Hmdb loader

Showing metabocard for Ginsenoside B2 (HMDB0035749)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 20:46:08 UTC
Update Date2022-03-07 02:54:37 UTC
HMDB IDHMDB0035749
Secondary Accession Numbers
  • HMDB35749
Metabolite Identification
Common NameGinsenoside B2
DescriptionGinsenoside B2 belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Ginsenoside B2 is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563862766
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035749 (Ginsenoside B2)


  Mrv0541 02241220282D          

 66 72  0  0  0  0            999 V2000
    0.4358    5.0432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2227    4.2457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8056    3.6627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5925    2.8653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2049    3.0797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4468    1.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3382    0.7465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8222    1.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3382    2.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4468    1.8259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1619    2.2383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8754    1.8259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.1619    0.5885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.1619    3.0633    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1619   -0.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8754   -0.6489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5903   -0.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5903    0.5885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5903    1.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9431    5.4130    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1470    5.6261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0660    6.4236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3039    1.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0189    0.5885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.7338   -0.6489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3900    2.6522    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.7691    3.0220    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.1494    3.3919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7338    3.9748    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.7598    4.0326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.1389    4.4025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.1297    5.4130    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8754   -1.4739    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1619   -1.8863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4468   -1.4739    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2680   -1.8863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.6967   -1.8863    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3039   -3.9487    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5903   -4.3611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.1619   -4.3611    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1619   -5.1862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8754   -5.5986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  2  3  1  0  0  0  0
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  4 32  1  0  0  0  0
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 62 63  1  0  0  0  0
M  END
Download

3D MOL for HMDB0035749 (Ginsenoside B2)

HMDB0252725
     RDKit          3D
Ginsenoside Re
148154  0  0  0  0  0  0  0  0999 V2000
   -5.8274    6.9264    0.8156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3802    5.5834    1.2475 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7572    5.0769    2.5854 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6558    4.8492    0.4514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1533    3.4573    0.8154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6739    2.4548   -0.1274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1941    0.9963    0.1982 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8242    0.9769    1.6839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9920    0.1042   -0.3484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3133   -0.0811   -1.6195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6533    0.5474   -1.7325 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6328   -0.3276   -1.3907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8193    0.5141   -0.8828 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.2971   -1.2579   -0.2528 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4287   -2.0248    0.0395 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.2534   -1.5252    0.3276 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0048    0.1893    0.9976 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3459    1.3654    1.6129 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5639    1.1111    3.0831 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6057    0.1686    3.2230 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.9052    3.4439   -0.5398 O   0  0  0  0  0  0  0  0  0  0  0  0
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    6.2368   -0.2468   -3.4829 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.0625    0.9570   -3.2127 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4711    1.1057   -1.8898 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4811    2.2394   -3.7604 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8715    3.2740   -2.9160 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9715    2.1994   -3.7843 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3638    3.4115   -3.5828 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1457   -1.4081   -0.7493 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1514   -1.7036   -0.0953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7349   -3.0100   -0.6891 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2024    7.7254    1.2840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8621    7.1004    1.2063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8272    7.0293   -0.2999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3175    4.1199    2.4324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4240    5.7913    3.1089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8162    4.8868    3.1604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3629    5.1947   -0.5394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5315    3.3287    1.8660 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0757    3.5975    0.8950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5022    2.6619   -1.1889 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.1226    1.4358    2.3641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0380   -0.0555    1.9587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8122    1.4851    1.6230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7443    0.4160   -2.4208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0643   -0.8835   -2.2591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4911    1.0915    0.0185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6747   -0.1359   -0.6117 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8529    0.8483   -2.4980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9346   -0.7017    0.6050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1913   -2.5190    0.8860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4774   -2.3882   -0.0258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7161   -3.5453   -0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2666   -1.5900   -2.8667 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0035749 (Ginsenoside B2)


  Mrv0541 02241220282D          

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M  END
> <DATABASE_ID>
HMDB0035749

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1OC(OC2C(O)C(O)C(CO)OC2OC2CC3(C)C(CC(O)C4C(CCC34C)C(C)(CCC=C(C)C)OC3OC(CO)C(O)C(O)C3O)C3(C)CCC(O)C(C)(C)C23)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C48H82O18/c1-21(2)11-10-14-48(9,66-42-38(60)35(57)32(54)26(19-49)63-42)23-12-16-46(7)30(23)24(51)17-28-45(6)15-13-29(52)44(4,5)40(45)25(18-47(28,46)8)62-43-39(36(58)33(55)27(20-50)64-43)65-41-37(59)34(56)31(53)22(3)61-41/h11,22-43,49-60H,10,12-20H2,1-9H3

