Hmdb loader

Showing metabocard for Notoginsenoside R6 (HMDB0040492)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 02:02:31 UTC
Update Date2022-03-07 02:56:36 UTC
HMDB IDHMDB0040492
Secondary Accession Numbers
  • HMDB40492
Metabolite Identification
Common NameNotoginsenoside R6
DescriptionNotoginsenoside R6 belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Notoginsenoside R6 is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563863556
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040492 (Notoginsenoside R6)


  Mrv0541 02241215462D          

 67 73  0  0  0  0            999 V2000
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M  END
Download

3D MOL for HMDB0040492 (Notoginsenoside R6)

HMDB0040492
     RDKit          3D
Notoginsenoside R6
149155  0  0  0  0  0  0  0  0999 V2000
    3.2866   -5.8674   -5.2808 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9160   -5.0462   -4.0373 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8301   -5.8144   -2.7840 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7047   -3.7921   -4.2692 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3468   -2.6815   -3.4020 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4837   -2.9388   -1.9630 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.4668    3.6915   -3.2316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6765    3.2547   -3.8261 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7560    2.5342   -2.5862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3715    1.3618   -3.0223 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6664    0.2313   -0.7039 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2621    0.5096   -0.2404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9949    1.9690   -0.6828 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9766   -5.2866   -5.9067 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7730   -6.7884   -4.9725 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3429   -6.0566   -5.7904 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4540   -5.4792   -1.9505 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7606   -5.8981   -2.4929 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2322   -6.8688   -2.9824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8108   -3.4899   -5.3511 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.0397   -0.7296   -1.3352 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5926    0.2851   -0.8083 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.0212   -1.3980    0.4560 H   0  0  0  0  0  0  0  0  0  0  0  0
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    7.6696    3.0111    3.3517 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5240    3.4441    1.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0040492 (Notoginsenoside R6)


  Mrv0541 02241215462D          

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M  END
> <DATABASE_ID>
HMDB0040492

> <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(O)C(C)(C)C3C(CC21C)OC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C48H82O19/c1-21(2)10-9-13-48(8,67-43-39(61)36(58)33(55)27(66-43)20-62-41-37(59)34(56)31(53)25(18-49)64-41)22-11-15-46(6)30(22)23(51)16-28-45(5)14-12-29(52)44(3,4)40(45)24(17-47(28,46)7)63-42-38(60)35(57)32(54)26(19-50)65-42/h10,22-43,49-61H,9,11-20H2,1-8H3

> <INCHI_KEY>
YPUHYSBFIMWSEC-UHFFFAOYSA-N

> <FORMULA>
C48H82O19

> <MOLECULAR_WEIGHT>
963.1533

> <EXACT_MASS>
962.545030442

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
103.23408740366666

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
13

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[2-(5,16-dihydroxy-2,6,6,10,11-pentamethyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[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>
0.17

> <JCHEM_LOGP>
-1.0893339289999995

> <ALOGPS_LOGS>
-2.92

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.201383965172505

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.756395913472188

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6483775346041236

> <JCHEM_POLAR_SURFACE_AREA>
318.37

> <JCHEM_REFRACTIVITY>
236.0683000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.17e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[2-(5,16-dihydroxy-2,6,6,10,11-pentamethyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[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 HMDB0040492 (Notoginsenoside R6)

