Hmdb loader

Showing metabocard for Ginsenoside Rb1 (HMDB0035892)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 20:56:13 UTC
Update Date2022-03-07 02:54:41 UTC
HMDB IDHMDB0035892
Secondary Accession Numbers
  • HMDB35892
Metabolite Identification
Common NameGinsenoside Rb1
DescriptionGinsenoside Rb1, also known as GRB 1 or gynosaponin C, belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Ginsenoside Rb1 is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563862788
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035892 (Ginsenoside Rb1)


  Mrv0541 05061308462D          

 77 84  0  0  0  0            999 V2000
    4.8506    1.9496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6375    1.1522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.6270    0.1416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.7092   -2.5388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5875   -1.7228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3904   -1.9083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8565   -1.3103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3712   -0.6421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0035892 (Ginsenoside Rb1)

HMDB0035892
     RDKit          3D
Ginsenoside Rb1
169176  0  0  0  0  0  0  0  0999 V2000
    4.4585   -5.8805   -1.8817 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5894   -4.9932   -2.2183 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1535   -4.9949   -3.5871 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1397   -4.1783   -1.3116 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6942   -4.0673    0.0969 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4714   -2.6902    0.5979 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4627   -1.7964    0.0328 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7833   -1.5942   -1.4746 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4483   -0.5122    0.4720 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5438    0.2796    0.3542 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9497    0.5504    1.6224 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7226    1.7422    2.1841 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8829    2.1377    3.0729 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0489    2.1817    2.3144 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1515    2.5486    3.0609 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7021    3.6870    2.4938 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9691    3.5715    1.1521 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2196    4.3922    0.8123 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0153    5.7289    1.1231 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2511    2.1622    0.6865 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1504    2.2074   -0.3942 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9093    1.3229    1.7620 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2600    1.6837    1.7854 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2409    1.4882    3.0962 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1995    1.9250    4.0096 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.1384   -0.6934    1.2238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9007   -1.6705    0.7768 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -12.7917    2.7356    1.9711 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6955    1.8961    2.5278 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7232    2.9990    3.3743 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0035892 (Ginsenoside Rb1)


  Mrv0541 05061308462D          

 77 84  0  0  0  0            999 V2000
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    5.3194    4.8658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1169    4.6527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6999    5.2356    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2360    0.7823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8191    1.3653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6059    2.1627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1888    2.7457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9757    3.5431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9284    5.5066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7259    5.2934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3088    5.8764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1063    5.6632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6893    6.2462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8097    2.3758    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0957    6.6724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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 74 75  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035892

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCCC(C)(OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C

> <INCHI_IDENTIFIER>
InChI=1S/C54H92O23/c1-23(2)10-9-14-54(8,77-48-44(69)40(65)37(62)29(74-48)22-70-46-42(67)38(63)34(59)26(19-55)71-46)24-11-16-53(7)33(24)25(58)18-31-51(5)15-13-32(50(3,4)30(51)12-17-52(31,53)6)75-49-45(41(66)36(61)28(21-57)73-49)76-47-43(68)39(64)35(60)27(20-56)72-47/h10,24-49,55-69H,9,11-22H2,1-8H3

> <INCHI_KEY>
GZYPWOGIYAIIPV-UHFFFAOYSA-N

> <FORMULA>
C54H92O23

> <MOLECULAR_WEIGHT>
1109.2945

> <EXACT_MASS>
1108.60293925

> <JCHEM_ACCEPTOR_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
119.44170608059684

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
15

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.24

> <JCHEM_LOGP>
-1.5514047776666662

> <ALOGPS_LOGS>
-3.02

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.185134421885058

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.751605954439546

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6486743719488306

> <JCHEM_POLAR_SURFACE_AREA>
377.29

> <JCHEM_REFRACTIVITY>
266.88910000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.07e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0035892 (Ginsenoside Rb1)