> <INCHI_KEY>
PWAOOJDMFUQOKB-UHFFFAOYSA-N

> <FORMULA>
C48H82O18

> <MOLECULAR_WEIGHT>
947.1539

> <EXACT_MASS>
946.55011582

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
102.73881678941798

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2-{[5,16-dihydroxy-2,6,6,10,11-pentamethyl-14-(6-methyl-2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}hept-5-en-2-yl)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-8-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl)oxy]-6-methyloxane-3,4,5-triol

> <ALOGPS_LOGP>
0.60

> <JCHEM_LOGP>
-0.04242396233333251

> <ALOGPS_LOGS>
-3.07

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.320196356268337

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.8523276816068

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6121826294395536

> <JCHEM_POLAR_SURFACE_AREA>
298.14

> <JCHEM_REFRACTIVITY>
234.5246000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.12e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2-{[5,16-dihydroxy-2,6,6,10,11-pentamethyl-14-(6-methyl-2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}hept-5-en-2-yl)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-8-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl)oxy]-6-methyloxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0035749 (Ginsenoside B2)

HMDB0252725
     RDKit          3D
Ginsenoside Re
148154  0  0  0  0  0  0  0  0999 V2000
   -5.8274    6.9264    0.8156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3802    5.5834    1.2475 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7572    5.0769    2.5854 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6558    4.8492    0.4514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1533    3.4573    0.8154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6739    2.4548   -0.1274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1941    0.9963    0.1982 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8242    0.9769    1.6839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9920    0.1042   -0.3484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3133   -0.0811   -1.6195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6533    0.5474   -1.7325 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6328   -0.3276   -1.3907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8193    0.5141   -0.8828 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2633    1.3749   -1.8857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2971   -1.2579   -0.2528 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4287   -2.0248    0.0395 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2473   -2.2155   -0.7765 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7626   -3.4101   -1.2131 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6066   -1.5002   -1.9628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4648   -2.1970   -2.2666 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7543    0.9500    0.3858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9067    1.4929   -0.7530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5525    0.7572   -0.6437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1562   -0.6650   -0.4648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6416   -0.9107   -1.8086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0025   -0.2812    0.6911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4878   -1.3147    1.5986 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6624   -0.7054    2.8809 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4436   -2.3969    1.8081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0746   -1.9975    1.3676 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0348   -2.9009    1.8287 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5835   -4.2910    2.2064 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6238   -2.3334    3.1316 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0747   -2.2051    3.2092 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9018   -3.2723    2.6076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0061   -4.4139    3.4360 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4195   -3.5781    1.2488 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5036   -3.2695    0.2000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3164   -5.1133    1.1550 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1747   -2.9176    0.8022 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2534   -1.5252    0.3276 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4413   -1.0316   -0.1480 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8024    0.2166    0.3454 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0048    0.1893    0.9976 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3459    1.3654    1.6129 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5639    1.1111    3.0831 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6057    0.1686    3.2230 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2761    2.4337    1.4602 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8287    3.6359    1.8978 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9368    2.6181   -0.0261 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9052    3.4439   -0.5398 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8149    1.2831   -0.7181 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8698    1.1417   -1.5983 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4468    1.0788   -2.9243 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8874   -0.1179   -3.4604 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2368   -0.2468   -3.4829 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6482   -0.9066   -4.8126 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0625    0.9570   -3.2127 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4711    1.1057   -1.8898 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4811    2.2394   -3.7604 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8715    3.2740   -2.9160 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9715    2.1994   -3.7843 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3638    3.4115   -3.5828 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1457   -1.4081   -0.7493 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1514   -1.7036   -0.0953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7349   -3.0100   -0.6891 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2024    7.7254    1.2840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8621    7.1004    