0.000  0.00  0.00           C+0
HETATM   74  O   UNK     0      17.507   6.251   0.000  0.00  0.00           O+0
HETATM   75  O   UNK     0      14.094   0.074   0.000  0.00  0.00           O+0
HETATM   76  O   UNK     0     -12.071  -6.297   0.000  0.00  0.00           O+0
HETATM   77  C   UNK     0     -12.071  -7.837   0.000  0.00  0.00           C+0
HETATM   78  C   UNK     0     -13.403  -8.608   0.000  0.00  0.00           C+0
CONECT    1    2   24                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10   55                                             
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   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   21                                                  
CONECT   15    7   14   16   18                                             
CONECT   16   15                                                            
CONECT   17   12                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   53                                                  
CONECT   21   14   20   22   26                                             
CONECT   22   21                                                            
CONECT   23   24                                                            
CONECT   24    1   23   25                                                  
CONECT   25   24                                                            
CONECT   26   21   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   53                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   45                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   47                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   36                                                            
CONECT   36   35   37   43                                                  
CONECT   37   36   38   49                                                  
CONECT   38   37                                                            
CONECT   39   40   77                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42   49                                                  
CONECT   42   41   43                                                       
CONECT   43   36   42   44                                                  
CONECT   44   43   45                                                       
CONECT   45   30   44   46                                                  
CONECT   46   45   47   51                                                  
CONECT   47   32   46   48                                                  
CONECT   48   47                                                            
CONECT   49   37   41   50                                                  
CONECT   50   49                                                            
CONECT   51   46                                                            
CONECT   52   53                                                            
CONECT   53   20   28   52   54                                             
CONECT   54   53                                                            
CONECT   55    4   56                                                       
CONECT   56   55   57   67                                                  
CONECT   57   56   58                                                       
CONECT   58   57   59   69                                                  
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62   73                                                  