HMDB0040492
     RDKit          3D
Notoginsenoside R6
149155  0  0  0  0  0  0  0  0999 V2000
    3.2866   -5.8674   -5.2808 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9160   -5.0462   -4.0373 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8301   -5.8144   -2.7840 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7047   -3.7921   -4.2692 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3468   -2.6815   -3.4020 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4837   -2.9388   -1.9630 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1086   -1.7718   -1.0453 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9729   -0.5976   -1.4220 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5402   -2.1506    0.2091 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8205   -2.4073    0.4490 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3710   -1.6878    1.5350 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7280   -1.8081    1.4728 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3991   -0.9959    2.5093 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2898    0.3475    2.5225 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7525    1.0687    1.4644 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9660    1.7081    1.7309 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9007    2.9441    2.2851 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3011    3.5587    2.1242 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2281    2.7373    2.7854 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9560    3.8867    1.5687 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8832    5.0502    2.3545 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5919    3.2338    1.6058 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7282    4.0439    0.8644 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7068    1.9226    0.8571 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4994    1.2492    0.8354 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2503   -3.2154    1.5722 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4419   -3.5673    2.9088 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3771   -4.2503    0.9555 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7438   -4.4656   -0.3938 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9186   -3.8716    0.9284 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4126   -3.8714    2.2254 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7055   -1.4442   -1.1718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3102   -2.4824   -0.8341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5657   -1.7148   -1.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2811   -0.2762   -1.0766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2621    0.3371   -2.4915 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1449   -0.2266   -0.5629 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2830    0.0712    0.8527 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3619   -0.3574    1.5640 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9158   -0.2565    1.7384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1611    0.3945    1.2143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3659   -0.0873    2.0110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0766    0.3879    3.4552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5224   -1.5537    2.0747 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7886   -2.2093    1.6814 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9401   -1.3680    1.2819 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1186   -1.9930    1.7678 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8699   -0.0506    1.9615 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0574    0.8583    1.6184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0365   -0.3156    3.4382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6344    0.6590    1.5873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5672    1.1224    0.1852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7119    1.3024   -0.5254 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8553    2.5627   -1.0783 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9395    3.2861   -0.6326 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8464    4.6394   -0.9109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9402    5.4443   -0.2627 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2093    5.0640   -0.6674 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7037    4.8712   -2.3672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6421    5.7887   -2.5682 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4668    3.6915   -3.2316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6765    3.2547   -3.8261 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7560    2.5342   -2.5862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3715    1.3618   -3.0223 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6664    0.2313   -0.7039 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2621    0.5096   -0.2404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9949    1.9690   -0.6828 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9766   -5.2866   -5.9067 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7730   -6.7884   -4.9725 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3429   -6.0566   -5.7904 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4540   -5.4792   -1.9505 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7606   -5.8981   -2.4929 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2322   -6.8688   -2.9824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8108   -3.4899   -5.3511 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3180   -2.3638   -3.7196 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9780   -1.7916   -3.7221 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8987   -3.7821   -1.5779 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5705   -3.2041   -1.7924 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0397   -0.7296   -1.3352 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5926    0.2851   -0.8083 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7732   -0.2541   -2.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5706   -2.3361   -0.3425 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0212   -1.3980    0.4560 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9638   -1.3492    3.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4558   -1.3680    2.5802 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0633    0.2970    0.6832 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6696    3.0111    3.3517 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5240    3.4441    1.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3429    4.6081    2.4471 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9647    2.4662    2.1846 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2231    4.0821    0.5329 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9391    5.8745    1.8322 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2276    3.0512    2.6170 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1088    4.9613    0.7859 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0171    2.1863   -0.1935 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7769    1.9367    0.8129 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2498   -3.2550    1.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3368   -3.3008    3.2351 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4620   -5.2392    1.4475 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2625   -3.6661   -0.6616 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3094   -4.5041    0.2837 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0625   -4.2115    2.8894 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5223   -1.2987   -2.2934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3337   -2.8322    0.1918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1852   -3.4170   -1.4527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6653   -1.9902   -2.3606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4688   -2.1205   -0.8129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1026    0.9913   -2.6974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2929   -0.4592   -3.2784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3350    0.9715   -2.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6185    0.6362   -1.1765 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3343    1.2159    0.9359 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2314   -0.1474    2.5055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6150    0.1831    2.7368 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9250   -1.3168    1.9059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0386    1.4654    1.6081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2378    1.1347    3.4824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9315    0.9937    3.8599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7807   -0.4330    4.1007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2820   -1.9285    3.1266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7067   -2.1038    1.5038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6456   -2.9141    0.7965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1339   -2.9534    2.4674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1198   -1.3135    0.1900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8549   -1.9684    1.1384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5527    0.5415    0.6793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7828    1.9111    1.6846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8906    0.7521    2.3776 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.3051   -0.9571    3.9027 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.7750    5.3985    0.8260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3077    4.1050   -0.4392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6167    5.4084   -2.7183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9771    6.7070   -2.7361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8539    4.0303   -4.1151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4814    2.5773   -4.5247 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.1034    1.1411   -2.3961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9769   -0.8045   -0.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8321    0.6094   -1.7360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9974    2.1141   -1.0825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7302    2.3642   -1.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0632    2.6038    0.2506 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
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 22 93  1  0
 23 94  1  0
 24 95  1  0
 25 96  1  0
 26 97  1  0
 27 98  1  0
 28 99  1  0
 29100  1  0
 30101  1  0
 31102  1  0
 32103  1  0
 33104  1  0
 33105  1  0
 34106  1  0
 34107  1  0
 36108  1  0
 36109  1  0
 36110  1  0
 37111  1  0
 38112  1  0
 39113  1  0
 40114  1  0
 40115  1  0
 41116  1  0
 43117  1  0
 43118  1  0
 43119  1  0
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 61141  1  0
 62142  1  0
 63143  1  0
 64144  1  0
 65145  1  0
 65146  1  0
 67147  1  0
 67148  1  0
 67149  1  0
M  END
Download