1.2063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8272    7.0293   -0.2999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3175    4.1199    2.4324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4240    5.7913    3.1089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8162    4.8868    3.1604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3629    5.1947   -0.5394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5315    3.3287    1.8660 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0757    3.5975    0.8950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5022    2.6619   -1.1889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7778    2.3987   -0.0044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1226    1.4358    2.3641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0380   -0.0555    1.9587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8122    1.4851    1.6230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7443    0.4160   -2.4208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0643   -0.8835   -2.2591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4911    1.0915    0.0185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6747   -0.1359   -0.6117 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8529    0.8483   -2.4980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9346   -0.7017    0.6050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1913   -2.5190    0.8860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4774   -2.3882   -0.0258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7161   -3.5453   -0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2666   -1.5900   -2.8667 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3192   -2.3893   -3.2076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5780    1.7388    1.2174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5783    2.5659   -0.5691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3405    1.5096   -1.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0078    1.0700    0.2332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1032    0.9093   -1.6193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5063   -0.3368   -2.1862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8170   -0.5371   -2.5175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7817   -1.9270   -2.2029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2017    0.2141    1.4023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4890   -1.7467    1.3950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9135   -0.0392    2.9927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8555   -3.3095    1.3373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3467   -2.5866    2.9236 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1360   -1.0333    1.8956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5076   -4.3611    2.4160 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8020   -5.0825    1.5055 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0272   -4.6386    3.1924 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2200   -2.8813    4.0328 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1902   -1.2960    3.2788 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4800   -1.2177    2.8356 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3409   -2.1745    4.3107 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9625   -2.8896    2.5436 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7771   -4.0735    4.3533 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0697   -3.1710   -0.8083 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2158   -4.1495    0.0946 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1728   -2.4718    0.5185 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3678   -5.5236    0.9961 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0334   -5.5729    2.1004 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7844   -5.4421    0.2545 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8690   -3.5787   -0.0717 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9060   -0.7382    1.0533 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9839    0.5302    1.0597 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3102    1.7883    1.2243 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6840    0.6995    3.6005 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8305    2.0463    3.6205 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7044   -0.3302    2.3726 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3886    2.2473    2.0702 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7823    3.5600    2.1462 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9674    3.1904   -0.0365 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7594    3.2488   -0.0862 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8577    1.3218   -1.2851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3269    1.1598   -2.9800 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5266   -1.0156   -2.7044 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9752   -1.7252   -5.0666 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5216   -0.1040   -5.5949 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7194   -1.1683   -4.8065 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0305    0.8107   -3.7860 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1537    0.4324   -1.6856 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8962    2.4817   -4.7704 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6275    2.9871   -2.3128 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7118    1.8964   -4.8441 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9549    4.1870   -3.5387 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3863   -2.2000   -1.5120 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2873   -0.4634   -1.2346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4894   -3.8930   -0.0306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405   -3.0294   -0.6311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3541   -3.1948   -1.6999 H   0  0  0  0  0  0  0  0  0  0  0  0
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 40121  1  0
 41122  1  0
 43123  1  0
 45124  1  0
 46125  1  0
 46126  1  0
 47127  1  0
 48128  1  0
 49129  1  0
 50130  1  0
 51131  1  0
 52132  1  0
 54133  1  0
 56134  1  0
 57135  1  0
 57136  1  0
 57137  1  0
 58138  1  0
 59139  1  0
 60140  1  0
 61141  1  0
 62142  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 HMDB0035749 (Ginsenoside B2)