HMDB0035892
     RDKit          3D
Ginsenoside Rb1
169176  0  0  0  0  0  0  0  0999 V2000
    4.4585   -5.8805   -1.8817 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5894   -4.9932   -2.2183 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1535   -4.9949   -3.5871 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1397   -4.1783   -1.3116 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6942   -4.0673    0.0969 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4714   -2.6902    0.5979 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4627   -1.7964    0.0328 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7833   -1.5942   -1.4746 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4483   -0.5122    0.4720 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5438    0.2796    0.3542 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9497    0.5504    1.6224 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7226    1.7422    2.1841 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8829    2.1377    3.0729 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0489    2.1817    2.3144 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1515    2.5486    3.0609 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7021    3.6870    2.4938 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9691    3.5715    1.1521 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2196    4.3922    0.8123 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0153    5.7289    1.1231 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2511    2.1622    0.6865 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1504    2.2074   -0.3942 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9093    1.3229    1.7620 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2600    1.6837    1.7854 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2409    1.4882    3.0962 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1995    1.9250    4.0096 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3314    2.8938    1.3338 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5935    4.1022    1.9607 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0874    2.7142    0.0378 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8162    3.7362   -0.8732 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4528    1.4508   -0.5707 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1901    1.2761   -1.7585 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1309   -2.4028    0.0871 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5744   -2.8498    1.4200 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3151   -3.5427    0.8484 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9321   -2.8231   -0.3985 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2329   -3.5696   -1.6777 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9190   -1.6253   -0.3706 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3954   -0.5374    0.4542 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2786    0.0923    1.3319 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1384   -0.6934    1.2238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9007   -1.6705    0.7768 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2800   -1.0315    0.7351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3752   -0.1919    2.0198 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4137   -1.9886    0.8306 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4327   -1.8260   -0.2611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9209   -0.3941   -0.3142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9533   -0.1574   -1.1561 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1772    0.0826   -0.6544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1531   -0.7436   -1.1992 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7946   -0.9850   -2.5214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8043   -1.8808   -3.1844 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3910   -2.0789   -4.5112 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5853    0.3117   -3.2152 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3919    0.2841   -4.3822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9685    1.5428   -2.4463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2943    1.8478   -2.7563 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7133    1.4962   -0.9788 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9712    1.5058   -0.3186 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0437    2.4182    0.7015 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0137    3.3830    0.5941 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2158    2.8007    0.2350 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2452    3.8702   -0.1573 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4630    4.7183    0.9345 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7223    2.0176    1.4271 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7917    2.7356    1.9711 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6955    1.8961    2.5278 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7232    2.9990    3.3743 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3102    1.6396    1.9798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3966    2.0882    2.9304 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7558    0.4645   -0.6936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9663    0.8813   -2.1310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9849    1.7757    0.0997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3949   -0.0539   -0.4034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6692   -0.4408   -1.6493 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8005   -1.6080   -1.6870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5141   -2.3944   -0.4723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2552   -3.7373   -0.6071 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5590   -5.2781   -1.8249 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7341   -6.4007   -0.9364 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3575   -6.6229   -2.7222 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5919   -4.3419   -4.2545 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1808   -6.0160   -4.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2195   -4.6597   -3.5948 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9875   -3.5368   -1.5974 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5355   -4.5850    0.6712 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8351   -4.7585    0.3068 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5069   -2.2475    0.6515 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2737   -2.8362    1.7236 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1498   -0.7293   -1.8400 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3872   -2.4375   -2.0686 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8312   -1.4676   -1.6782 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3618   -0.3510   -0.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8604    1.6009    2.9174 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9463    1.4712    3.9567 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7429    3.1737    3.4754 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8359    2.7526    4.1076 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1557    3.9628    0.4971 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4023    4.3359   -0.2960 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.1094    3.9740    1.2973 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3318    6.3124    0.3852 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3672    1.6172    0.3349 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.5447    1.3243   -0.5598 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8651    0.2711    1.4460 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6393    1.6678    2.7119 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8609    0.5210    3.4858 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2258    2.9235    3.9865 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2414    2.8093    1.0975 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8562    4.7595    1.2611 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1660    2.5650    0.1903 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6467    3.3762   -1.7979 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4314    1.7746   -0.8329 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6392    1.3537   -2.5620 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1165   -3.3685   -0.4911 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2212   -3.6143    1.8970 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2338   -2.0918    2.0898 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7095   -4.5506    0.5181 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.1301   -1.3541   -1.4264 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2004    0.3181   -0.2877 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8464    0.9527    1.5994 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3328   -0.8042    2.3136 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.0275   -1.8862    1.7856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9624   -2.0526   -1.2252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2995   -2.4710   -0.0755 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.8439   -1.5972   -2.4562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6679   -2.8988   -2.7089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8365   -1.5590   -3.0824 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.5404    0.4085   -3.6396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1739    1.1592   -4.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.8852    1.0624   -2.8059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0520    2.2579   -0.5639 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0606    2.9630    0.7656 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1263    2.0770   -0.6051 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9161    4.4622   -1.0183 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.2204    3.4113   -0.3961 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.4076    4.9097    1.0921 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1331    1.0381    1.1220 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.4211    2.1785    2.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.9665    1.0068    3.1318 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8925    2.7345    4.3134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1718    0.5512    1.8538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4202    1.4093    3.6754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0873    1.4184   -2.4796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3474    0.0714   -2.7790 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8012    1.6287   -2.1211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0202    2.3337    0.1501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7232    2.4065   -0.4351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4163    1.5485    1.0948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8347    0.8825   -0.0771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4874   -0.5510   -2.4405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0962    0.4493   -2.0848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1761   -2.2704   -2.5431 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2118   -1.3038   -2.1150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6277   -4.4041   -1.2733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1886   -3.6656   -1.1497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2520   -4.3095    0.3381 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0035892 (Ginsenoside Rb1)

