Hmdb loader

Showing metabocard for Ginsenoside Ro (HMDB0034534)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 19:23:35 UTC
Update Date2022-03-07 02:54:08 UTC
HMDB IDHMDB0034534
Secondary Accession Numbers
  • HMDB34534
Metabolite Identification
Common NameGinsenoside Ro
DescriptionGinsenoside Ro belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton. Based on a literature review a significant number of articles have been published on Ginsenoside Ro.
Structure
Data?1563862577
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0034534 (Ginsenoside Ro)


  Mrv0541 02241217122D          

 67 74  0  0  0  0            999 V2000
    3.9299    2.9845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9299    2.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2149    1.7470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2149    0.9221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5342    0.5728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7861    0.9221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1986    0.2070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5011    2.9845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5011    2.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7299    1.7140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0712    2.1595    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 HMDB0034534 (Ginsenoside Ro)

HMDB0034534
     RDKit          3D
Ginsenoside Ro
143150  0  0  0  0  0  0  0  0999 V2000
    6.9181   -2.9040   -2.1819 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2255   -3.7049   -1.1452 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2950   -5.1724   -1.5972 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8391   -3.6459    0.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0047   -2.8517    1.1973 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4042   -1.6080    0.5699 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4756   -0.6674    0.2079 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6731   -1.0128    0.5011 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3329    0.5458   -0.4109 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4774    1.3305   -0.6852 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4336    2.5118    0.0553 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6017    3.2388   -0.0543 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3385    4.7273   -0.0066 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7295    5.0780    1.1967 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4071    2.9094   -1.2702 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3444    1.9075   -1.0275 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5941    2.5827   -2.4908 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0510    3.7111   -3.0754 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5161    1.6013   -2.1666 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7349    0.3947   -2.8342 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5216   -0.9751    1.6182 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6341    0.1213    1.1039 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6651   -0.3121    0.0428 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0300    0.4706   -1.2259 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0722   -1.7303   -0.2721 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2555   -2.7386   -0.2090 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8553   -2.5325    0.1940 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.3922    2.9237    2.4996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6079    2.2305    2.3691 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.5702    2.1495   -2.7804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2799    2.6222   -2.7990 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9790   -0.2500   -2.7526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8103   -0.7077   -3.7814 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8405   -1.4102   -1.7693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2040   -2.4467   -2.4557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1301   -1.0176   -0.5103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8633   -1.6080   -0.5654 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8296   -1.1359    1.6631 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8843   -0.7292    3.1228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5775   -2.4794    1.6215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3804   -1.3218    1.2856 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5709   -0.3981    2.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8943   -0.3208    1.8593 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2174   -0.1666    0.3725 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8679    1.2757    0.0590 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4979   -1.9737   -0.6133 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7521   -3.4243   -0.9725 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2520   -3.5267   -3.0682 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3653   -2.0742   -2.6168 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9072   -2.5778   -1.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6411   -5.3165   -2.5074 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3115   -5.4217   -1.9280 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8846   -5.8402   -0.8217 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8936   -3.3088    0.1746 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9073   -4.6796    0.6786 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2013   -3.4161    1.6825 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6817   -2.4940    1.9995 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4150    0.8092   -0.3351 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2367    2.9938    0.8330 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7325    5.0378   -0.8654 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2925    5.2860   -0.0668 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5003    6.0325    1.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0149    3.8323   -1.5068 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7877    1.7155   -1.8946 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3131    2.1259   -3.2352 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1057    3.6089   -4.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5219    2.0114   -2.4384 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0034534 (Ginsenoside Ro)


  Mrv0541 02241217122D          

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M  END
> <DATABASE_ID>
HMDB0034534

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(OC6OC(C(O)C(O)C6OC6OC(CO)C(O)C(O)C6O)C(O)=O)C(C)(C)C5CCC34C)C2C1)C(=O)OC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C48H76O19/c1-43(2)14-16-48(42(61)67-40-35(58)31(54)29(52)24(20-50)63-40)17-15-46(6)21(22(48)18-43)8-9-26-45(5)12-11-27(44(3,4)25(45)10-13-47(26,46)7)64-41-37(33(56)32(55)36(65-41)38(59)60)66-39-34(57)30(53)28(51)23(19-49)62-39/h8,22-37,39-41,49-58H,9-20H2,1-7H3,(H,59,60)

> <INCHI_KEY>
NFZYDZXHKFHPGA-UHFFFAOYSA-N

> <FORMULA>
C48H76O19

> <MOLECULAR_WEIGHT>
957.1056

> <EXACT_MASS>
956.49808025

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
101.24325279233244

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.03

> <JCHEM_LOGP>
1.1053685866666676

> <ALOGPS_LOGS>
-3.72

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.904039820548087

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4135826523807378

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6786228428984202

> <JCHEM_POLAR_SURFACE_AREA>
312.04999999999995

> <JCHEM_REFRACTIVITY>
230.7497000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.84e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0034534 (Ginsenoside Ro)