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       0.813   9.414   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.416   7.925   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.504   6.837   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.106   5.349   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.382   5.749   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.834   1.868   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.631   1.393   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.535   2.638   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.631   3.886   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.834   3.408   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.169   4.178   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.501   3.408   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.501   1.868   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.169   1.099   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.834   0.329   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.169   5.718   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -2.169  -0.441   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.501  -1.211   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.835  -0.441   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.835   1.099   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -4.835   2.638   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.760  10.104   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.274  10.502   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.123  11.991   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -6.167   1.868   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -7.502   1.099   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -7.502  -0.441   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -8.836  -1.211   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -7.158  -2.389   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -6.167  -1.211   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -5.179  -2.389   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       2.595   4.951   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       3.683   6.039   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       5.169   5.641   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       6.260   6.729   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       7.746   6.332   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       8.836   7.420   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       1.796   7.925   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       3.285   7.528   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       4.373   8.616   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       5.859   8.218   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       6.950   9.306   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       3.975  10.104   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      -3.501  -2.751   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -2.169  -3.521   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      -0.834  -2.751   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0       0.500  -3.521   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       1.833  -2.751   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0       3.167  -3.521   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      -6.167  -7.371   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      -4.835  -8.141   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -4.835  -9.681   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0      -6.167 -10.451   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       1.833  -5.831   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0       0.500  -5.061   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -0.834  -5.831   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -2.169  -5.061   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      -3.501  -5.831   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      -3.501  -7.371   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0      -2.169  -8.141   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0      -2.169  -9.681   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      -3.501 -10.451   0.000  0.00  0.00           C+0
HETATM   63  O   UNK     0      -3.501 -11.991   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      -0.834  -7.371   0.000  0.00  0.00           O+0
HETATM   65  C   UNK     0      -0.064   0.534   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      -0.834 -10.451   0.000  0.00  0.00           C+0
CONECT    1    2   23                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9   32                                             
CONECT    5    4                                                            
CONECT    6    7   10   14   65                                             
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    4    8   10                                                  
CONECT   10    6    9   11                                                  
CONECT   11   10   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14    6   13   15   17                                             
CONECT   15   14                                                            
CONECT   16   11                                                            
CONECT   17   14   18                                                       
CONECT   18   17   19   44                                                  
CONECT   19   18   20   30                                                  
CONECT   20   13   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   30                                                  
CONECT   28   27                                                            
CONECT   29   30                                                            
CONECT   30   19   27   29   31                                             
CONECT   31   30                                                            
CONECT   32    4   33                                                       
CONECT   33   32   34   39                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   41                                                  
CONECT   36   35   37                                                       
CONECT   37   36                                                            
CONECT   38   39                                                            
CONECT   39   33   38   40                                                  
CONECT   40   39   41   43                                                  
CONECT   41   35   40   42                                                  
CONECT   42   41                                                            
CONECT   43   40                                                            
CONECT   44   18   45                                                       
CONECT   45   44   46   57                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48   55                                                  
CONECT   48   47   49                                                       
CONECT   49   48                                                            
CONECT   50   51                                                            
CONECT   51   50   52   59                                                  
CONECT   52   51   53   62                                                  
CONECT   53   52                                                            
CONECT   54   55                                                            
CONECT   55   47   54   56                                                  
CONECT   56   55   57   64                                                  
CONECT   57   45   56   58                                                  
CONECT   58   57   59                                                       
CONECT   59   51   58   60                                                  
CONECT   60   59   61                                                       
CONECT   61   60   62   66                                                  
CONECT   62   52   61   63                                                  
CONECT   63   62                                                            
CONECT   64   56                                                            
CONECT   65    6                                                            
CONECT   66   61                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  144    0
END
Download