PDB for HMDB0040492 (Notoginsenoside R6)

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      -2.160   7.488   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.558   6.002   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.469   4.911   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.867   3.425   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.356   3.823   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.808  -0.055   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.345  -0.533   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.439   0.715   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.345   1.959   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.808   1.485   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.142   2.255   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -5.142   3.795   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -6.477   1.485   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.477  -0.055   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.142  -0.825   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.808  -1.595   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -5.142  -2.365   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.477  -3.135   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -7.809  -2.365   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -7.809  -0.825   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -7.809   0.715   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -4.737   8.179   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.248   8.579   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.850  10.065   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -9.144  -0.055   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -10.476  -0.825   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -10.476  -2.365   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0     -11.811  -3.135   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0     -10.132  -4.316   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -9.144  -3.135   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -8.153  -4.316   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -0.381   3.027   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.710   4.116   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.309   5.602   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.177   6.002   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       2.196   3.718   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       3.284   4.806   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.773   4.408   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       5.861   5.497   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       7.350   5.099   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       8.438   6.187   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       8.040   7.673   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       7.748   3.610   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0       9.236   3.212   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       9.634   1.723   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      11.120   1.326   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0       3.974   7.383   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0       2.886   6.292   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       1.400   6.693   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0       1.000   8.179   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      11.811   3.903   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      10.325   4.300   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       9.927   5.789   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      11.015   6.878   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      -6.477  -4.675   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0      -5.142  -5.445   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -3.808  -4.675   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      -3.808  -3.135   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      -5.142  -6.985   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0      -3.808  -7.755   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      -3.808  -9.295   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0      -2.475 -10.065   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      -1.141  -7.755   0.000  0.00  0.00           O+0
HETATM   64  C   UNK     0      -2.475  -6.985   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      -2.475  -5.445   0.000  0.00  0.00           C+0
HETATM   66  O   UNK     0      -1.141  -4.675   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0      -3.410  -1.544   0.000  0.00  0.00           C+0
CONECT    1    2   23                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9   32                                             
CONECT    5    4                                                            
CONECT    6    7   10   15   67                                             
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    4    8   10                                                  
CONECT   10    6    9   11                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   20                                                  
CONECT   15    6   14   16   17                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   55                                                  
CONECT   19   18   20   30                                                  
CONECT   20   14   19   21   25                                             
CONECT   21   20                                                            
CONECT   22   23                                                            
CONECT   23    1   22   24                                                  
CONECT   24   23                                                            
CONECT   25   20   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   30                                                  
CONECT   28   27                                                            
CONECT   29   30                                                            
CONECT   30   19   27   29   31                                             
CONECT   31   30                                                            
CONECT   32    4   33                                                       
CONECT   33   32   34   36                                                  
CONECT   34   33   35   49                                                  
CONECT   35   34                                                            
CONECT   36   33   37                                                       
CONECT   37   36   38   48                                                  
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41   43                                                  
CONECT   41   40   42   53                                                  
CONECT   42   41                                                            
CONECT   43   40   44                                                       
CONECT   44   43   45   52                                                  
CONECT   45   44   46                                                       
CONECT   46   45                                                            
CONECT   47   48                                                            
CONECT   48   37   47   49                                                  
CONECT   49   34   48   50                                                  
CONECT   50   49                                                            
CONECT   51   52                                                            
CONECT   52   44   51   53                                                  
CONECT   53   41   52   54                                                  
CONECT   54   53                                                            
CONECT   55   18   56                                                       
CONECT   56   55   57   59                                                  
CONECT   57   56   58   65                                                  
CONECT   58   57                                                            
CONECT   59   56   60                                                       
CONECT   60   59   61   64                                                  
CONECT   61   60   62                                                       
CONECT   62   61                                                            
CONECT   63   64                                                            
CONECT   64   60   63   65                                                  
CONECT   65   57   64   66                                                  
CONECT   66   65                                                            
CONECT   67    6                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  146    0
END
Download