HMDB0034534
     RDKit          3D
Ginsenoside Ro
143150  0  0  0  0  0  0  0  0999 V2000
    6.9181   -2.9040   -2.1819 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2255   -3.7049   -1.1452 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2950   -5.1724   -1.5972 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8391   -3.6459    0.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0047   -2.8517    1.1973 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4042   -1.6080    0.5699 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4756   -0.6674    0.2079 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6731   -1.0128    0.5011 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3329    0.5458   -0.4109 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4774    1.3305   -0.6852 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4336    2.5118    0.0553 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6017    3.2388   -0.0543 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3385    4.7273   -0.0066 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7295    5.0780    1.1967 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4071    2.9094   -1.2702 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3444    1.9075   -1.0275 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5941    2.5827   -2.4908 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0510    3.7111   -3.0754 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5161    1.6013   -2.1666 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7349    0.3947   -2.8342 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5216   -0.9751    1.6182 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6341    0.1213    1.1039 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6651   -0.3121    0.0428 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0300    0.4706   -1.2259 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0722   -1.7303   -0.2721 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2555   -2.7386   -0.2090 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8553   -2.5325    0.1940 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4100   -1.1924   -0.3415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0677   -1.2031   -0.1710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5050   -2.4864   -0.9189 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8372   -0.1067   -0.8159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3347   -0.2248   -0.6107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5782   -0.1221    0.8800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8868   -0.1187    1.2385 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3976    1.0285    1.7408 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0032    0.9888    2.9611 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5324    2.1399    3.4543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4514    3.0192    3.9557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2489    2.6303    3.9052 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6712    4.2834    4.4961 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3922    2.9237    2.4996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6079    2.2305    2.3691 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6869    3.0228    1.1712 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4385    3.6140    1.3485 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4284    1.5756    0.7320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6200    0.9175    0.8255 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0294    0.5099   -0.4456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3124    0.9994   -0.7171 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7021    0.8352   -2.0157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5702    2.1495   -2.7804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2799    2.6222   -2.7990 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9790   -0.2500   -2.7526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8103   -0.7077   -3.7814 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8405   -1.4102   -1.7693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2040   -2.4467   -2.4557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1301   -1.0176   -0.5103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8633   -1.6080   -0.5654 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8296   -1.1359    1.6631 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8843   -0.7292    3.1228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5775   -2.4794    1.6215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3804   -1.3218    1.2856 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5709   -0.3981    2.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8943   -0.3208    1.8593 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2174   -0.1666    0.3725 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8679    1.2757    0.0590 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4979   -1.9737   -0.6133 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7521   -3.4243   -0.9725 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2520   -3.5267   -3.0682 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3653   -2.0742   -2.6168 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9072   -2.5778   -1.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6411   -5.3165   -2.5074 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3115   -5.4217   -1.9280 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8846   -5.8402   -0.8217 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8936   -3.3088    0.1746 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9073   -4.6796    0.6786 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2013   -3.4161    1.6825 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6817   -2.4940    1.9995 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4150    0.8092   -0.3351 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2367    2.9938    0.8330 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7325    5.0378   -0.8654 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2925    5.2860   -0.0668 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5003    6.0325    1.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0149    3.8323   -1.5068 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7877    1.7155   -1.8946 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3131    2.1259   -3.2352 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1057    3.6089   -4.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5219    2.0114   -2.4384 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2656    0.4198   -3.7070 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9671   -1.8040    2.0935 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1905   -0.4820    2.3826 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3410    0.9318    0.7457 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1582    0.5768    1.9939 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7703    1.2808   -1.0086 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1429    0.8595   -1.7627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5151   -0.1531   -2.0035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6453   -3.7344   -0.4778 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7558   -2.5913    1.3061 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2960   -3.4035   -0.1736 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6395   -1.1458   -1.4243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7587   -2.7399   -1.7330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7151   -3.3101   -0.2357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4230   -2.3367   -1.5161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6355    0.8986   -0.3889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5892   -0.0719   -1.8910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8379   -1.0232   -1.1192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7686    0.7294   -1.0403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1628    0.8947    1.1466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6384    1.8704    1.7830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1678    1.9381    4.3739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6775    5.0784    3.8697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6472    3.9291    2.9063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3444    2.8752    2.1488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2263    3.5759    0.4092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2048    4.1736    0.5671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0761    1.6077   -0.2874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3337    0.7945   -1.2502 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8068    0.5907   -2.0753 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2442    2.8672   -2.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9183    2.0101   -3.8204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9920    2.9235   -3.7066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0376    0.0456   -3.2151 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6123   -1.0983   -3.3403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8926   -1.7611   -1.5765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6254   -3.3032   -2.2032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7034   -1.4136    0.3612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5166   -1.3748   -1.4666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4238   -1.4967    3.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5801    0.2994    3.3093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9823   -0.7885    3.3912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4730   -2.3927    2.2731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9494   -3.2613    2.0573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9436   -2.6939    0.6081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1663   -2.3917    1.5956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6874   -0.6402    3.1960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0467    0.6251    2.0172 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4736   -1.0621    2.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1830    0.6624    2.3599 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2121    1.7455    0.8554 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5066    1.4685   -0.9425 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7940    1.9299    0.1600 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8976   -1.3981   -1.4448 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1919   -3.6631   -1.8717 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4787   -4.0617   -0.0736 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
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M  END
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PDB for HMDB0034534 (Ginsenoside Ro)