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       9.054   3.639   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.657   2.151   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.168   1.753   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.770   0.264   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.256  -0.133   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.057  -4.739   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.830  -3.216   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.329  -3.562   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.199  -2.446   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.293  -1.199   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.694  -1.681   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.496  -0.906   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.164  -1.676   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.164  -3.216   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.496  -3.986   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.514  -2.454   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       3.496   0.634   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       3.496  -5.526   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.164  -6.296   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.829  -5.526   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.829  -3.986   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.829  -2.446   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.631   2.949   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.543   4.037   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.941   5.523   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.506  -3.216   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.838  -3.986   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.838  -5.526   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -3.172  -6.296   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -4.507  -5.526   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.507  -3.986   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -5.839  -3.216   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.839  -1.676   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -7.173  -0.906   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -5.839 -10.915   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -7.173 -10.145   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -8.505 -10.915   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -8.505 -12.455   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0     -12.506  -8.605   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0     -11.175  -7.836   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -9.840  -8.605   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      -8.505  -7.836   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -7.173  -8.605   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      -5.839  -7.836   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -5.839  -6.296   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -7.173  -5.526   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -7.173  -3.986   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0      -8.505  -3.216   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0      -9.840 -10.145   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0     -11.175 -10.915   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -8.505  -6.296   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      -1.494  -7.474   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      -0.506  -6.296   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       0.485  -7.474   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0       5.282   0.665   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0       4.884   2.151   0.000  0.00  0.00           C+0
HETATM   57  O   UNK     0       5.972   3.239   0.000  0.00  0.00           O+0
HETATM   58  C   UNK     0       5.574   4.728   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0       6.662   5.816   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0       6.265   7.304   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0       7.353   8.393   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0       8.841   7.995   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0       9.930   9.083   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      11.418   8.685   0.000  0.00  0.00           C+0
HETATM   65  O   UNK     0      12.506   9.773   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       2.307   1.460   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0       3.396   2.549   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0       2.998   4.037   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0       4.086   5.125   0.000  0.00  0.00           C+0
HETATM   70  O   UNK     0       3.688   6.614   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0       5.466  10.279   0.000  0.00  0.00           O+0
HETATM   72  C   UNK     0       6.955   9.881   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0       8.043  10.969   0.000  0.00  0.00           C+0
HETATM   74  C   UNK     0       9.532  10.571   0.000  0.00  0.00           C+0
HETATM   75  O   UNK     0      10.620  11.660   0.000  0.00  0.00           O+0
HETATM   76  O   UNK     0       1.511   4.435   0.000  0.00  0.00           O+0
HETATM   77  O   UNK     0       7.645  12.455   0.000  0.00  0.00           O+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                                                            
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   72                                                  
CONECT   62   61   63                                                       
CONECT   63   62   64   74                                                  
CONECT   64   63   65                                                       
CONECT   65   64                                                            
CONECT   66   67                                                            
CONECT   67   56   66   68                                                  
CONECT   68   67   69   76                                                  
CONECT   69   58   68   70                                                  
CONECT   70   69                                                            
CONECT   71   72                                                            
CONECT   72   61   71   73                                                  
CONECT   73   72   74   77                                                  
CONECT   74   63   73   75                                                  
CONECT   75   74                                                            
CONECT   76   68                                                            
CONECT   77   73                                                            
MASTER        0    0    0    0    0    0    0    0   77    0  168    0
END
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3D PDB for HMDB0035892 (Ginsenoside Rb1)