3D PDB for HMDB0040492 (Notoginsenoside R6)

COMPND    HMDB0040492
HETATM    1  C1  UNL     1       3.287  -5.867  -5.281  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.916  -5.046  -4.037  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.830  -5.814  -2.784  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.705  -3.792  -4.269  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.347  -2.682  -3.402  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.484  -2.939  -1.963  1.00  0.00           C  
HETATM    7  C7  UNL     1       2.109  -1.772  -1.045  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.973  -0.598  -1.422  1.00  0.00           C  
HETATM    9  O1  UNL     1       2.540  -2.151   0.209  1.00  0.00           O  
HETATM   10  C9  UNL     1       3.820  -2.407   0.449  1.00  0.00           C  
HETATM   11  O2  UNL     1       4.371  -1.688   1.535  1.00  0.00           O  
HETATM   12  C10 UNL     1       5.728  -1.808   1.473  1.00  0.00           C  
HETATM   13  C11 UNL     1       6.399  -0.996   2.509  1.00  0.00           C  
HETATM   14  O3  UNL     1       6.290   0.348   2.522  1.00  0.00           O  
HETATM   15  C12 UNL     1       6.753   1.069   1.464  1.00  0.00           C  
HETATM   16  O4  UNL     1       7.966   1.708   1.731  1.00  0.00           O  
HETATM   17  C13 UNL     1       7.901   2.944   2.285  1.00  0.00           C  
HETATM   18  C14 UNL     1       9.301   3.559   2.124  1.00  0.00           C  
HETATM   19  O5  UNL     1      10.228   2.737   2.785  1.00  0.00           O  
HETATM   20  C15 UNL     1       6.956   3.887   1.569  1.00  0.00           C  
HETATM   21  O6  UNL     1       6.883   5.050   2.354  1.00  0.00           O  
HETATM   22  C16 UNL     1       5.592   3.234   1.606  1.00  0.00           C  
HETATM   23  O7  UNL     1       4.728   4.044   0.864  1.00  0.00           O  
HETATM   24  C17 UNL     1       5.707   1.923   0.857  1.00  0.00           C  
HETATM   25  O8  UNL     1       4.499   1.249   0.835  1.00  0.00           O  
HETATM   26  C18 UNL     1       6.250  -3.215   1.572  1.00  0.00           C  
HETATM   27  O9  UNL     1       6.442  -3.567   2.909  1.00  0.00           O  
HETATM   28  C19 UNL     1       5.377  -4.250   0.955  1.00  0.00           C  
HETATM   29  O10 UNL     1       5.744  -4.466  -0.394  1.00  0.00           O  
HETATM   30  C20 UNL     1       3.919  -3.872   0.928  1.00  0.00           C  
HETATM   31  O11 UNL     1       3.413  -3.871   2.225  1.00  0.00           O  
HETATM   32  C21 UNL     1       0.705  -1.444  -1.172  1.00  0.00           C  
HETATM   33  C22 UNL     1      -0.310  -2.482  -0.834  1.00  0.00           C  
HETATM   34  C23 UNL     1      -1.566  -1.715  -1.256  1.00  0.00           C  
HETATM   35  C24 UNL     1      -1.281  -0.276  -1.077  1.00  0.00           C  
HETATM   36  C25 UNL     1      -1.262   0.337  -2.492  1.00  0.00           C  
HETATM   37  C26 UNL     1       0.145  -0.227  -0.563  1.00  0.00           C  
HETATM   38  C27 UNL     1       0.283   0.071   0.853  1.00  0.00           C  
HETATM   39  O12 UNL     1       1.362  -0.357   1.564  1.00  0.00           O  
HETATM   40  C28 UNL     1      -0.916  -0.257   1.738  1.00  0.00           C  
HETATM   41  C29 UNL     1      -2.161   0.395   1.214  1.00  0.00           C  
HETATM   42  C30 UNL     1      -3.366  -0.087   2.011  1.00  0.00           C  