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       7.336   5.571   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.336   4.031   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.001   3.261   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.001   1.721   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.731   1.069   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.334   1.721   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.104   0.386   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.669   5.571   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.669   4.031   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.229   3.199   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.000   4.031   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.667   3.261   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.667   1.721   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.000   0.951   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.334   0.181   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.000  -0.589   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.667  -1.359   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.667  -0.589   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.667   0.951   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.667   2.491   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.992   7.519   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.001   6.341   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.013   7.519   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.999   1.721   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.334   0.951   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -3.334  -0.589   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -4.669  -1.359   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -6.001  -0.589   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -6.001   0.951   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -7.336   1.721   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -8.670   0.951   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0     -10.002   1.721   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -7.336  -5.979   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -8.670  -5.209   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -10.002  -5.979   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0     -10.002  -7.519   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -6.001   4.031   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -7.336   3.261   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -8.670   4.031   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0     -10.002  -1.359   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      -8.670  -0.589   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -7.336  -1.359   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      -7.336  -2.899   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      -8.670  -3.669   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0     -10.002  -2.899   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0     -12.669  -5.979   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0     -11.337  -5.209   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -11.337  -3.669   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -12.669  -2.899   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0     -14.004  -3.669   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      -2.990  -2.540   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -1.999  -1.359   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      -1.011  -2.540   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0       7.336   0.951   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0       7.336   2.491   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0       8.668   3.261   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0      10.003   2.491   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      10.003   0.951   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      11.337   0.181   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      11.337  -1.359   0.000  0.00  0.00           C+0
HETATM   61  O   UNK     0      12.669  -2.129   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      11.337   4.801   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0      11.337   3.261   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      12.669   2.491   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      12.669   0.951   0.000  0.00  0.00           C+0
HETATM   66  O   UNK     0      14.004   0.181   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0      14.004   3.261   0.000  0.00  0.00           O+0
CONECT    1    2   22                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    9   55                                             
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   10   14                                             
CONECT    7    6                                                            
CONECT    8    9   22                                                       
CONECT    9    3    8   10                                                  
CONECT   10    6    9   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   19                                                  
CONECT   14    6   13   15   16                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   52                                                  
CONECT   19   13   18   20   24                                             
CONECT   20   19                                                            
CONECT   21   22                                                            
CONECT   22    1    8   21   23                                             
CONECT   23   22                                                            
CONECT   24   19   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   52                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   42                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   38                                                  
CONECT   31   30   32   41                                                  
CONECT   32   31                                                            
CONECT   33   34                                                            
CONECT   34   33   35   44                                                  
CONECT   35   34   36   47                                                  
CONECT   36   35                                                            
CONECT   37   38                                                            
CONECT   38   30   37   39                                                  
CONECT   39   38                                                            
CONECT   40   41                                                            
CONECT   41   31   40   42                                                  
CONECT   42   28   41   43                                                  
CONECT   43   42   44                                                       
CONECT   44   34   43   45                                                  
CONECT   45   44   48                                                       
CONECT   46   47                                                            
CONECT   47   35   46   48                                                  
CONECT   48   45   47   49                                                  
CONECT   49   48   50                                                       
CONECT   50   49                                                            
CONECT   51   52                                                            
CONECT   52   18   26   51   53                                             
CONECT   53   52                                                            
CONECT   54   55                                                            
CONECT   55    3   54   56                                                  
CONECT   56   55   57                                                       
CONECT   57   56   58   63                                                  
CONECT   58   57   59                                                       
CONECT   59   58   60   65                                                  
CONECT   60   59   61                                                       
CONECT   61   60                                                            
CONECT   62   63                                                            
CONECT   63   57   62   64                                                  
CONECT   64   63   65   67                                                  
CONECT   65   59   64   66                                                  
CONECT   66   65                                                            
CONECT   67   64                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  148    0
END
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3D PDB for HMDB0034534 (Ginsenoside Ro)