COMPND    HMDB0035892
HETATM    1  C1  UNL     1       4.458  -5.881  -1.882  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.589  -4.993  -2.218  1.00  0.00           C  
HETATM    3  C3  UNL     1       6.154  -4.995  -3.587  1.00  0.00           C  
HETATM    4  C4  UNL     1       6.140  -4.178  -1.312  1.00  0.00           C  
HETATM    5  C5  UNL     1       5.694  -4.067   0.097  1.00  0.00           C  
HETATM    6  C6  UNL     1       5.471  -2.690   0.598  1.00  0.00           C  
HETATM    7  C7  UNL     1       4.463  -1.796   0.033  1.00  0.00           C  
HETATM    8  C8  UNL     1       4.783  -1.594  -1.475  1.00  0.00           C  
HETATM    9  O1  UNL     1       4.448  -0.512   0.472  1.00  0.00           O  
HETATM   10  C9  UNL     1       5.544   0.280   0.354  1.00  0.00           C  
HETATM   11  O2  UNL     1       5.950   0.550   1.622  1.00  0.00           O  
HETATM   12  C10 UNL     1       5.723   1.742   2.184  1.00  0.00           C  
HETATM   13  C11 UNL     1       6.883   2.138   3.073  1.00  0.00           C  
HETATM   14  O3  UNL     1       8.049   2.182   2.314  1.00  0.00           O  
HETATM   15  C12 UNL     1       9.152   2.549   3.061  1.00  0.00           C  
HETATM   16  O4  UNL     1       9.702   3.687   2.494  1.00  0.00           O  
HETATM   17  C13 UNL     1       9.969   3.572   1.152  1.00  0.00           C  
HETATM   18  C14 UNL     1      11.220   4.392   0.812  1.00  0.00           C  
HETATM   19  O5  UNL     1      11.015   5.729   1.123  1.00  0.00           O  
HETATM   20  C15 UNL     1      10.251   2.162   0.687  1.00  0.00           C  
HETATM   21  O6  UNL     1      11.150   2.207  -0.394  1.00  0.00           O  
HETATM   22  C16 UNL     1      10.909   1.323   1.762  1.00  0.00           C  
HETATM   23  O7  UNL     1      12.260   1.684   1.785  1.00  0.00           O  
HETATM   24  C17 UNL     1      10.241   1.488   3.096  1.00  0.00           C  
HETATM   25  O8  UNL     1      11.199   1.925   4.010  1.00  0.00           O  
HETATM   26  C18 UNL     1       5.331   2.894   1.334  1.00  0.00           C  
HETATM   27  O9  UNL     1       5.593   4.102   1.961  1.00  0.00           O  
HETATM   28  C19 UNL     1       6.087   2.714   0.038  1.00  0.00           C  
HETATM   29  O10 UNL     1       5.816   3.736  -0.873  1.00  0.00           O  
HETATM   30  C20 UNL     1       5.453   1.451  -0.571  1.00  0.00           C  
HETATM   31  O11 UNL     1       6.190   1.276  -1.758  1.00  0.00           O  
HETATM   32  C21 UNL     1       3.131  -2.403   0.087  1.00  0.00           C  
HETATM   33  C22 UNL     1       2.574  -2.850   1.420  1.00  0.00           C  
HETATM   34  C23 UNL     1       1.315  -3.543   0.848  1.00  0.00           C  
HETATM   35  C24 UNL     1       0.932  -2.823  -0.398  1.00  0.00           C  
HETATM   36  C25 UNL     1       1.233  -3.570  -1.678  1.00  0.00           C  
HETATM   37  C26 UNL     1       1.919  -1.625  -0.371  1.00  0.00           C  
HETATM   38  C27 UNL     1       1.395  -0.537   0.454  1.00  0.00           C  
HETATM   39  O12 UNL     1       2.279   0.092   1.332  1.00  0.00           O  
HETATM   40  C28 UNL     1       0.138  -0.693   1.224  1.00  0.00           C  
HETATM   41  C29 UNL     1      -0.901  -1.670   0.777  1.00  0.00           C  
HETATM   42  C30 UNL     1      -2.280  -1.032   0.735  1.00  0.00           C  
HETATM   43  C31 UNL     1      -2.375  -0.192   2.020  1.00  0.00           C  
HETATM   44  C32 UNL     1      -3.414  -1.989   0.831  1.00  0.00           C  
HETATM   45  C33 UNL     1      -4.433  -1.826  -0.261  1.00  0.00           C  
HETATM   46  C34 UNL     1      -4.921  -0.394  -0.314  1.00  0.00           C  
HETATM   47  O13 UNL     1      -5.953  -0.157  -1.156  1.00  0.00           O  
HETATM   48  C35 UNL     1      -7.177   0.083  -0.654  1.00  0.00           C  