HETATM   43  C31 UNL     1      -3.077   0.388   3.455  1.00  0.00           C  
HETATM   44  C32 UNL     1      -3.522  -1.554   2.075  1.00  0.00           C  
HETATM   45  C33 UNL     1      -4.789  -2.209   1.681  1.00  0.00           C  
HETATM   46  C34 UNL     1      -5.940  -1.368   1.282  1.00  0.00           C  
HETATM   47  O13 UNL     1      -7.119  -1.993   1.768  1.00  0.00           O  
HETATM   48  C35 UNL     1      -5.870  -0.051   1.961  1.00  0.00           C  
HETATM   49  C36 UNL     1      -7.057   0.858   1.618  1.00  0.00           C  
HETATM   50  C37 UNL     1      -6.036  -0.316   3.438  1.00  0.00           C  
HETATM   51  C38 UNL     1      -4.634   0.659   1.587  1.00  0.00           C  
HETATM   52  C39 UNL     1      -4.567   1.122   0.185  1.00  0.00           C  
HETATM   53  O14 UNL     1      -5.712   1.302  -0.525  1.00  0.00           O  
HETATM   54  C40 UNL     1      -5.855   2.563  -1.078  1.00  0.00           C  
HETATM   55  O15 UNL     1      -6.939   3.286  -0.633  1.00  0.00           O  
HETATM   56  C41 UNL     1      -6.846   4.639  -0.911  1.00  0.00           C  
HETATM   57  C42 UNL     1      -7.940   5.444  -0.263  1.00  0.00           C  
HETATM   58  O16 UNL     1      -9.209   5.064  -0.667  1.00  0.00           O  
HETATM   59  C43 UNL     1      -6.704   4.871  -2.367  1.00  0.00           C  
HETATM   60  O17 UNL     1      -5.642   5.789  -2.568  1.00  0.00           O  
HETATM   61  C44 UNL     1      -6.467   3.692  -3.232  1.00  0.00           C  
HETATM   62  O18 UNL     1      -7.676   3.255  -3.826  1.00  0.00           O  
HETATM   63  C45 UNL     1      -5.756   2.534  -2.586  1.00  0.00           C  
HETATM   64  O19 UNL     1      -6.371   1.362  -3.022  1.00  0.00           O  
HETATM   65  C46 UNL     1      -3.666   0.231  -0.704  1.00  0.00           C  
HETATM   66  C47 UNL     1      -2.262   0.510  -0.240  1.00  0.00           C  
HETATM   67  C48 UNL     1      -1.995   1.969  -0.683  1.00  0.00           C  
HETATM   68  H1  UNL     1       3.977  -5.287  -5.907  1.00  0.00           H  
HETATM   69  H2  UNL     1       3.773  -6.788  -4.973  1.00  0.00           H  
HETATM   70  H3  UNL     1       2.343  -6.057  -5.790  1.00  0.00           H  
HETATM   71  H4  UNL     1       3.454  -5.479  -1.951  1.00  0.00           H  
HETATM   72  H5  UNL     1       1.761  -5.898  -2.493  1.00  0.00           H  
HETATM   73  H6  UNL     1       3.232  -6.869  -2.982  1.00  0.00           H  
HETATM   74  H7  UNL     1       2.811  -3.490  -5.351  1.00  0.00           H  
HETATM   75  H8  UNL     1       1.318  -2.364  -3.720  1.00  0.00           H  
HETATM   76  H9  UNL     1       2.978  -1.792  -3.722  1.00  0.00           H  
HETATM   77  H10 UNL     1       1.899  -3.782  -1.578  1.00  0.00           H  
HETATM   78  H11 UNL     1       3.571  -3.204  -1.792  1.00  0.00           H  
HETATM   79  H12 UNL     1       4.040  -0.730  -1.335  1.00  0.00           H  
HETATM   80  H13 UNL     1       2.593   0.285  -0.808  1.00  0.00           H  
HETATM   81  H14 UNL     1       2.773  -0.254  -2.469  1.00  0.00           H  
HETATM   82  H15 UNL     1       4.571  -2.336  -0.342  1.00  0.00           H  
HETATM   83  H16 UNL     1       6.021  -1.398   0.456  1.00  0.00           H  
HETATM   84  H17 UNL     1       5.964  -1.349   3.508  1.00  0.00           H  
HETATM   85  H18 UNL     1       7.456  -1.368   2.580  1.00  0.00           H  