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65   72                                                  
CONECT   65   64                                                            
CONECT   66   67                                                            
CONECT   67   56   66   68                                                  
CONECT   68   67   69   75                                                  
CONECT   69   58   68   70                                                  
CONECT   70   69                                                            
CONECT   71   72                                                            
CONECT   72   64   71   73                                                  
CONECT   73   61   72   74                                                  
CONECT   74   73                                                            
CONECT   75   68                                                            
CONECT   76   77                                                            
CONECT   77   39   76   78                                                  
CONECT   78   77                                                            
MASTER        0    0    0    0    0    0    0    0   78    0  170    0
END
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3D PDB for HMDB0039548 (Ginsenoside Rs1)

COMPND    HMDB0039548
HETATM    1  C1  UNL     1       9.417  -1.769  -1.292  1.00  0.00           C  
HETATM    2  C2  UNL     1       9.547  -1.820   0.192  1.00  0.00           C  
HETATM    3  O1  UNL     1      10.460  -1.153   0.713  1.00  0.00           O  
HETATM    4  O2  UNL     1       8.713  -2.563   1.004  1.00  0.00           O  
HETATM    5  C3  UNL     1       8.800  -2.634   2.407  1.00  0.00           C  
HETATM    6  C4  UNL     1       8.590  -1.302   3.009  1.00  0.00           C  
HETATM    7  O3  UNL     1       7.319  -0.787   2.657  1.00  0.00           O  
HETATM    8  C5  UNL     1       7.492   0.616   2.734  1.00  0.00           C  
HETATM    9  O4  UNL     1       6.576   1.312   1.976  1.00  0.00           O  
HETATM   10  C6  UNL     1       7.092   1.843   0.835  1.00  0.00           C  
HETATM   11  C7  UNL     1       6.293   1.522  -0.385  1.00  0.00           C  
HETATM   12  O5  UNL     1       5.643   0.329  -0.403  1.00  0.00           O  
HETATM   13  C8  UNL     1       4.305   0.507  -0.627  1.00  0.00           C  
HETATM   14  C9  UNL     1       3.466   0.237   0.621  1.00  0.00           C  
HETATM   15  C10 UNL     1       2.244   1.099   0.402  1.00  0.00           C  
HETATM   16  C11 UNL     1       1.543   0.839  -0.875  1.00  0.00           C  
HETATM   17  C12 UNL     1       1.349   2.234  -1.520  1.00  0.00           C  
HETATM   18  C13 UNL     1       2.219  -0.051  -1.871  1.00  0.00           C  
HETATM   19  C14 UNL     1       1.433  -1.237  -2.329  1.00  0.00           C  
HETATM   20  C15 UNL     1       0.439  -1.872  -1.448  1.00  0.00           C  
HETATM   21  C16 UNL     1      -0.063  -1.033  -0.277  1.00  0.00           C  
HETATM   22  C17 UNL     1       0.542  -1.584   0.926  1.00  0.00           C  
HETATM   23  C18 UNL     1       0.120   0.352  -0.717  1.00  0.00           C  
HETATM   24  C19 UNL     1      -0.824   1.367  -0.149  1.00  0.00           C  
HETATM   25  C20 UNL     1      -2.199   1.081  -0.722  1.00  0.00           C  
HETATM   26  O6  UNL     1      -2.211   1.847  -1.921  1.00  0.00           O  
HETATM   27  C21 UNL     1      -2.367  -0.409  -1.108  1.00  0.00           C  
HETATM   28  C22 UNL     1      -3.760  -0.893  -0.878  1.00  0.00           C  