HETATM   49  O14 UNL     1      -8.153  -0.744  -1.199  1.00  0.00           O  
HETATM   50  C36 UNL     1      -7.795  -0.985  -2.521  1.00  0.00           C  
HETATM   51  C37 UNL     1      -8.804  -1.881  -3.184  1.00  0.00           C  
HETATM   52  O15 UNL     1      -8.391  -2.079  -4.511  1.00  0.00           O  
HETATM   53  C38 UNL     1      -7.585   0.312  -3.215  1.00  0.00           C  
HETATM   54  O16 UNL     1      -8.392   0.284  -4.382  1.00  0.00           O  
HETATM   55  C39 UNL     1      -7.969   1.543  -2.446  1.00  0.00           C  
HETATM   56  O17 UNL     1      -9.294   1.848  -2.756  1.00  0.00           O  
HETATM   57  C40 UNL     1      -7.713   1.496  -0.979  1.00  0.00           C  
HETATM   58  O18 UNL     1      -8.971   1.506  -0.319  1.00  0.00           O  
HETATM   59  C41 UNL     1      -9.044   2.418   0.702  1.00  0.00           C  
HETATM   60  O19 UNL     1     -10.014   3.383   0.594  1.00  0.00           O  
HETATM   61  C42 UNL     1     -11.216   2.801   0.235  1.00  0.00           C  
HETATM   62  C43 UNL     1     -12.245   3.870  -0.157  1.00  0.00           C  
HETATM   63  O20 UNL     1     -12.463   4.718   0.934  1.00  0.00           O  
HETATM   64  C44 UNL     1     -11.722   2.018   1.427  1.00  0.00           C  
HETATM   65  O21 UNL     1     -12.792   2.736   1.971  1.00  0.00           O  
HETATM   66  C45 UNL     1     -10.695   1.896   2.528  1.00  0.00           C  
HETATM   67  O22 UNL     1     -10.723   2.999   3.374  1.00  0.00           O  
HETATM   68  C46 UNL     1      -9.310   1.640   1.980  1.00  0.00           C  
HETATM   69  O23 UNL     1      -8.397   2.088   2.930  1.00  0.00           O  
HETATM   70  C47 UNL     1      -3.756   0.464  -0.694  1.00  0.00           C  
HETATM   71  C48 UNL     1      -3.966   0.881  -2.131  1.00  0.00           C  
HETATM   72  C49 UNL     1      -3.985   1.776   0.100  1.00  0.00           C  
HETATM   73  C50 UNL     1      -2.395  -0.054  -0.403  1.00  0.00           C  
HETATM   74  C51 UNL     1      -1.669  -0.441  -1.649  1.00  0.00           C  
HETATM   75  C52 UNL     1      -0.801  -1.608  -1.687  1.00  0.00           C  
HETATM   76  C53 UNL     1      -0.514  -2.394  -0.472  1.00  0.00           C  
HETATM   77  C54 UNL     1      -1.255  -3.737  -0.607  1.00  0.00           C  
HETATM   78  H1  UNL     1       3.559  -5.278  -1.825  1.00  0.00           H  
HETATM   79  H2  UNL     1       4.734  -6.401  -0.936  1.00  0.00           H  
HETATM   80  H3  UNL     1       4.358  -6.623  -2.722  1.00  0.00           H  
HETATM   81  H4  UNL     1       5.592  -4.342  -4.254  1.00  0.00           H  
HETATM   82  H5  UNL     1       6.181  -6.016  -4.028  1.00  0.00           H  
HETATM   83  H6  UNL     1       7.220  -4.660  -3.595  1.00  0.00           H  
HETATM   84  H7  UNL     1       6.988  -3.537  -1.597  1.00  0.00           H  
HETATM   85  H8  UNL     1       6.535  -4.585   0.671  1.00  0.00           H  
HETATM   86  H9  UNL     1       4.835  -4.759   0.307  1.00  0.00           H  
HETATM   87  H10 UNL     1       6.507  -2.247   0.652  1.00  0.00           H  
HETATM   88  H11 UNL     1       5.274  -2.836   1.724  1.00  0.00           H  
HETATM   89  H12 UNL     1       4.150  -0.729  -1.840  1.00  0.00           H  
HETATM   90  H13 UNL     1       4.387  -2.438  -2.069  1.00  0.00           H  
HETATM   91  H14 UNL     1       5.831  -1.468  -1.678  1.00  0.00           H  
HETATM   92  H15 UNL     1       6.362  -0.351  -0.086  1.00  0.00           H  
HETATM   93  H16 UNL     1       4.860   1.601   2.917  1.00  0.00           H  
HETATM   94  H17 UNL     1       6.946   1.471   3.957  1.00  0.00           H  
HETATM   95  H18 UNL     1       6.743   3.174   3.475  1.00  0.00           H  
HETATM   96  H19 UNL     1       8.836   2.753   4.108  1.00  0.00           H  