3D PDB for HMDB0035749 (Ginsenoside B2)

COMPND    HMDB0252725
HETATM    1  C1  UNL     1      -5.827   6.926   0.816  1.00  0.00           C  
HETATM    2  C2  UNL     1      -5.380   5.583   1.248  1.00  0.00           C  
HETATM    3  C3  UNL     1      -5.757   5.077   2.585  1.00  0.00           C  
HETATM    4  C4  UNL     1      -4.656   4.849   0.451  1.00  0.00           C  
HETATM    5  C5  UNL     1      -4.153   3.457   0.815  1.00  0.00           C  
HETATM    6  C6  UNL     1      -4.674   2.455  -0.127  1.00  0.00           C  
HETATM    7  C7  UNL     1      -4.194   0.996   0.198  1.00  0.00           C  
HETATM    8  C8  UNL     1      -4.824   0.977   1.684  1.00  0.00           C  
HETATM    9  O1  UNL     1      -4.992   0.104  -0.348  1.00  0.00           O  
HETATM   10  C9  UNL     1      -5.313  -0.081  -1.619  1.00  0.00           C  
HETATM   11  O2  UNL     1      -6.653   0.547  -1.732  1.00  0.00           O  
HETATM   12  C10 UNL     1      -7.633  -0.328  -1.391  1.00  0.00           C  
HETATM   13  C11 UNL     1      -8.819   0.514  -0.883  1.00  0.00           C  
HETATM   14  O3  UNL     1      -9.263   1.375  -1.886  1.00  0.00           O  
HETATM   15  C12 UNL     1      -7.297  -1.258  -0.253  1.00  0.00           C  
HETATM   16  O4  UNL     1      -8.429  -2.025   0.039  1.00  0.00           O  
HETATM   17  C13 UNL     1      -6.247  -2.215  -0.777  1.00  0.00           C  
HETATM   18  O5  UNL     1      -6.763  -3.410  -1.213  1.00  0.00           O  
HETATM   19  C14 UNL     1      -5.607  -1.500  -1.963  1.00  0.00           C  
HETATM   20  O6  UNL     1      -4.465  -2.197  -2.267  1.00  0.00           O  
HETATM   21  C15 UNL     1      -2.754   0.950   0.386  1.00  0.00           C  
HETATM   22  C16 UNL     1      -1.907   1.493  -0.753  1.00  0.00           C  
HETATM   23  C17 UNL     1      -0.552   0.757  -0.644  1.00  0.00           C  
HETATM   24  C18 UNL     1      -1.156  -0.665  -0.465  1.00  0.00           C  
HETATM   25  C19 UNL     1      -1.642  -0.911  -1.809  1.00  0.00           C  
HETATM   26  C20 UNL     1      -2.003  -0.281   0.691  1.00  0.00           C  
HETATM   27  C21 UNL     1      -2.488  -1.315   1.599  1.00  0.00           C  
HETATM   28  O7  UNL     1      -2.662  -0.705   2.881  1.00  0.00           O  
HETATM   29  C22 UNL     1      -1.444  -2.397   1.808  1.00  0.00           C  
HETATM   30  C23 UNL     1      -0.075  -1.998   1.368  1.00  0.00           C  
HETATM   31  C24 UNL     1       1.035  -2.901   1.829  1.00  0.00           C  
HETATM   32  C25 UNL     1       0.584  -4.291   2.206  1.00  0.00           C  
HETATM   33  C26 UNL     1       1.624  -2.333   3.132  1.00  0.00           C  
HETATM   34  C27 UNL     1       3.075  -2.205   3.209  1.00  0.00           C  
HETATM   35  C28 UNL     1       3.902  -3.272   2.608  1.00  0.00           C  
HETATM   36  O8  UNL     1       4.006  -4.414   3.436  1.00  0.00           O  
HETATM   37  C29 UNL     1       3.419  -3.578   1.249  1.00  0.00           C  
HETATM   38  C30 UNL     1       4.504  -3.270   0.200  1.00  0.00           C  
HETATM   39  C31 UNL     1       3.316  -5.113   1.155  1.00  0.00           C  
HETATM   40  C32 UNL     1       2.175  -2.918   0.802  1.00  0.00           C  
HETATM   41  C33 UNL     1       2.253  -1.525   0.328  1.00  0.00           C  
HETATM   42  O9  UNL     1       3.441  -1.032  -0.148  1.00  0.00           O  
HETATM   43  C34 UNL     1       3.802   0.217   0.345  1.00  0.00           C  
HETATM   44  O10 UNL     1       5.005   0.189   0.998  1.00  0.00           O  
HETATM   45  C35 UNL     1       5.346   1.365   1.613  1.00  0.00           C  
HETATM   46  C36 UNL     1       5.564   1.111   3.083  1.00  0.00           C  
HETATM   47  O11 UNL     1       6.606   0.169   3.223  1.00  0.00           O  
HETATM   48  C37 UNL     1       4.276   2.434   1.460  1.00  0.00           C  
HETATM   49  O12 UNL     1       4.829   3.636   1.898  1.00  0.00           O  
HETATM   50  C38 UNL     1       3.937   2.618  -0.026  1.00  0.00           C  
HETATM   51  O13 UNL     1       4.905   3.444  -0.540  1.00  0.00           O  
HETATM   52  C39 UNL     1       3.815   1.283  -0.718  1.00  0.00           C  
HETATM   53  O14 UNL     1       4.870   1.142  -1.598  1.00  0.00           O  