COMPND    HMDB0034534
HETATM    1  C1  UNL     1       6.918  -2.904  -2.182  1.00  0.00           C  
HETATM    2  C2  UNL     1       6.226  -3.705  -1.145  1.00  0.00           C  
HETATM    3  C3  UNL     1       6.295  -5.172  -1.597  1.00  0.00           C  
HETATM    4  C4  UNL     1       6.839  -3.646   0.232  1.00  0.00           C  
HETATM    5  C5  UNL     1       6.005  -2.852   1.197  1.00  0.00           C  
HETATM    6  C6  UNL     1       5.404  -1.608   0.570  1.00  0.00           C  
HETATM    7  C7  UNL     1       6.476  -0.667   0.208  1.00  0.00           C  
HETATM    8  O1  UNL     1       7.673  -1.013   0.501  1.00  0.00           O  
HETATM    9  O2  UNL     1       6.333   0.546  -0.411  1.00  0.00           O  
HETATM   10  C8  UNL     1       7.477   1.330  -0.685  1.00  0.00           C  
HETATM   11  O3  UNL     1       7.434   2.512   0.055  1.00  0.00           O  
HETATM   12  C9  UNL     1       8.602   3.239  -0.054  1.00  0.00           C  
HETATM   13  C10 UNL     1       8.338   4.727  -0.007  1.00  0.00           C  
HETATM   14  O4  UNL     1       7.730   5.078   1.197  1.00  0.00           O  
HETATM   15  C11 UNL     1       9.407   2.909  -1.270  1.00  0.00           C  
HETATM   16  O5  UNL     1      10.344   1.907  -1.027  1.00  0.00           O  
HETATM   17  C12 UNL     1       8.594   2.583  -2.491  1.00  0.00           C  
HETATM   18  O6  UNL     1       8.051   3.711  -3.075  1.00  0.00           O  
HETATM   19  C13 UNL     1       7.516   1.601  -2.167  1.00  0.00           C  
HETATM   20  O7  UNL     1       7.735   0.395  -2.834  1.00  0.00           O  
HETATM   21  C14 UNL     1       4.522  -0.975   1.618  1.00  0.00           C  
HETATM   22  C15 UNL     1       3.634   0.121   1.104  1.00  0.00           C  
HETATM   23  C16 UNL     1       2.665  -0.312   0.043  1.00  0.00           C  
HETATM   24  C17 UNL     1       3.030   0.471  -1.226  1.00  0.00           C  
HETATM   25  C18 UNL     1       3.072  -1.730  -0.272  1.00  0.00           C  
HETATM   26  C19 UNL     1       2.256  -2.739  -0.209  1.00  0.00           C  
HETATM   27  C20 UNL     1       0.855  -2.533   0.194  1.00  0.00           C  
HETATM   28  C21 UNL     1       0.410  -1.192  -0.341  1.00  0.00           C  
HETATM   29  C22 UNL     1      -1.068  -1.203  -0.171  1.00  0.00           C  
HETATM   30  C23 UNL     1      -1.505  -2.486  -0.919  1.00  0.00           C  
HETATM   31  C24 UNL     1      -1.837  -0.107  -0.816  1.00  0.00           C  
HETATM   32  C25 UNL     1      -3.335  -0.225  -0.611  1.00  0.00           C  
HETATM   33  C26 UNL     1      -3.578  -0.122   0.880  1.00  0.00           C  
HETATM   34  O8  UNL     1      -4.887  -0.119   1.238  1.00  0.00           O  
HETATM   35  C27 UNL     1      -5.398   1.028   1.741  1.00  0.00           C  
HETATM   36  O9  UNL     1      -6.003   0.989   2.961  1.00  0.00           O  
HETATM   37  C28 UNL     1      -6.532   2.140   3.454  1.00  0.00           C  
HETATM   38  C29 UNL     1      -5.451   3.019   3.956  1.00  0.00           C  
HETATM   39  O10 UNL     1      -4.249   2.630   3.905  1.00  0.00           O  
HETATM   40  O11 UNL     1      -5.671   4.283   4.496  1.00  0.00           O  
HETATM   41  C30 UNL     1      -7.392   2.924   2.500  1.00  0.00           C  