HETATM   97  H20 UNL     1       9.156   3.963   0.497  1.00  0.00           H  
HETATM   98  H21 UNL     1      11.402   4.336  -0.296  1.00  0.00           H  
HETATM   99  H22 UNL     1      12.109   3.974   1.297  1.00  0.00           H  
HETATM  100  H23 UNL     1      11.332   6.312   0.385  1.00  0.00           H  
HETATM  101  H24 UNL     1       9.367   1.617   0.335  1.00  0.00           H  
HETATM  102  H25 UNL     1      11.545   1.324  -0.560  1.00  0.00           H  
HETATM  103  H26 UNL     1      10.865   0.271   1.446  1.00  0.00           H  
HETATM  104  H27 UNL     1      12.639   1.668   2.712  1.00  0.00           H  
HETATM  105  H28 UNL     1       9.861   0.521   3.486  1.00  0.00           H  
HETATM  106  H29 UNL     1      11.226   2.923   3.987  1.00  0.00           H  
HETATM  107  H30 UNL     1       4.241   2.809   1.097  1.00  0.00           H  
HETATM  108  H31 UNL     1       5.856   4.760   1.261  1.00  0.00           H  
HETATM  109  H32 UNL     1       7.166   2.565   0.190  1.00  0.00           H  
HETATM  110  H33 UNL     1       5.647   3.376  -1.798  1.00  0.00           H  
HETATM  111  H34 UNL     1       4.431   1.775  -0.833  1.00  0.00           H  
HETATM  112  H35 UNL     1       5.639   1.354  -2.562  1.00  0.00           H  
HETATM  113  H36 UNL     1       3.116  -3.368  -0.491  1.00  0.00           H  
HETATM  114  H37 UNL     1       3.221  -3.614   1.897  1.00  0.00           H  
HETATM  115  H38 UNL     1       2.234  -2.092   2.090  1.00  0.00           H  
HETATM  116  H39 UNL     1       1.710  -4.551   0.518  1.00  0.00           H  
HETATM  117  H40 UNL     1       0.575  -3.732   1.595  1.00  0.00           H  
HETATM  118  H41 UNL     1       1.320  -4.661  -1.525  1.00  0.00           H  
HETATM  119  H42 UNL     1       0.482  -3.358  -2.499  1.00  0.00           H  
HETATM  120  H43 UNL     1       2.160  -3.181  -2.206  1.00  0.00           H  
HETATM  121  H44 UNL     1       2.130  -1.354  -1.426  1.00  0.00           H  
HETATM  122  H45 UNL     1       1.200   0.318  -0.288  1.00  0.00           H  
HETATM  123  H46 UNL     1       1.846   0.953   1.599  1.00  0.00           H  
HETATM  124  H47 UNL     1       0.333  -0.804   2.314  1.00  0.00           H  
HETATM  125  H48 UNL     1      -0.379   0.322   1.217  1.00  0.00           H  
HETATM  126  H49 UNL     1      -0.986  -2.451   1.565  1.00  0.00           H  
HETATM  127  H50 UNL     1      -1.738  -0.605   2.817  1.00  0.00           H  
HETATM  128  H51 UNL     1      -3.423  -0.226   2.446  1.00  0.00           H  
HETATM  129  H52 UNL     1      -2.210   0.887   1.837  1.00  0.00           H  
HETATM  130  H53 UNL     1      -3.083  -3.016   0.878  1.00  0.00           H  
HETATM  131  H54 UNL     1      -4.027  -1.886   1.786  1.00  0.00           H  
HETATM  132  H55 UNL     1      -3.962  -2.053  -1.225  1.00  0.00           H  
HETATM  133  H56 UNL     1      -5.300  -2.471  -0.075  1.00  0.00           H  
HETATM  134  H57 UNL     1      -5.293  -0.222   0.748  1.00  0.00           H  
HETATM  135  H58 UNL     1      -7.275  -0.003   0.449  1.00  0.00           H  
HETATM  136  H59 UNL     1      -6.844  -1.597  -2.456  1.00  0.00           H  
HETATM  137  H60 UNL     1      -8.668  -2.899  -2.709  1.00  0.00           H  
HETATM  138  H61 UNL     1      -9.836  -1.559  -3.082  1.00  0.00           H  
HETATM  139  H62 UNL     1      -7.397  -2.002  -4.550  1.00  0.00           H  
HETATM  140  H63 UNL     1      -6.540   0.408  -3.640  1.00  0.00           H  
HETATM  141  H64 UNL     1      -8.174   1.159  -4.837  1.00  0.00           H  
HETATM  142  H65 UNL     1      -7.375   2.383  -2.910  1.00  0.00           H  
HETATM  143  H66 UNL     1      -9.885   1.062  -2.806  1.00  0.00           H  
HETATM  144  H67 UNL     1      -7.052   2.258  -0.564  1.00  0.00           H  