HETATM   29  C23 UNL     1      -4.699  -1.003  -2.029  1.00  0.00           C  
HETATM   30  C24 UNL     1      -4.779   0.368  -2.783  1.00  0.00           C  
HETATM   31  C25 UNL     1      -4.565  -2.087  -2.991  1.00  0.00           C  
HETATM   32  C26 UNL     1      -3.362  -2.311  -3.781  1.00  0.00           C  
HETATM   33  C27 UNL     1      -3.243  -3.356  -4.770  1.00  0.00           C  
HETATM   34  C28 UNL     1      -4.014  -4.250  -5.241  1.00  0.00           C  
HETATM   35  C29 UNL     1      -3.430  -5.173  -6.318  1.00  0.00           C  
HETATM   36  C30 UNL     1      -5.415  -4.497  -4.874  1.00  0.00           C  
HETATM   37  O7  UNL     1      -5.970  -0.901  -1.466  1.00  0.00           O  
HETATM   38  C31 UNL     1      -6.561  -1.599  -0.570  1.00  0.00           C  
HETATM   39  O8  UNL     1      -6.914  -0.692   0.481  1.00  0.00           O  
HETATM   40  C32 UNL     1      -8.115  -0.084   0.293  1.00  0.00           C  
HETATM   41  C33 UNL     1      -8.220   1.218   1.022  1.00  0.00           C  
HETATM   42  O9  UNL     1      -8.076   1.180   2.378  1.00  0.00           O  
HETATM   43  C34 UNL     1      -8.236   2.485   2.867  1.00  0.00           C  
HETATM   44  O10 UNL     1      -7.073   2.992   3.441  1.00  0.00           O  
HETATM   45  C35 UNL     1      -7.108   2.984   4.825  1.00  0.00           C  
HETATM   46  C36 UNL     1      -8.035   4.076   5.274  1.00  0.00           C  
HETATM   47  O11 UNL     1      -8.210   4.124   6.652  1.00  0.00           O  
HETATM   48  C37 UNL     1      -9.344   3.917   4.530  1.00  0.00           C  
HETATM   49  O12 UNL     1      -9.635   4.978   3.698  1.00  0.00           O  
HETATM   50  C38 UNL     1      -9.419   2.613   3.784  1.00  0.00           C  
HETATM   51  O13 UNL     1     -10.630   2.582   3.103  1.00  0.00           O  
HETATM   52  C39 UNL     1      -9.292  -1.018   0.616  1.00  0.00           C  
HETATM   53  O14 UNL     1     -10.412  -0.525  -0.011  1.00  0.00           O  
HETATM   54  C40 UNL     1      -8.845  -2.366   0.064  1.00  0.00           C  
HETATM   55  O15 UNL     1      -9.924  -3.184  -0.230  1.00  0.00           O  
HETATM   56  C41 UNL     1      -7.905  -2.193  -1.070  1.00  0.00           C  
HETATM   57  O16 UNL     1      -8.372  -1.588  -2.195  1.00  0.00           O  
HETATM   58  C42 UNL     1      -3.607  -2.239  -0.178  1.00  0.00           C  
HETATM   59  C43 UNL     1      -2.098  -2.558  -0.148  1.00  0.00           C  
HETATM   60  C44 UNL     1      -1.584  -1.188  -0.071  1.00  0.00           C  
HETATM   61  C45 UNL     1      -1.944  -0.713   1.344  1.00  0.00           C  
HETATM   62  C46 UNL     1       3.689  -0.305  -1.711  1.00  0.00           C  
HETATM   63  C47 UNL     1       4.486   0.135  -2.972  1.00  0.00           C  
HETATM   64  C48 UNL     1       4.062  -1.774  -1.604  1.00  0.00           C  
HETATM   65  O17 UNL     1       7.190   1.712  -1.476  1.00  0.00           O  
HETATM   66  C49 UNL     1       7.321   3.098  -1.656  1.00  0.00           C  
HETATM   67  C50 UNL     1       8.015   3.384  -2.936  1.00  0.00           C  
HETATM   68  O18 UNL     1       9.282   2.861  -3.051  1.00  0.00           O  
HETATM   69  C51 UNL     1       7.852   3.822  -0.466  1.00  0.00           C  
HETATM   70  O19 UNL     1       9.204   3.430  -0.334  1.00  0.00           O  
HETATM   71  C52 UNL     1       7.174   3.388   0.848  1.00  0.00           C  
HETATM   72  O20 UNL     1       5.895   3.927   0.814  1.00  0.00           O  