HETATM   42  O12 UNL     1      -8.608   2.231   2.369  1.00  0.00           O  
HETATM   43  C31 UNL     1      -6.687   3.023   1.171  1.00  0.00           C  
HETATM   44  O13 UNL     1      -5.438   3.614   1.348  1.00  0.00           O  
HETATM   45  C32 UNL     1      -6.428   1.576   0.732  1.00  0.00           C  
HETATM   46  O14 UNL     1      -7.620   0.917   0.826  1.00  0.00           O  
HETATM   47  C33 UNL     1      -8.029   0.510  -0.446  1.00  0.00           C  
HETATM   48  O15 UNL     1      -9.312   0.999  -0.717  1.00  0.00           O  
HETATM   49  C34 UNL     1      -9.702   0.835  -2.016  1.00  0.00           C  
HETATM   50  C35 UNL     1      -9.570   2.150  -2.780  1.00  0.00           C  
HETATM   51  O16 UNL     1      -8.280   2.622  -2.799  1.00  0.00           O  
HETATM   52  C36 UNL     1      -8.979  -0.250  -2.753  1.00  0.00           C  
HETATM   53  O17 UNL     1      -9.810  -0.708  -3.781  1.00  0.00           O  
HETATM   54  C37 UNL     1      -8.841  -1.410  -1.769  1.00  0.00           C  
HETATM   55  O18 UNL     1      -8.204  -2.447  -2.456  1.00  0.00           O  
HETATM   56  C38 UNL     1      -8.130  -1.018  -0.510  1.00  0.00           C  
HETATM   57  O19 UNL     1      -6.863  -1.608  -0.565  1.00  0.00           O  
HETATM   58  C39 UNL     1      -2.830  -1.136   1.663  1.00  0.00           C  
HETATM   59  C40 UNL     1      -2.884  -0.729   3.123  1.00  0.00           C  
HETATM   60  C41 UNL     1      -3.578  -2.479   1.621  1.00  0.00           C  
HETATM   61  C42 UNL     1      -1.380  -1.322   1.286  1.00  0.00           C  
HETATM   62  C43 UNL     1      -0.571  -0.398   2.096  1.00  0.00           C  
HETATM   63  C44 UNL     1       0.894  -0.321   1.859  1.00  0.00           C  
HETATM   64  C45 UNL     1       1.217  -0.167   0.372  1.00  0.00           C  
HETATM   65  C46 UNL     1       0.868   1.276   0.059  1.00  0.00           C  
HETATM   66  C47 UNL     1       4.498  -1.974  -0.613  1.00  0.00           C  
HETATM   67  C48 UNL     1       4.752  -3.424  -0.973  1.00  0.00           C  
HETATM   68  H1  UNL     1       7.252  -3.527  -3.068  1.00  0.00           H  
HETATM   69  H2  UNL     1       6.365  -2.074  -2.617  1.00  0.00           H  
HETATM   70  H3  UNL     1       7.907  -2.578  -1.739  1.00  0.00           H  
HETATM   71  H4  UNL     1       5.641  -5.317  -2.507  1.00  0.00           H  
HETATM   72  H5  UNL     1       7.312  -5.422  -1.928  1.00  0.00           H  
HETATM   73  H6  UNL     1       5.885  -5.840  -0.822  1.00  0.00           H  
HETATM   74  H7  UNL     1       7.894  -3.309   0.175  1.00  0.00           H  
HETATM   75  H8  UNL     1       6.907  -4.680   0.679  1.00  0.00           H  
HETATM   76  H9  UNL     1       5.201  -3.416   1.682  1.00  0.00           H  
HETATM   77  H10 UNL     1       6.682  -2.494   1.999  1.00  0.00           H  
HETATM   78  H11 UNL     1       8.415   0.809  -0.335  1.00  0.00           H  
HETATM   79  H12 UNL     1       9.237   2.994   0.833  1.00  0.00           H  
HETATM   80  H13 UNL     1       7.732   5.038  -0.865  1.00  0.00           H  
HETATM   81  H14 UNL     1       9.293   5.286  -0.067  1.00  0.00           H  
HETATM   82  H15 UNL     1       7.500   6.032   1.187  1.00  0.00           H  