HETATM  145  H68 UNL     1      -8.061   2.963   0.766  1.00  0.00           H  
HETATM  146  H69 UNL     1     -11.126   2.077  -0.605  1.00  0.00           H  
HETATM  147  H70 UNL     1     -11.916   4.462  -1.018  1.00  0.00           H  
HETATM  148  H71 UNL     1     -13.220   3.411  -0.396  1.00  0.00           H  
HETATM  149  H72 UNL     1     -13.408   4.910   1.092  1.00  0.00           H  
HETATM  150  H73 UNL     1     -12.133   1.038   1.122  1.00  0.00           H  
HETATM  151  H74 UNL     1     -13.421   2.179   2.480  1.00  0.00           H  
HETATM  152  H75 UNL     1     -10.966   1.007   3.132  1.00  0.00           H  
HETATM  153  H76 UNL     1     -10.892   2.735   4.313  1.00  0.00           H  
HETATM  154  H77 UNL     1      -9.172   0.551   1.854  1.00  0.00           H  
HETATM  155  H78 UNL     1      -8.420   1.409   3.675  1.00  0.00           H  
HETATM  156  H79 UNL     1      -3.087   1.418  -2.480  1.00  0.00           H  
HETATM  157  H80 UNL     1      -4.347   0.071  -2.779  1.00  0.00           H  
HETATM  158  H81 UNL     1      -4.801   1.629  -2.121  1.00  0.00           H  
HETATM  159  H82 UNL     1      -3.020   2.334   0.150  1.00  0.00           H  
HETATM  160  H83 UNL     1      -4.723   2.406  -0.435  1.00  0.00           H  
HETATM  161  H84 UNL     1      -4.416   1.549   1.095  1.00  0.00           H  
HETATM  162  H85 UNL     1      -1.835   0.883  -0.077  1.00  0.00           H  
HETATM  163  H86 UNL     1      -2.487  -0.551  -2.441  1.00  0.00           H  
HETATM  164  H87 UNL     1      -1.096   0.449  -2.085  1.00  0.00           H  
HETATM  165  H88 UNL     1      -1.176  -2.270  -2.543  1.00  0.00           H  
HETATM  166  H89 UNL     1       0.212  -1.304  -2.115  1.00  0.00           H  
HETATM  167  H90 UNL     1      -0.628  -4.404  -1.273  1.00  0.00           H  
HETATM  168  H91 UNL     1      -2.189  -3.666  -1.150  1.00  0.00           H  
HETATM  169  H92 UNL     1      -1.252  -4.309   0.338  1.00  0.00           H  
CONECT    1    2   78   79   80
CONECT    2    3    4    4
CONECT    3   81   82   83
CONECT    4    5   84
CONECT    5    6   85   86
CONECT    6    7   87   88
CONECT    7    8    9   32
CONECT    8   89   90   91
CONECT    9   10
CONECT   10   11   30   92
CONECT   11   12
CONECT   12   13   26   93
CONECT   13   14   94   95
CONECT   14   15
CONECT   15   16   24   96
CONECT   16   17
CONECT   17   18   20   97
CONECT   18   19   98   99
CONECT   19  100
CONECT   20   21   22  101
CONECT   21  102
CONECT   22   23   24  103
CONECT   23  104
CONECT   24   25  105
CONECT   25  106
CONECT   26   27   28  107
CONECT   27  108
CONECT   28   29   30  109
CONECT   29  110
CONECT   30   31  111
CONECT   31  112
CONECT   32   33   37  113
CONECT   33   34  114  115
CONECT   34   35  116  117
CONECT   35   36   37   76
CONECT   36  118  119  120
CONECT   37   38  121
CONECT   38   39   40  122
CONECT   39  123
CONECT   40   41  124  125
CONECT   41   42   76  126
CONECT   42   43   44   73
CONECT   43  127  128  129
CONECT   44   45  130  131
CONECT   45   46  132  133
CONECT   46   47   70  134
CONECT   47   48
CONECT   48   49   57  135
CONECT   49   50
CONECT   50   51   53  136
CONECT   51   52  137  138
CONECT   52  139
CONECT   53   54   55  140
CONECT   54  141
CONECT   55   56   57  142
CONECT   56  143
CONECT   57   58  144
CONECT   58   59
CONECT   59   60   68  145
CONECT   60   61
CONECT   61   62   64  146
CONECT   62   63  147  148
CONECT   63  149
CONECT   64   65   66  150
CONECT   65  151
CONECT   66   67   68  152
CONECT   67  153
CONECT   68   69  154
CONECT   69  155
CONECT   70   71   72   73
CONECT   71  156  157  158
CONECT   72  159  160  161
CONECT   73   74  162
CONECT   74   75  163  164
CONECT   75   76  165  166
CONECT   76   77
CONECT   77  167  168  169
END
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SMILES for HMDB0035892 (Ginsenoside Rb1)