HETATM   73  C53 UNL     1       7.556   0.990   4.161  1.00  0.00           C  
HETATM   74  O21 UNL     1       7.772   2.349   4.377  1.00  0.00           O  
HETATM   75  C54 UNL     1       8.667   0.254   4.860  1.00  0.00           C  
HETATM   76  O22 UNL     1       8.538   0.339   6.256  1.00  0.00           O  
HETATM   77  C55 UNL     1       8.725  -1.228   4.511  1.00  0.00           C  
HETATM   78  O23 UNL     1       9.984  -1.693   4.861  1.00  0.00           O  
HETATM   79  H1  UNL     1      10.311  -2.187  -1.766  1.00  0.00           H  
HETATM   80  H2  UNL     1       9.290  -0.690  -1.601  1.00  0.00           H  
HETATM   81  H3  UNL     1       8.468  -2.269  -1.642  1.00  0.00           H  
HETATM   82  H4  UNL     1       8.071  -3.379   2.783  1.00  0.00           H  
HETATM   83  H5  UNL     1       9.819  -3.048   2.622  1.00  0.00           H  
HETATM   84  H6  UNL     1       9.377  -0.588   2.627  1.00  0.00           H  
HETATM   85  H7  UNL     1       8.489   0.769   2.242  1.00  0.00           H  
HETATM   86  H8  UNL     1       8.154   1.526   0.745  1.00  0.00           H  
HETATM   87  H9  UNL     1       5.505   2.343  -0.500  1.00  0.00           H  
HETATM   88  H10 UNL     1       4.109   1.597  -0.842  1.00  0.00           H  
HETATM   89  H11 UNL     1       4.030   0.637   1.475  1.00  0.00           H  
HETATM   90  H12 UNL     1       3.309  -0.813   0.779  1.00  0.00           H  
HETATM   91  H13 UNL     1       1.566   1.189   1.259  1.00  0.00           H  
HETATM   92  H14 UNL     1       2.729   2.141   0.400  1.00  0.00           H  
HETATM   93  H15 UNL     1       2.278   2.337  -2.167  1.00  0.00           H  
HETATM   94  H16 UNL     1       1.424   3.046  -0.809  1.00  0.00           H  
HETATM   95  H17 UNL     1       0.526   2.255  -2.240  1.00  0.00           H  
HETATM   96  H18 UNL     1       2.228   0.588  -2.832  1.00  0.00           H  
HETATM   97  H19 UNL     1       2.214  -2.040  -2.535  1.00  0.00           H  
HETATM   98  H20 UNL     1       1.022  -1.092  -3.385  1.00  0.00           H  
HETATM   99  H21 UNL     1       0.696  -2.910  -1.124  1.00  0.00           H  
HETATM  100  H22 UNL     1      -0.491  -2.024  -2.074  1.00  0.00           H  
HETATM  101  H23 UNL     1      -0.138  -2.359   1.408  1.00  0.00           H  
HETATM  102  H24 UNL     1       1.437  -2.239   0.668  1.00  0.00           H  
HETATM  103  H25 UNL     1       0.890  -0.970   1.734  1.00  0.00           H  
HETATM  104  H26 UNL     1      -0.205   0.352  -1.822  1.00  0.00           H  
HETATM  105  H27 UNL     1      -0.447   2.378  -0.508  1.00  0.00           H  
HETATM  106  H28 UNL     1      -0.796   1.507   0.937  1.00  0.00           H  
HETATM  107  H29 UNL     1      -3.032   1.464  -0.139  1.00  0.00           H  
HETATM  108  H30 UNL     1      -1.843   1.284  -2.635  1.00  0.00           H  
HETATM  109  H31 UNL     1      -2.036  -0.594  -2.107  1.00  0.00           H  
HETATM  110  H32 UNL     1      -4.191  -0.214  -0.084  1.00  0.00           H  
HETATM  111  H33 UNL     1      -5.712   0.320  -3.381  1.00  0.00           H  
HETATM  112  H34 UNL     1      -4.916   1.117  -2.021  1.00  0.00           H  
HETATM  113  H35 UNL     1      -3.949   0.460  -3.480  1.00  0.00           H  
HETATM  114  H36 UNL     1      -4.717  -3.046  -2.409  1.00  0.00           H  
HETATM  115  H37 UNL     1      -5.444  -2.131  -3.712  1.00  0.00           H  
HETATM  116  H38 UNL     1      -2.887  -1.364  -4.184  1.00  0.00           H  
HETATM  117  H39 UNL     1      -2.568  -2.616  -2.996  1.00  0.00           H  