HETATM   83  H16 UNL     1      10.015   3.832  -1.507  1.00  0.00           H  
HETATM   84  H17 UNL     1      10.788   1.715  -1.895  1.00  0.00           H  
HETATM   85  H18 UNL     1       9.313   2.126  -3.235  1.00  0.00           H  
HETATM   86  H19 UNL     1       8.106   3.609  -4.053  1.00  0.00           H  
HETATM   87  H20 UNL     1       6.522   2.011  -2.438  1.00  0.00           H  
HETATM   88  H21 UNL     1       7.266   0.420  -3.707  1.00  0.00           H  
HETATM   89  H22 UNL     1       3.967  -1.804   2.093  1.00  0.00           H  
HETATM   90  H23 UNL     1       5.190  -0.482   2.383  1.00  0.00           H  
HETATM   91  H24 UNL     1       4.341   0.932   0.746  1.00  0.00           H  
HETATM   92  H25 UNL     1       3.158   0.577   1.994  1.00  0.00           H  
HETATM   93  H26 UNL     1       3.770   1.281  -1.009  1.00  0.00           H  
HETATM   94  H27 UNL     1       2.143   0.860  -1.763  1.00  0.00           H  
HETATM   95  H28 UNL     1       3.515  -0.153  -2.003  1.00  0.00           H  
HETATM   96  H29 UNL     1       2.645  -3.734  -0.478  1.00  0.00           H  
HETATM   97  H30 UNL     1       0.756  -2.591   1.306  1.00  0.00           H  
HETATM   98  H31 UNL     1       0.296  -3.404  -0.174  1.00  0.00           H  
HETATM   99  H32 UNL     1       0.639  -1.146  -1.424  1.00  0.00           H  
HETATM  100  H33 UNL     1      -0.759  -2.740  -1.733  1.00  0.00           H  
HETATM  101  H34 UNL     1      -1.715  -3.310  -0.236  1.00  0.00           H  
HETATM  102  H35 UNL     1      -2.423  -2.337  -1.516  1.00  0.00           H  
HETATM  103  H36 UNL     1      -1.636   0.899  -0.389  1.00  0.00           H  
HETATM  104  H37 UNL     1      -1.589  -0.072  -1.891  1.00  0.00           H  
HETATM  105  H38 UNL     1      -3.838  -1.023  -1.119  1.00  0.00           H  
HETATM  106  H39 UNL     1      -3.769   0.729  -1.040  1.00  0.00           H  
HETATM  107  H40 UNL     1      -3.163   0.895   1.147  1.00  0.00           H  
HETATM  108  H41 UNL     1      -4.638   1.870   1.783  1.00  0.00           H  
HETATM  109  H42 UNL     1      -7.168   1.938   4.374  1.00  0.00           H  
HETATM  110  H43 UNL     1      -5.677   5.078   3.870  1.00  0.00           H  
HETATM  111  H44 UNL     1      -7.647   3.929   2.906  1.00  0.00           H  
HETATM  112  H45 UNL     1      -9.344   2.875   2.149  1.00  0.00           H  
HETATM  113  H46 UNL     1      -7.226   3.576   0.409  1.00  0.00           H  
HETATM  114  H47 UNL     1      -5.205   4.174   0.567  1.00  0.00           H  
HETATM  115  H48 UNL     1      -6.076   1.608  -0.287  1.00  0.00           H  
HETATM  116  H49 UNL     1      -7.334   0.794  -1.250  1.00  0.00           H  
HETATM  117  H50 UNL     1     -10.807   0.591  -2.075  1.00  0.00           H  
HETATM  118  H51 UNL     1     -10.244   2.867  -2.248  1.00  0.00           H  
HETATM  119  H52 UNL     1      -9.918   2.010  -3.820  1.00  0.00           H  
HETATM  120  H53 UNL     1      -7.992   2.924  -3.707  1.00  0.00           H  
HETATM  121  H54 UNL     1      -8.038   0.046  -3.215  1.00  0.00           H  
HETATM  122  H55 UNL     1     -10.612  -1.098  -3.340  1.00  0.00           H  