HETATM   86  H19 UNL     1       7.063   0.297   0.683  1.00  0.00           H  
HETATM   87  H20 UNL     1       7.670   3.011   3.352  1.00  0.00           H  
HETATM   88  H21 UNL     1       9.524   3.444   1.028  1.00  0.00           H  
HETATM   89  H22 UNL     1       9.343   4.608   2.447  1.00  0.00           H  
HETATM   90  H23 UNL     1      10.965   2.466   2.185  1.00  0.00           H  
HETATM   91  H24 UNL     1       7.223   4.082   0.533  1.00  0.00           H  
HETATM   92  H25 UNL     1       6.939   5.875   1.832  1.00  0.00           H  
HETATM   93  H26 UNL     1       5.228   3.051   2.617  1.00  0.00           H  
HETATM   94  H27 UNL     1       5.109   4.961   0.786  1.00  0.00           H  
HETATM   95  H28 UNL     1       6.017   2.186  -0.194  1.00  0.00           H  
HETATM   96  H29 UNL     1       3.777   1.937   0.813  1.00  0.00           H  
HETATM   97  H30 UNL     1       7.250  -3.255   1.090  1.00  0.00           H  
HETATM   98  H31 UNL     1       7.337  -3.301   3.235  1.00  0.00           H  
HETATM   99  H32 UNL     1       5.462  -5.239   1.448  1.00  0.00           H  
HETATM  100  H33 UNL     1       6.262  -3.666  -0.662  1.00  0.00           H  
HETATM  101  H34 UNL     1       3.309  -4.504   0.284  1.00  0.00           H  
HETATM  102  H35 UNL     1       4.063  -4.211   2.889  1.00  0.00           H  
HETATM  103  H36 UNL     1       0.522  -1.299  -2.293  1.00  0.00           H  
HETATM  104  H37 UNL     1      -0.334  -2.832   0.192  1.00  0.00           H  
HETATM  105  H38 UNL     1      -0.185  -3.417  -1.453  1.00  0.00           H  
HETATM  106  H39 UNL     1      -1.665  -1.990  -2.361  1.00  0.00           H  
HETATM  107  H40 UNL     1      -2.469  -2.121  -0.813  1.00  0.00           H  
HETATM  108  H41 UNL     1      -2.103   0.991  -2.697  1.00  0.00           H  
HETATM  109  H42 UNL     1      -1.293  -0.459  -3.278  1.00  0.00           H  
HETATM  110  H43 UNL     1      -0.335   0.971  -2.621  1.00  0.00           H  
HETATM  111  H44 UNL     1       0.618   0.636  -1.177  1.00  0.00           H  
HETATM  112  H45 UNL     1       0.334   1.216   0.936  1.00  0.00           H  
HETATM  113  H46 UNL     1       1.231  -0.147   2.506  1.00  0.00           H  
HETATM  114  H47 UNL     1      -0.615   0.183   2.737  1.00  0.00           H  
HETATM  115  H48 UNL     1      -0.925  -1.317   1.906  1.00  0.00           H  
HETATM  116  H49 UNL     1      -2.039   1.465   1.608  1.00  0.00           H  
HETATM  117  H50 UNL     1      -2.238   1.135   3.482  1.00  0.00           H  
HETATM  118  H51 UNL     1      -3.932   0.994   3.860  1.00  0.00           H  
HETATM  119  H52 UNL     1      -2.781  -0.433   4.101  1.00  0.00           H  
HETATM  120  H53 UNL     1      -3.282  -1.928   3.127  1.00  0.00           H  
HETATM  121  H54 UNL     1      -2.707  -2.104   1.504  1.00  0.00           H  
HETATM  122  H55 UNL     1      -4.646  -2.914   0.797  1.00  0.00           H  
HETATM  123  H56 UNL     1      -5.134  -2.953   2.467  1.00  0.00           H  
HETATM  124  H57 UNL     1      -6.120  -1.314   0.190  1.00  0.00           H  
HETATM  125  H58 UNL     1      -7.855  -1.968   1.138  1.00  0.00           H  
HETATM  126  H59 UNL     1      -7.553   0.541   0.679  1.00  0.00           H  
HETATM  127  H60 UNL     1      -6.783   1.911   1.685  1.00  0.00           H  