CC(C)=CCCC(C)(OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C
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INCHI for HMDB0035892 (Ginsenoside Rb1)

InChI=1S/C54H92O23/c1-23(2)10-9-14-54(8,77-48-44(69)40(65)37(62)29(74-48)22-70-46-42(67)38(63)34(59)26(19-55)71-46)24-11-16-53(7)33(24)25(58)18-31-51(5)15-13-32(50(3,4)30(51)12-17-52(31,53)6)75-49-45(41(66)36(61)28(21-57)73-49)76-47-43(68)39(64)35(60)27(20-56)72-47/h10,24-49,55-69H,9,11-22H2,1-8H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
GRB 1HMDB
Gynosaponin CHMDB
Gypenoside IIIHMDB
Sanchinoside e1HMDB
Sanchinoside RB1HMDB
Chemical FormulaC54H92O23
Average Molecular Weight1109.2945
Monoisotopic Molecular Weight1108.60293925
IUPAC Name2-{[2-(5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-6-methylhept-5-en-2-yl]oxy}-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxane-3,4,5-triol
Traditional Name2-{[2-(5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-6-methylhept-5-en-2-yl]oxy}-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxane-3,4,5-triol
CAS Registry Number41753-43-9
SMILES
CC(C)=CCCC(C)(OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C
InChI Identifier
InChI=1S/C54H92O23/c1-23(2)10-9-14-54(8,77-48-44(69)40(65)37(62)29(74-48)22-70-46-42(67)38(63)34(59)26(19-55)71-46)24-11-16-53(7)33(24)25(58)18-31-51(5)15-13-32(50(3,4)30(51)12-17-52(31,53)6)75-49-45(41(66)36(61)28(21-57)73-49)76-47-43(68)39(64)35(60)27(20-56)72-47/h10,24-49,55-69H,9,11-22H2,1-8H3
InChI KeyGZYPWOGIYAIIPV-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
  • Steroidal glycoside
  • 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
  • Polyol
  • Acetal
  • Organoheterocyclic compound
  • Oxacycle
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Alcohol
  • Primary alcohol
  • Organooxygen compound
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
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 Point197 - 198 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.07 g/LALOGPS
logP-0.24ALOGPS
logP-1.6ChemAxon
logS-3ALOGPS
pKa (Strongest Acidic)11.75ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count23ChemAxon
Hydrogen Donor Count15ChemAxon
Polar Surface Area377.29 ŲChemAxon
Rotatable Bond Count16ChemAxon
Refractivity266.89 m³·mol⁻¹ChemAxon
Polarizability119.44 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]-352.64630932474
DeepCCS[M+Na]+326.66630932474
AllCCS[M+H]+329.932859911
AllCCS[M+H-H2O]+330.232859911
AllCCS[M+NH4]+329.632859911
AllCCS[M+Na]+329.532859911
AllCCS[M-H]-281.832859911
AllCCS[M+Na-2H]-288.432859911
AllCCS[M+HCOO]-295.632859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-0a4i-0900000000-51177c0113617d95fcd82021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-004i-2910000000-d7fdc31e47ae79a41b6c2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-0a4i-0900000000-281827a3bdc07fdd06692021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-0a4i-0900000000-3451c8d9db6a83e00baf2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-0a4i-0900000000-68cc5a03ccee98ab006d2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-004i-0129503201-a15114dfba33d8ddcf5b2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-0a4i-0900000000-572beb81205d6acf65402021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-0a4i-0900000000-abbdb7cac81ef6d63b452021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-01t9-1910000000-c7e56908c1c275d2741c2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-0mmr-1910000000-f216da3b07e37fdbd7f62021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-004i-0129503201-7023fb058b6f0ccbbb5a2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Negative-QTOFsplash10-0a4i-0900000000-68f2a89937eadcbd947b2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Rb1 6V, Positive-QTOFsplash10-0a4i-0900000000-91fa87d785090f9e9a372021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 10V, Positive-QTOFsplash10-0173-4100101904-10bb8cba28885805c23b2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 20V, Positive-QTOFsplash10-01bi-1100405903-d4402afa719645ee82842015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 40V, Positive-QTOFsplash10-0avi-4401907601-f6216a287dfd117116602015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 10V, Positive-QTOFsplash10-0173-4100101904-10bb8cba28885805c23b2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 20V, Positive-QTOFsplash10-01bi-1100405903-d4402afa719645ee82842015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 40V, Positive-QTOFsplash10-0avi-4401907601-f6216a287dfd117116602015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 10V, Negative-QTOFsplash10-05s0-7920002705-3c44fd62e183b9751d672015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 20V, Negative-QTOFsplash10-01u9-8901102804-734e6c50d043e5e5df132015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 40V, Negative-QTOFsplash10-057i-3921405601-d2146dcfc3738bc7535a2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 10V, Negative-QTOFsplash10-05s0-7920002705-3c44fd62e183b9751d672015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 20V, Negative-QTOFsplash10-01u9-8901102804-734e6c50d043e5e5df132015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Rb1 40V, Negative-QTOFsplash10-057i-3921405601-d2146dcfc3738bc7535a2015-04-25Wishart 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 IDFDB014677
KNApSAcK IDC00030394
Chemspider ID382521
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound432524
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.