HETATM  123  H56 UNL     1      -9.893  -1.761  -1.576  1.00  0.00           H  
HETATM  124  H57 UNL     1      -8.625  -3.303  -2.203  1.00  0.00           H  
HETATM  125  H58 UNL     1      -8.703  -1.414   0.361  1.00  0.00           H  
HETATM  126  H59 UNL     1      -6.517  -1.375  -1.467  1.00  0.00           H  
HETATM  127  H60 UNL     1      -2.424  -1.497   3.779  1.00  0.00           H  
HETATM  128  H61 UNL     1      -2.580   0.299   3.309  1.00  0.00           H  
HETATM  129  H62 UNL     1      -3.982  -0.789   3.391  1.00  0.00           H  
HETATM  130  H63 UNL     1      -4.473  -2.393   2.273  1.00  0.00           H  
HETATM  131  H64 UNL     1      -2.949  -3.261   2.057  1.00  0.00           H  
HETATM  132  H65 UNL     1      -3.944  -2.694   0.608  1.00  0.00           H  
HETATM  133  H66 UNL     1      -1.166  -2.392   1.596  1.00  0.00           H  
HETATM  134  H67 UNL     1      -0.687  -0.640   3.196  1.00  0.00           H  
HETATM  135  H68 UNL     1      -1.047   0.625   2.017  1.00  0.00           H  
HETATM  136  H69 UNL     1       1.474  -1.062   2.384  1.00  0.00           H  
HETATM  137  H70 UNL     1       1.183   0.662   2.360  1.00  0.00           H  
HETATM  138  H71 UNL     1       0.212   1.746   0.855  1.00  0.00           H  
HETATM  139  H72 UNL     1       0.507   1.468  -0.942  1.00  0.00           H  
HETATM  140  H73 UNL     1       1.794   1.930   0.160  1.00  0.00           H  
HETATM  141  H74 UNL     1       4.898  -1.398  -1.445  1.00  0.00           H  
HETATM  142  H75 UNL     1       4.192  -3.663  -1.872  1.00  0.00           H  
HETATM  143  H76 UNL     1       4.479  -4.062  -0.074  1.00  0.00           H  
CONECT    1    2   68   69   70
CONECT    2    3    4   67
CONECT    3   71   72   73
CONECT    4    5   74   75
CONECT    5    6   76   77
CONECT    6    7   21   66
CONECT    7    8    8    9
CONECT    9   10
CONECT   10   11   19   78
CONECT   11   12
CONECT   12   13   15   79
CONECT   13   14   80   81
CONECT   14   82
CONECT   15   16   17   83
CONECT   16   84
CONECT   17   18   19   85
CONECT   18   86
CONECT   19   20   87
CONECT   20   88
CONECT   21   22   89   90
CONECT   22   23   91   92
CONECT   23   24   25   64
CONECT   24   93   94   95
CONECT   25   26   26   66
CONECT   26   27   96
CONECT   27   28   97   98
CONECT   28   29   64   99
CONECT   29   30   31   61
CONECT   30  100  101  102
CONECT   31   32  103  104
CONECT   32   33  105  106
CONECT   33   34   58  107
CONECT   34   35
CONECT   35   36   45  108
CONECT   36   37
CONECT   37   38   41  109
CONECT   38   39   39   40
CONECT   40  110
CONECT   41   42   43  111
CONECT   42  112
CONECT   43   44   45  113
CONECT   44  114
CONECT   45   46  115
CONECT   46   47
CONECT   47   48   56  116
CONECT   48   49
CONECT   49   50   52  117
CONECT   50   51  118  119
CONECT   51  120
CONECT   52   53   54  121
CONECT   53  122
CONECT   54   55   56  123
CONECT   55  124
CONECT   56   57  125
CONECT   57  126
CONECT   58   59   60   61
CONECT   59  127  128  129
CONECT   60  130  131  132
CONECT   61   62  133
CONECT   62   63  134  135
CONECT   63   64  136  137
CONECT   64   65
CONECT   65  138  139  140
CONECT   66   67  141
CONECT   67  142  143
END
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SMILES for HMDB0034534 (Ginsenoside Ro)