HETATM  128  H61 UNL     1      -7.891   0.752   2.378  1.00  0.00           H  
HETATM  129  H62 UNL     1      -6.282   0.621   4.018  1.00  0.00           H  
HETATM  130  H63 UNL     1      -5.305  -0.957   3.903  1.00  0.00           H  
HETATM  131  H64 UNL     1      -7.008  -0.898   3.511  1.00  0.00           H  
HETATM  132  H65 UNL     1      -4.655   1.604   2.223  1.00  0.00           H  
HETATM  133  H66 UNL     1      -4.030   2.128   0.148  1.00  0.00           H  
HETATM  134  H67 UNL     1      -4.948   3.159  -0.766  1.00  0.00           H  
HETATM  135  H68 UNL     1      -5.890   4.962  -0.415  1.00  0.00           H  
HETATM  136  H69 UNL     1      -7.792   6.501  -0.567  1.00  0.00           H  
HETATM  137  H70 UNL     1      -7.775   5.399   0.826  1.00  0.00           H  
HETATM  138  H71 UNL     1      -9.308   4.105  -0.439  1.00  0.00           H  
HETATM  139  H72 UNL     1      -7.617   5.408  -2.718  1.00  0.00           H  
HETATM  140  H73 UNL     1      -5.977   6.707  -2.736  1.00  0.00           H  
HETATM  141  H74 UNL     1      -5.854   4.030  -4.115  1.00  0.00           H  
HETATM  142  H75 UNL     1      -7.481   2.577  -4.525  1.00  0.00           H  
HETATM  143  H76 UNL     1      -4.706   2.488  -2.935  1.00  0.00           H  
HETATM  144  H77 UNL     1      -7.103   1.141  -2.396  1.00  0.00           H  
HETATM  145  H78 UNL     1      -3.977  -0.804  -0.704  1.00  0.00           H  
HETATM  146  H79 UNL     1      -3.832   0.609  -1.736  1.00  0.00           H  
HETATM  147  H80 UNL     1      -0.997   2.114  -1.082  1.00  0.00           H  
HETATM  148  H81 UNL     1      -2.730   2.364  -1.367  1.00  0.00           H  
HETATM  149  H82 UNL     1      -2.063   2.604   0.251  1.00  0.00           H  
CONECT    1    2   68   69   70
CONECT    2    3    4    4
CONECT    3   71   72   73
CONECT    4    5   74
CONECT    5    6   75   76
CONECT    6    7   77   78
CONECT    7    8    9   32
CONECT    8   79   80   81
CONECT    9   10
CONECT   10   11   30   82
CONECT   11   12
CONECT   12   13   26   83
CONECT   13   14   84   85
CONECT   14   15
CONECT   15   16   24   86
CONECT   16   17
CONECT   17   18   20   87
CONECT   18   19   88   89
CONECT   19   90
CONECT   20   21   22   91
CONECT   21   92
CONECT   22   23   24   93
CONECT   23   94
CONECT   24   25   95
CONECT   25   96
CONECT   26   27   28   97
CONECT   27   98
CONECT   28   29   30   99
CONECT   29  100
CONECT   30   31  101
CONECT   31  102
CONECT   32   33   37  103
CONECT   33   34  104  105
CONECT   34   35  106  107
CONECT   35   36   37   66
CONECT   36  108  109  110
CONECT   37   38  111
CONECT   38   39   40  112
CONECT   39  113
CONECT   40   41  114  115
CONECT   41   42   66  116
CONECT   42   43   44   51
CONECT   43  117  118  119
CONECT   44   45  120  121
CONECT   45   46  122  123
CONECT   46   47   48  124
CONECT   47  125
CONECT   48   49   50   51
CONECT   49  126  127  128
CONECT   50  129  130  131
CONECT   51   52  132
CONECT   52   53   65  133
CONECT   53   54
CONECT   54   55   63  134
CONECT   55   56
CONECT   56   57   59  135
CONECT   57   58  136  137
CONECT   58  138
CONECT   59   60   61  139
CONECT   60  140
CONECT   61   62   63  141
CONECT   62  142
CONECT   63   64  143
CONECT   64  144
CONECT   65   66  145  146
CONECT   66   67
CONECT   67  147  148  149
END
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SMILES for HMDB0040492 (Notoginsenoside R6)