HETATM   54  C40 UNL     1       4.447   1.079  -2.924  1.00  0.00           C  
HETATM   55  O15 UNL     1       4.887  -0.118  -3.460  1.00  0.00           O  
HETATM   56  C41 UNL     1       6.237  -0.247  -3.483  1.00  0.00           C  
HETATM   57  C42 UNL     1       6.648  -0.907  -4.813  1.00  0.00           C  
HETATM   58  C43 UNL     1       7.062   0.957  -3.213  1.00  0.00           C  
HETATM   59  O16 UNL     1       7.471   1.106  -1.890  1.00  0.00           O  
HETATM   60  C44 UNL     1       6.481   2.239  -3.760  1.00  0.00           C  
HETATM   61  O17 UNL     1       6.871   3.274  -2.916  1.00  0.00           O  
HETATM   62  C45 UNL     1       4.971   2.199  -3.784  1.00  0.00           C  
HETATM   63  O18 UNL     1       4.364   3.412  -3.583  1.00  0.00           O  
HETATM   64  C46 UNL     1       1.146  -1.408  -0.749  1.00  0.00           C  
HETATM   65  C47 UNL     1      -0.151  -1.704  -0.095  1.00  0.00           C  
HETATM   66  C48 UNL     1      -0.735  -3.010  -0.689  1.00  0.00           C  
HETATM   67  H1  UNL     1      -5.202   7.725   1.284  1.00  0.00           H  
HETATM   68  H2  UNL     1      -6.862   7.100   1.206  1.00  0.00           H  
HETATM   69  H3  UNL     1      -5.827   7.029  -0.300  1.00  0.00           H  
HETATM   70  H4  UNL     1      -6.318   4.120   2.432  1.00  0.00           H  
HETATM   71  H5  UNL     1      -6.424   5.791   3.109  1.00  0.00           H  
HETATM   72  H6  UNL     1      -4.816   4.887   3.160  1.00  0.00           H  
HETATM   73  H7  UNL     1      -4.363   5.195  -0.539  1.00  0.00           H  
HETATM   74  H8  UNL     1      -4.532   3.329   1.866  1.00  0.00           H  
HETATM   75  H9  UNL     1      -3.076   3.598   0.895  1.00  0.00           H  
HETATM   76  H10 UNL     1      -4.502   2.662  -1.189  1.00  0.00           H  
HETATM   77  H11 UNL     1      -5.778   2.399  -0.004  1.00  0.00           H  
HETATM   78  H12 UNL     1      -4.123   1.436   2.364  1.00  0.00           H  
HETATM   79  H13 UNL     1      -5.038  -0.056   1.959  1.00  0.00           H  
HETATM   80  H14 UNL     1      -5.812   1.485   1.623  1.00  0.00           H  
HETATM   81  H15 UNL     1      -4.744   0.416  -2.421  1.00  0.00           H  
HETATM   82  H16 UNL     1      -8.064  -0.883  -2.259  1.00  0.00           H  
HETATM   83  H17 UNL     1      -8.491   1.091   0.019  1.00  0.00           H  
HETATM   84  H18 UNL     1      -9.675  -0.136  -0.612  1.00  0.00           H  
HETATM   85  H19 UNL     1      -9.853   0.848  -2.498  1.00  0.00           H  
HETATM   86  H20 UNL     1      -6.935  -0.702   0.605  1.00  0.00           H  
HETATM   87  H21 UNL     1      -8.191  -2.519   0.886  1.00  0.00           H  
HETATM   88  H22 UNL     1      -5.477  -2.388  -0.026  1.00  0.00           H  
HETATM   89  H23 UNL     1      -7.716  -3.545  -0.981  1.00  0.00           H  
HETATM   90  H24 UNL     1      -6.267  -1.590  -2.867  1.00  0.00           H  
HETATM   91  H25 UNL     1      -4.319  -2.389  -3.208  1.00  0.00           H  
HETATM   92  H26 UNL     1      -2.578   1.739   1.217  1.00  0.00           H  
HETATM   93  H27 UNL     1      -1.578   2.566  -0.569  1.00  0.00           H  
HETATM   94  H28 UNL     1      -2.340   1.510  -1.724  1.00  0.00           H  
HETATM   95  H29 UNL     1       0.008   1.070   0.233  1.00  0.00           H  
HETATM   96  H30 UNL     1      -0.103   0.909  -1.619  1.00  0.00           H  
HETATM   97  H31 UNL     1      -2.506  -0.337  -2.186  1.00  0.00           H  
HETATM   98  H32 UNL     1      -0.817  -0.537  -2.517  1.00  0.00           H  
HETATM   99  H33 UNL     1      -1.782  -1.927  -2.203  1.00  0.00           H  
HETATM  100  H34 UNL     1      -1.202   0.214   1.402  1.00  0.00           H  
HETATM  101  H35 UNL     1      -3.489  -1.747   1.395  1.00  0.00           H  
HETATM  102  H36 UNL     1      -1.913  -0.039   2.993  1.00  0.00           H  
HETATM  103  H37 UNL     1      -1.856  -3.310   1.337  1.00  0.00           H  
HETATM  104  H38 UNL     1      -1.347  -2.587   2.924  1.00  0.00           H  
HETATM  105  H39 UNL     1       0.136  -1.033   1.896  1.00  0.00           H  
HETATM  106  H40 UNL     1      -0.508  -4.361   2.416  1.00  0.00           H  