HETATM  118  H40 UNL     1      -2.187  -3.379  -5.247  1.00  0.00           H  
HETATM  119  H41 UNL     1      -4.212  -5.366  -7.049  1.00  0.00           H  
HETATM  120  H42 UNL     1      -3.059  -6.054  -5.759  1.00  0.00           H  
HETATM  121  H43 UNL     1      -2.571  -4.706  -6.816  1.00  0.00           H  
HETATM  122  H44 UNL     1      -5.770  -5.428  -5.418  1.00  0.00           H  
HETATM  123  H45 UNL     1      -5.513  -4.620  -3.802  1.00  0.00           H  
HETATM  124  H46 UNL     1      -6.135  -3.723  -5.232  1.00  0.00           H  
HETATM  125  H47 UNL     1      -6.132  -2.443  -0.022  1.00  0.00           H  
HETATM  126  H48 UNL     1      -8.294   0.206  -0.789  1.00  0.00           H  
HETATM  127  H49 UNL     1      -7.350   1.836   0.640  1.00  0.00           H  
HETATM  128  H50 UNL     1      -9.169   1.701   0.695  1.00  0.00           H  
HETATM  129  H51 UNL     1      -8.447   3.177   2.004  1.00  0.00           H  
HETATM  130  H52 UNL     1      -6.086   3.225   5.195  1.00  0.00           H  
HETATM  131  H53 UNL     1      -7.469   2.006   5.227  1.00  0.00           H  
HETATM  132  H54 UNL     1      -7.612   5.059   4.939  1.00  0.00           H  
HETATM  133  H55 UNL     1      -8.459   3.224   6.975  1.00  0.00           H  
HETATM  134  H56 UNL     1     -10.175   3.897   5.296  1.00  0.00           H  
HETATM  135  H57 UNL     1      -9.636   5.818   4.262  1.00  0.00           H  
HETATM  136  H58 UNL     1      -9.465   1.750   4.506  1.00  0.00           H  
HETATM  137  H59 UNL     1     -10.989   3.518   3.015  1.00  0.00           H  
HETATM  138  H60 UNL     1      -9.387  -1.045   1.732  1.00  0.00           H  
HETATM  139  H61 UNL     1     -11.259  -0.757   0.403  1.00  0.00           H  
HETATM  140  H62 UNL     1      -8.298  -2.875   0.896  1.00  0.00           H  
HETATM  141  H63 UNL     1     -10.656  -2.636  -0.664  1.00  0.00           H  
HETATM  142  H64 UNL     1      -7.627  -3.245  -1.402  1.00  0.00           H  
HETATM  143  H65 UNL     1      -7.834  -1.882  -2.987  1.00  0.00           H  
HETATM  144  H66 UNL     1      -4.003  -2.222   0.867  1.00  0.00           H  
HETATM  145  H67 UNL     1      -4.037  -3.094  -0.661  1.00  0.00           H  
HETATM  146  H68 UNL     1      -1.764  -3.253  -0.875  1.00  0.00           H  
HETATM  147  H69 UNL     1      -1.948  -3.073   0.852  1.00  0.00           H  
HETATM  148  H70 UNL     1      -2.500  -1.508   1.932  1.00  0.00           H  
HETATM  149  H71 UNL     1      -2.675   0.118   1.339  1.00  0.00           H  
HETATM  150  H72 UNL     1      -1.060  -0.557   1.989  1.00  0.00           H  
HETATM  151  H73 UNL     1       4.476   1.242  -2.935  1.00  0.00           H  
HETATM  152  H74 UNL     1       5.493  -0.267  -2.850  1.00  0.00           H  
HETATM  153  H75 UNL     1       3.970  -0.188  -3.885  1.00  0.00           H  
HETATM  154  H76 UNL     1       5.074  -1.779  -1.127  1.00  0.00           H  
HETATM  155  H77 UNL     1       4.218  -2.214  -2.601  1.00  0.00           H  
HETATM  156  H78 UNL     1       3.405  -2.335  -0.929  1.00  0.00           H  
HETATM  157  H79 UNL     1       6.257   3.455  -1.788  1.00  0.00           H  
HETATM  158  H80 UNL     1       7.392   2.948  -3.763  1.00  0.00           H  
HETATM  159  H81 UNL     1       8.009   4.488  -3.110  1.00  0.00           H  
HETATM  160  H82 UNL     1       9.236   2.011  -3.552  1.00  0.00           H  
HETATM  161  H83 UNL     1       7.856   4.911  -0.578  1.00  0.00           H  