CC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(OC6OC(C(O)C(O)C6OC6OC(CO)C(O)C(O)C6O)C(O)=O)C(C)(C)C5CCC34C)C2C1)C(=O)OC1OC(CO)C(O)C(O)C1O
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INCHI for HMDB0034534 (Ginsenoside Ro)

InChI=1S/C48H76O19/c1-43(2)14-16-48(42(61)67-40-35(58)31(54)29(52)24(20-50)63-40)17-15-46(6)21(22(48)18-43)8-9-26-45(5)12-11-27(44(3,4)25(45)10-13-47(26,46)7)64-41-37(33(56)32(55)36(65-41)38(59)60)66-39-34(57)30(53)28(51)23(19-49)62-39/h8,22-37,39-41,49-58H,9-20H2,1-7H3,(H,59,60)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Chikusetsusaponin 5HMDB
Chikusetsusaponin VHMDB
Polysciasaponin P3HMDB
6-{[4,4,6a,6b,11,11,14b-heptamethyl-8a-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}carbonyl)-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,14,14a,14b-icosahydropicen-3-yl]oxy}-3,4-dihydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylateGenerator
Chemical FormulaC48H76O19
Average Molecular Weight957.1056
Monoisotopic Molecular Weight956.49808025
IUPAC Name6-{[4,4,6a,6b,11,11,14b-heptamethyl-8a-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}carbonyl)-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,14,14a,14b-icosahydropicen-3-yl]oxy}-3,4-dihydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid
Traditional Name6-{[4,4,6a,6b,11,11,14b-heptamethyl-8a-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}carbonyl)-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy}-3,4-dihydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid
CAS Registry Number34367-04-9
SMILES
CC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(OC6OC(C(O)C(O)C6OC6OC(CO)C(O)C(O)C6O)C(O)=O)C(C)(C)C5CCC34C)C2C1)C(=O)OC1OC(CO)C(O)C(O)C1O
InChI Identifier
InChI=1S/C48H76O19/c1-43(2)14-16-48(42(61)67-40-35(58)31(54)29(52)24(20-50)63-40)17-15-46(6)21(22(48)18-43)8-9-26-45(5)12-11-27(44(3,4)25(45)10-13-47(26,46)7)64-41-37(33(56)32(55)36(65-41)38(59)60)66-39-34(57)30(53)28(51)23(19-49)62-39/h8,22-37,39-41,49-58H,9-20H2,1-7H3,(H,59,60)
InChI KeyNFZYDZXHKFHPGA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene glycosides
Direct ParentTriterpene saponins
Alternative Parents
Substituents
  • Triterpene saponin
  • Triterpenoid
  • Fatty acyl glycoside
  • Fatty acyl glycoside of mono- or disaccharide
  • 1-o-glucuronide
  • O-glucuronide
  • Glucuronic acid or derivatives
  • Disaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • Beta-hydroxy acid
  • Fatty acyl
  • Dicarboxylic acid or derivatives
  • Pyran
  • Hydroxy acid
  • Oxane
  • Secondary alcohol
  • Carboxylic acid ester
  • Acetal
  • Oxacycle
  • Organoheterocyclic compound
  • Carboxylic acid
  • Carboxylic acid derivative
  • Polyol
  • Organic oxide
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Alcohol
  • Primary alcohol
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point239 - 241 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.18 g/LALOGPS
logP2.03ALOGPS
logP1.11ChemAxon
logS-3.7ALOGPS
pKa (Strongest Acidic)3.41ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area312.05 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity230.75 m³·mol⁻¹ChemAxon
Polarizability101.24 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]-326.33730932474
DeepCCS[M+Na]+300.21430932474
AllCCS[M+H]+303.832859911
AllCCS[M+H-H2O]+304.032859911
AllCCS[M+NH4]+303.532859911
AllCCS[M+Na]+303.432859911
AllCCS[M-H]-255.132859911
AllCCS[M+Na-2H]-261.332859911
AllCCS[M+HCOO]-268.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.6.65 minutes32390414
Predicted by Siyang on May 30, 202216.1308 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.96 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid158.2 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3408.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid149.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid201.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid192.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid267.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid519.7 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid806.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)581.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1123.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid674.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1823.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid467.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid496.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate306.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA338.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water11.5 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Ro 6V, Positive-QTOFsplash10-000i-0214901000-097f85483f6f7ad3fa582021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Ro 6V, Positive-QTOFsplash10-0a4i-0000000009-6b544d20a929e6283a642021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Ro 6V, Positive-QTOFsplash10-00kf-3500172901-89303227282f144d01952021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Ro 6V, Negative-QTOFsplash10-0a4i-0000000009-317ac4da29735e77f3eb2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Ro 6V, Positive-QTOFsplash10-00kf-2400171902-28c74ed7a777138290102021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Ro 6V, Positive-QTOFsplash10-0a4i-0000000009-a8fccee8f212369586db2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ginsenoside Ro 6V, Positive-QTOFsplash10-0a4i-0000000009-2dcf9dfbe5f55a10ab312021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 10V, Positive-QTOFsplash10-004r-0100306904-3c006b72e3fe9cef37772015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 20V, Positive-QTOFsplash10-0lfr-0200509400-c21b1d4827759e3fa2322015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 40V, Positive-QTOFsplash10-0a7i-0400917101-2eb0e93223580e9497782015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 10V, Positive-QTOFsplash10-004r-0100306904-3c006b72e3fe9cef37772015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 20V, Positive-QTOFsplash10-0lfr-0200509400-c21b1d4827759e3fa2322015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 40V, Positive-QTOFsplash10-0a7i-0400917101-2eb0e93223580e9497782015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 10V, Positive-QTOFsplash10-004r-0100306904-3c006b72e3fe9cef37772015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 20V, Positive-QTOFsplash10-0lfr-0200509400-c21b1d4827759e3fa2322015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 40V, Positive-QTOFsplash10-0a7i-0400917101-2eb0e93223580e9497782015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 10V, Negative-QTOFsplash10-056u-0400124928-9a2fbaa572def5d71d9a2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 20V, Negative-QTOFsplash10-02dr-2900225702-2423a23b88c15a647a592015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 40V, Negative-QTOFsplash10-02dj-6900203100-731443439506818bb5bb2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 10V, Negative-QTOFsplash10-056u-0400124928-9a2fbaa572def5d71d9a2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 20V, Negative-QTOFsplash10-02dr-2900225702-2423a23b88c15a647a592015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 40V, Negative-QTOFsplash10-02dj-6900203100-731443439506818bb5bb2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 10V, Negative-QTOFsplash10-056u-0400124928-9a2fbaa572def5d71d9a2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 20V, Negative-QTOFsplash10-02dr-2900225702-2423a23b88c15a647a592015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ginsenoside Ro 40V, Negative-QTOFsplash10-02dj-6900203100-731443439506818bb5bb2015-04-25Wishart 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 IDFDB013036
KNApSAcK IDC00029947
Chemspider IDNot Available
KEGG Compound IDC17543
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12302914
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.