HETATM  107  H41 UNL     1       0.802  -5.082   1.506  1.00  0.00           H  
HETATM  108  H42 UNL     1       1.027  -4.639   3.192  1.00  0.00           H  
HETATM  109  H43 UNL     1       1.220  -2.881   4.033  1.00  0.00           H  
HETATM  110  H44 UNL     1       1.190  -1.296   3.279  1.00  0.00           H  
HETATM  111  H45 UNL     1       3.480  -1.218   2.836  1.00  0.00           H  
HETATM  112  H46 UNL     1       3.341  -2.174   4.311  1.00  0.00           H  
HETATM  113  H47 UNL     1       4.963  -2.890   2.544  1.00  0.00           H  
HETATM  114  H48 UNL     1       3.777  -4.074   4.353  1.00  0.00           H  
HETATM  115  H49 UNL     1       4.070  -3.171  -0.808  1.00  0.00           H  
HETATM  116  H50 UNL     1       5.216  -4.150   0.095  1.00  0.00           H  
HETATM  117  H51 UNL     1       5.173  -2.472   0.519  1.00  0.00           H  
HETATM  118  H52 UNL     1       4.368  -5.524   0.996  1.00  0.00           H  
HETATM  119  H53 UNL     1       3.033  -5.573   2.100  1.00  0.00           H  
HETATM  120  H54 UNL     1       2.784  -5.442   0.254  1.00  0.00           H  
HETATM  121  H55 UNL     1       1.869  -3.579  -0.072  1.00  0.00           H  
HETATM  122  H56 UNL     1       1.906  -0.738   1.053  1.00  0.00           H  
HETATM  123  H57 UNL     1       2.984   0.530   1.060  1.00  0.00           H  
HETATM  124  H58 UNL     1       6.310   1.788   1.224  1.00  0.00           H  
HETATM  125  H59 UNL     1       4.684   0.700   3.601  1.00  0.00           H  
HETATM  126  H60 UNL     1       5.831   2.046   3.620  1.00  0.00           H  
HETATM  127  H61 UNL     1       6.704  -0.330   2.373  1.00  0.00           H  
HETATM  128  H62 UNL     1       3.389   2.247   2.070  1.00  0.00           H  
HETATM  129  H63 UNL     1       5.782   3.560   2.146  1.00  0.00           H  
HETATM  130  H64 UNL     1       2.967   3.190  -0.037  1.00  0.00           H  
HETATM  131  H65 UNL     1       5.759   3.249  -0.086  1.00  0.00           H  
HETATM  132  H66 UNL     1       2.858   1.322  -1.285  1.00  0.00           H  
HETATM  133  H67 UNL     1       3.327   1.160  -2.980  1.00  0.00           H  
HETATM  134  H68 UNL     1       6.527  -1.016  -2.704  1.00  0.00           H  
HETATM  135  H69 UNL     1       5.975  -1.725  -5.067  1.00  0.00           H  
HETATM  136  H70 UNL     1       6.522  -0.104  -5.595  1.00  0.00           H  
HETATM  137  H71 UNL     1       7.719  -1.168  -4.807  1.00  0.00           H  
HETATM  138  H72 UNL     1       8.030   0.811  -3.786  1.00  0.00           H  
HETATM  139  H73 UNL     1       8.154   0.432  -1.686  1.00  0.00           H  
HETATM  140  H74 UNL     1       6.896   2.482  -4.770  1.00  0.00           H  
HETATM  141  H75 UNL     1       7.627   2.987  -2.313  1.00  0.00           H  
HETATM  142  H76 UNL     1       4.712   1.896  -4.844  1.00  0.00           H  
HETATM  143  H77 UNL     1       4.955   4.187  -3.539  1.00  0.00           H  
HETATM  144  H78 UNL     1       1.386  -2.200  -1.512  1.00  0.00           H  
HETATM  145  H79 UNL     1       1.287  -0.463  -1.235  1.00  0.00           H  
HETATM  146  H80 UNL     1      -0.489  -3.893  -0.031  1.00  0.00           H  
HETATM  147  H81 UNL     1      -1.840  -3.029  -0.631  1.00  0.00           H  
HETATM  148  H82 UNL     1      -0.354  -3.195  -1.700  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   40
CONECT   32  106  107  108
CONECT   33   34  109  110
CONECT   34   35  111  112
CONECT   35   36   37  113
CONECT   36  114
CONECT   37   38   39   40
CONECT   38  115  116  117
CONECT   39  118  119  120
CONECT   40   41  121
CONECT   41   42   64  122
CONECT   42   43
CONECT   43   44   52  123
CONECT   44   45
CONECT   45   46   48  124
CONECT   46   47  125  126
CONECT   47  127
CONECT   48   49   50  128
CONECT   49  129
CONECT   50   51   52  130
CONECT   51  131
CONECT   52   53  132
CONECT   53   54
CONECT   54   55   62  133
CONECT   55   56
CONECT   56   57   58  134
CONECT   57  135  136  137
CONECT   58   59   60  138
CONECT   59  139
CONECT   60   61   62  140
CONECT   61  141
CONECT   62   63  142
CONECT   63  143
CONECT   64   65  144  145
CONECT   65   66
CONECT   66  146  147  148
END
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SMILES for HMDB0035749 (Ginsenoside B2)