HETATM  162  H84 UNL     1       9.713   3.986  -0.973  1.00  0.00           H  
HETATM  163  H85 UNL     1       7.816   3.758   1.655  1.00  0.00           H  
HETATM  164  H86 UNL     1       5.671   4.165   1.763  1.00  0.00           H  
HETATM  165  H87 UNL     1       6.608   0.658   4.679  1.00  0.00           H  
HETATM  166  H88 UNL     1       8.035   2.457   5.319  1.00  0.00           H  
HETATM  167  H89 UNL     1       9.643   0.689   4.558  1.00  0.00           H  
HETATM  168  H90 UNL     1       9.157  -0.335   6.624  1.00  0.00           H  
HETATM  169  H91 UNL     1       7.939  -1.801   4.998  1.00  0.00           H  
HETATM  170  H92 UNL     1      10.683  -1.016   4.685  1.00  0.00           H  
CONECT    1    2   79   80   81
CONECT    2    3    3    4
CONECT    4    5
CONECT    5    6   82   83
CONECT    6    7   77   84
CONECT    7    8
CONECT    8    9   73   85
CONECT    9   10
CONECT   10   11   71   86
CONECT   11   12   65   87
CONECT   12   13
CONECT   13   14   62   88
CONECT   14   15   89   90
CONECT   15   16   91   92
CONECT   16   17   18   23
CONECT   17   93   94   95
CONECT   18   19   62   96
CONECT   19   20   97   98
CONECT   20   21   99  100
CONECT   21   22   23   60
CONECT   22  101  102  103
CONECT   23   24  104
CONECT   24   25  105  106
CONECT   25   26   27  107
CONECT   26  108
CONECT   27   28   60  109
CONECT   28   29   58  110
CONECT   29   30   31   37
CONECT   30  111  112  113
CONECT   31   32  114  115
CONECT   32   33  116  117
CONECT   33   34   34  118
CONECT   34   35   36
CONECT   35  119  120  121
CONECT   36  122  123  124
CONECT   37   38
CONECT   38   39   56  125
CONECT   39   40
CONECT   40   41   52  126
CONECT   41   42  127  128
CONECT   42   43
CONECT   43   44   50  129
CONECT   44   45
CONECT   45   46  130  131
CONECT   46   47   48  132
CONECT   47  133
CONECT   48   49   50  134
CONECT   49  135
CONECT   50   51  136
CONECT   51  137
CONECT   52   53   54  138
CONECT   53  139
CONECT   54   55   56  140
CONECT   55  141
CONECT   56   57  142
CONECT   57  143
CONECT   58   59  144  145
CONECT   59   60  146  147
CONECT   60   61
CONECT   61  148  149  150
CONECT   62   63   64
CONECT   63  151  152  153
CONECT   64  154  155  156
CONECT   65   66
CONECT   66   67   69  157
CONECT   67   68  158  159
CONECT   68  160
CONECT   69   70   71  161
CONECT   70  162
CONECT   71   72  163
CONECT   72  164
CONECT   73   74   75  165
CONECT   74  166
CONECT   75   76   77  167
CONECT   76  168
CONECT   77   78  169
CONECT   78  170
END
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SMILES for HMDB0039548 (Ginsenoside Rs1)

CC(C)=CCCC(C)(OC1OC(COC2OCC(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(COC(C)=O)C(O)C(O)C4O)C(C)(C)C3CCC21C
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INCHI for HMDB0039548 (Ginsenoside Rs1)

InChI=1S/C55H92O23/c1-24(2)11-10-15-55(9,78-49-45(69)41(65)39(63)31(75-49)23-72-47-43(67)36(60)28(59)21-71-47)26-12-17-54(8)35(26)27(58)19-33-52(6)16-14-34(51(4,5)32(52)13-18-53(33,54)7)76-50-46(42(66)37(61)29(20-56)73-50)77-48-44(68)40(64)38(62)30(74-48)22-70-25(3)57/h11,26-50,56,58-69H,10,12-23H2,1-9H3
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Synonyms
ValueSource
[6-({4,5-dihydroxy-2-[(16-hydroxy-2,6,6,10,11-pentamethyl-14-{6-methyl-2-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]hept-5-en-2-yl}tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-5-yl)oxy]-6-(hydroxymethyl)oxan-3-yl}oxy)-3,4,5-trihydroxyoxan-2-yl]methyl acetic acidGenerator
Chemical FormulaC55H92O23
Average Molecular Weight1121.3052
Monoisotopic Molecular Weight1120.60293925