CC(C)=CCCC(C)(OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(O)C(C)(C)C3C(CC21C)OC1OC(CO)C(O)C(O)C1O
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INCHI for HMDB0040492 (Notoginsenoside R6)

InChI=1S/C48H82O19/c1-21(2)10-9-13-48(8,67-43-39(61)36(58)33(55)27(66-43)20-62-41-37(59)34(56)31(53)25(18-49)64-41)22-11-15-46(6)30(22)23(51)16-28-45(5)14-12-29(52)44(3,4)40(45)24(17-47(28,46)7)63-42-38(60)35(57)32(54)26(19-50)65-42/h10,22-43,49-61H,9,11-20H2,1-8H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(+)-Notoginsenoside R6HMDB
Chemical FormulaC48H82O19
Average Molecular Weight963.1533
Monoisotopic Molecular Weight962.545030442
IUPAC Name2-{[2-(5,16-dihydroxy-2,6,6,10,11-pentamethyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[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-(5,16-dihydroxy-2,6,6,10,11-pentamethyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[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 Number87741-78-4
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(O)C(C)(C)C3C(CC21C)OC1OC(CO)C(O)C(O)C1O
InChI Identifier
InChI=1S/C48H82O19/c1-21(2)10-9-13-48(8,67-43-39(61)36(58)33(55)27(66-43)20-62-41-37(59)34(56)31(53)25(18-49)64-41)22-11-15-46(6)30(22)23(51)16-28-45(5)14-12-29(52)44(3,4)40(45)24(17-47(28,46)7)63-42-38(60)35(57)32(54)26(19-50)65-42/h10,22-43,49-61H,9,11-20H2,1-8H3
InChI KeyYPUHYSBFIMWSEC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTriterpenoids
Direct ParentTriterpenoids
Alternative Parents
Substituents
  • Triterpenoid
  • 3-hydroxysteroid
  • 12-hydroxysteroid
  • Hydroxysteroid
  • Steroid
  • Fatty acyl glycoside
  • Fatty acyl glycoside of mono- or disaccharide
  • Alkyl glycoside
  • Disaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • Fatty acyl
  • Oxane
  • Cyclic alcohol
  • Secondary alcohol
  • Organoheterocyclic compound
  • Acetal
  • Oxacycle
  • Polyol
  • Organooxygen compound
  • Alcohol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.17 g/LALOGPS
logP0.17ALOGPS
logP-1.1ChemAxon
logS-2.9ALOGPS
pKa (Strongest Acidic)11.76ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area318.37 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity236.07 m³·mol⁻¹ChemAxon
Polarizability103.23 ųChemAxon
Number of Rings7ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-325.84330932474
DeepCCS[M+Na]+299.61930932474
AllCCS[M+H]+298.232859911
AllCCS[M+H-H2O]+298.432859911
AllCCS[M+NH4]+298.032859911
AllCCS[M+Na]+297.932859911
AllCCS[M-H]-265.432859911
AllCCS[M+Na-2H]-272.232859911
AllCCS[M+HCOO]-279.632859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 10V, Positive-QTOFsplash10-0fgk-0000207619-cb43498fd5faeacdca1e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 20V, Positive-QTOFsplash10-00c9-0100709611-8ab75d0b2a974b735f032017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 40V, Positive-QTOFsplash10-004i-1200903202-18eb319777bf9a21b5da2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 10V, Negative-QTOFsplash10-03ec-1310016529-8fd952eac6c2d66888a02017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 20V, Negative-QTOFsplash10-02d3-3601419805-974398cff52ae51d42792017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 40V, Negative-QTOFsplash10-00vr-4610946200-e21fb678673b135569f52017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 10V, Negative-QTOFsplash10-03di-0000000019-6bdefcb441e3bcc6edb02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 20V, Negative-QTOFsplash10-0btm-9010000466-d5b1f32cb88bb68c1a732021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 40V, Negative-QTOFsplash10-0a4i-9000001111-2eb0faa501106d70cbf92021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 10V, Positive-QTOFsplash10-0uk9-0000119012-d8b96e8f63f73cef95732021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 20V, Positive-QTOFsplash10-0irr-2500304229-29976a9645cdabb576ee2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside R6 40V, Positive-QTOFsplash10-0gvw-8901113050-ede19cd475a31ad1fd532021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB020253
KNApSAcK IDC00030857
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound73157231
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.