CC1OC(OC2C(O)C(O)C(CO)OC2OC2CC3(C)C(CC(O)C4C(CCC34C)C(C)(CCC=C(C)C)OC3OC(CO)C(O)C(O)C3O)C3(C)CCC(O)C(C)(C)C23)C(O)C(O)C1O
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INCHI for HMDB0035749 (Ginsenoside B2)

InChI=1S/C48H82O18/c1-21(2)11-10-14-48(9,66-42-38(60)35(57)32(54)26(19-49)63-42)23-12-16-46(7)30(23)24(51)17-28-45(6)15-13-29(52)44(4,5)40(45)25(18-47(28,46)8)62-43-39(36(58)33(55)27(20-50)64-43)65-41-37(59)34(56)31(53)22(3)61-41/h11,22-43,49-60H,10,12-20H2,1-9H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Chikusetsusaponin ivcHMDB
Ginsenoside reHMDB
Chemical FormulaC48H82O18
Average Molecular Weight947.1539
Monoisotopic Molecular Weight946.55011582
IUPAC Name2-[(2-{[5,16-dihydroxy-2,6,6,10,11-pentamethyl-14-(6-methyl-2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}hept-5-en-2-yl)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-8-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl)oxy]-6-methyloxane-3,4,5-triol
Traditional Name2-[(2-{[5,16-dihydroxy-2,6,6,10,11-pentamethyl-14-(6-methyl-2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}hept-5-en-2-yl)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-8-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl)oxy]-6-methyloxane-3,4,5-triol
CAS Registry Number52286-59-6
SMILES
CC1OC(OC2C(O)C(O)C(CO)OC2OC2CC3(C)C(CC(O)C4C(CCC34C)C(C)(CCC=C(C)C)OC3OC(CO)C(O)C(O)C3O)C3(C)CCC(O)C(C)(C)C23)C(O)C(O)C1O
InChI Identifier
InChI=1S/C48H82O18/c1-21(2)11-10-14-48(9,66-42-38(60)35(57)32(54)26(19-49)63-42)23-12-16-46(7)30(23)24(51)17-28-45(6)15-13-29(52)44(4,5)40(45)25(18-47(28,46)8)62-43-39(36(58)33(55)27(20-50)64-43)65-41-37(59)34(56)31(53)22(3)61-41/h11,22-43,49-60H,10,12-20H2,1-9H3
InChI KeyPWAOOJDMFUQOKB-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 Parents
Substituents
  • Triterpenoid
  • 3-hydroxysteroid
  • 12-hydroxysteroid
  • Hydroxysteroid
  • Steroid
  • Fatty acyl glycoside
  • Fatty acyl glycoside of mono- or disaccharide
  • Alkyl glycoside
  • Disaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • Fatty acyl
  • Oxane
  • Cyclic alcohol
  • Secondary alcohol
  • Organoheterocyclic compound
  • Acetal
  • Oxacycle
  • Polyol
  • Organooxygen compound
  • Alcohol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point201 - 203 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.81 g/LALOGPS
logP0.6ALOGPS
logP-0.042ChemAxon
logS-3.1ALOGPS
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 Count12ChemAxon
Refractivity234.52 m³·mol⁻¹ChemAxon
Polarizability102.74 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]-330.34630932474
DeepCCS[M+Na]+304.68530932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside B2 6V, Negative-QTOFsplash10-0002-0000003119-dc7a31ccd77743c6e1582021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside B2 6V, Positive-QTOFsplash10-0002-0300020009-165e6cc65a119bc814952021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside B2 6V, Positive-QTOFsplash10-0002-0300010109-a2cf2831898b0b5b08922021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside B2 6V, Positive-QTOFsplash10-0002-0300001009-c64b95b35c2b30f482902021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside B2 6V, Positive-QTOFsplash10-0002-0010000009-6da5506c80fe38427d492021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside B2 6V, Positive-QTOFsplash10-0002-0200000209-560f3fcaad80c828b79e2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside B2 6V, Positive-QTOFsplash10-03dr-3900000000-eb530eb1faaf1f5684942021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside B2 6V, Positive-QTOFsplash10-0fvi-2900300000-9641c26717c290ed1ef12021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside B2 6V, Positive-QTOFsplash10-0002-0000003119-505bec58da66de01e4432021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside B2 6V, Positive-QTOFsplash10-0w4r-3910201000-e6668ba9d2f93d7a1b3a2021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 10V, Negative-QTOFsplash10-00nb-2400007917-b80c56c6883503acda3a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 20V, Negative-QTOFsplash10-02u0-2900108702-f3c64a51970476ec55822016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 40V, Negative-QTOFsplash10-01w0-6700309000-18a025443d6d23c2703f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 10V, Negative-QTOFsplash10-0002-0000000239-78abb26dff53ee3a765d2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 20V, Negative-QTOFsplash10-0005-9300000584-0e4e186caa5a948a87182021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 40V, Negative-QTOFsplash10-0a4r-9200002400-8e1300be25d2e74849ba2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 10V, Positive-QTOFsplash10-00c9-0100107916-2812c9e885afd7077dbf2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 20V, Positive-QTOFsplash10-009i-0200409500-b2743b9b946e2f31936f2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 40V, Positive-QTOFsplash10-002r-1400709201-fd73d4ad5959064052962016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 10V, Positive-QTOFsplash10-00kb-0000002903-b80a4cd5cafaf6dfb2d72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 20V, Positive-QTOFsplash10-0fl1-2400308955-39d9e0c16dacdd53544f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside B2 40V, Positive-QTOFsplash10-0007-9100000110-c39f4e6c5f8a3a19ff412021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB014479
KNApSAcK IDC00003518
Chemspider ID382454
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound432449
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.