IUPAC Name[6-({4,5-dihydroxy-2-[(16-hydroxy-2,6,6,10,11-pentamethyl-14-{6-methyl-2-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]hept-5-en-2-yl}tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-5-yl)oxy]-6-(hydroxymethyl)oxan-3-yl}oxy)-3,4,5-trihydroxyoxan-2-yl]methyl acetate
Traditional Name[6-({4,5-dihydroxy-2-[(16-hydroxy-2,6,6,10,11-pentamethyl-14-{6-methyl-2-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]hept-5-en-2-yl}tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-5-yl)oxy]-6-(hydroxymethyl)oxan-3-yl}oxy)-3,4,5-trihydroxyoxan-2-yl]methyl acetate
CAS Registry Number87733-67-3
SMILES
CC(C)=CCCC(C)(OC1OC(COC2OCC(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(COC(C)=O)C(O)C(O)C4O)C(C)(C)C3CCC21C
InChI Identifier
InChI=1S/C55H92O23/c1-24(2)11-10-15-55(9,78-49-45(69)41(65)39(63)31(75-49)23-72-47-43(67)36(60)28(59)21-71-47)26-12-17-54(8)35(26)27(58)19-33-52(6)16-14-34(51(4,5)32(52)13-18-53(33,54)7)76-50-46(42(66)37(61)29(20-56)73-50)77-48-44(68)40(64)38(62)30(74-48)22-70-25(3)57/h11,26-50,56,58-69H,10,12-23H2,1-9H3
InChI KeyHAJTYGKLQDXTPO-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTriterpenoids
Direct ParentTriterpenoids
Alternative ParentsNot Available
SubstituentsNot Available
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.48 g/LALOGPS
logP-0.04ALOGPS
logP-0.48ChemAxon
logS-3.4ALOGPS
pKa (Strongest Acidic)11.75ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count22ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area363.13 ŲChemAxon
Rotatable Bond Count17ChemAxon
Refractivity270.08 m³·mol⁻¹ChemAxon
Polarizability120.23 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]-355.93730932474
DeepCCS[M+Na]+329.95730932474
AllCCS[M+H]+335.732859911
AllCCS[M+H-H2O]+336.032859911
AllCCS[M+NH4]+335.432859911
AllCCS[M+Na]+335.332859911
AllCCS[M-H]-271.932859911
AllCCS[M+Na-2H]-278.432859911
AllCCS[M+HCOO]-285.432859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 10V, Positive-QTOFsplash10-0pbj-3610102891-6731d8f7c4d8c37dff322016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 20V, Positive-QTOFsplash10-0ab9-0310607961-872423dd1aa0e9cdb8372016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 40V, Positive-QTOFsplash10-0ab9-4610907530-6c90610160a3ca96c8532016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 10V, Negative-QTOFsplash10-0pba-9720001231-143863411a13435e3f7b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 20V, Negative-QTOFsplash10-0pb9-9720001331-d2fb8386fe017e4f003f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 40V, Negative-QTOFsplash10-0a4i-9230202200-2c45b65a87bc29d1e6ec2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 10V, Negative-QTOFsplash10-014i-9700000001-91a8b5c7aa0d9cb4dc4b2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 20V, Negative-QTOFsplash10-0a4i-9100000004-d008167a28d1baa507952021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 40V, Negative-QTOFsplash10-0aou-9100000101-33f23b5903e51198fd1c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 10V, Positive-QTOFsplash10-0a6u-2500403940-8ae7fcf959ab3c79dd612021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 20V, Positive-QTOFsplash10-0h6r-1900204201-86616df54eef23e3a7b02021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rs1 40V, Positive-QTOFsplash10-0002-1900000010-b4a7cf0a2738cce46ea92021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • 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 IDFDB019167
KNApSAcK IDC00033882
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound85044013
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.