Hmdb loader

Showing metabocard for Notoginsenoside M (HMDB0039944)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:29:25 UTC
Update Date2022-03-07 02:56:24 UTC
HMDB IDHMDB0039944
Secondary Accession Numbers
  • HMDB39944
Metabolite Identification
Common NameNotoginsenoside M
DescriptionNotoginsenoside M belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Based on a literature review a significant number of articles have been published on Notoginsenoside M.
Structure
Data?1563863465
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039944 (Notoginsenoside M)


  Mrv0541 02241210462D          

 67 73  0  0  0  0            999 V2000
   -0.0323    3.8198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0323    2.9948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.6827    1.7573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1298    1.9003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3567   -0.1072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4270   -0.3616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9123    0.3053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4270    0.9735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3567    0.7177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    1.1302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    1.9552    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  4 33  1  0  0  0  0
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  6 15  1  0  0  0  0
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 60 62  1  0  0  0  0
 62 63  1  0  0  0  0
M  END
Download

3D MOL for HMDB0039944 (Notoginsenoside M)

HMDB0039944
     RDKit          3D
Notoginsenoside M
149155  0  0  0  0  0  0  0  0999 V2000
   -6.0666   -4.2146    4.4470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1635   -2.9686    5.2210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0004   -2.9378    6.4402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5223   -1.8740    4.8597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6384   -1.8144    3.6233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2088   -0.7961    2.7422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5568   -0.5123    1.4104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5058   -1.7784    0.6095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5071    0.2647    0.7339 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7226   -0.2840    0.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8932   -0.4680   -0.8658 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5220    0.4389   -1.6193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9155    0.7218   -2.9810 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7101    1.6898   -3.5853 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9403    1.7105   -0.8943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6567    2.5590   -1.6997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7709    1.1866    0.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7302    0.2804   -0.1603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7769    0.5124    1.1998 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1873    1.5758    1.9367 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3392    0.2952    1.5238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1973   -0.2760    2.3217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9531    0.4652    1.7851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2503    0.4296    0.3180 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.8105    0.8143   -1.7059 C   0  0  0  0  0  0  0  0  0  0  0  0
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    8.0400   -1.9772    3.1070 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4079   -1.8280    3.1016 C   0  0  0  0  0  0  0  0  0  0  0  0
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    9.4432    0.4191    2.1819 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3697    1.2640    2.7473 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1159    0.4205    2.8923 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3513    0.5710    4.2543 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7806   -2.5499   -0.8820 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1590   -2.4943   -1.0607 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0477   -2.7351   -2.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2745   -3.8892   -2.0614 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2595   -1.5550   -2.6525 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3539   -2.0850   -3.6133 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0165    0.9087   -0.4710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3763    1.4013   -0.5057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3736    2.7726    0.0837 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0629   -4.6426    4.4525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7502   -5.0074    4.8670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4798   -4.0278    3.4254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9880   -2.4520    6.2547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1932   -3.9564    6.8403 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.5794   -0.9450    5.4151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6374   -2.8519    3.2405 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.3028   -0.9037    2.7212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8097   -1.5722   -0.4252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5453   -2.2917    0.5995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2254   -2.5173    1.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8423   -1.3339    0.8764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5325   -0.0262   -1.8891 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8520    0.9232   -2.9813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0779   -0.2076   -3.6087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5978    1.2620   -3.7460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0499    2.1596   -0.4630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2643    3.1427   -1.1718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1942    2.0695    0.7837 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0039944 (Notoginsenoside M)


  Mrv0541 02241210462D          

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M  END
> <DATABASE_ID>
HMDB0039944

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(O)C(C)(C)C3C(CC21C)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C48H82O19/c1-21(2)10-9-13-48(8,67-43-39(61)35(57)32(54)26(19-50)65-43)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)36(58)33(55)27(66-42)20-62-41-37(59)34(56)31(53)25(18-49)64-41/h10,22-43,49-61H,9,11-20H2,1-8H3

> <INCHI_KEY>
SXNNDEIXKBANEP-UHFFFAOYSA-N

> <FORMULA>
C48H82O19

> <MOLECULAR_WEIGHT>
963.1533

> <EXACT_MASS>
962.545030442

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
103.73407943109108

> <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-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-6-methylhept-5-en-2-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
0.19

> <JCHEM_LOGP>
-1.0893339289999995

> <ALOGPS_LOGS>
-2.93

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.201383958312846

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.756395913709586

> <JCHEM_PKA_STRONGEST_BASIC>
-3.648377769780388

> <JCHEM_POLAR_SURFACE_AREA>
318.37

> <JCHEM_REFRACTIVITY>
236.0683000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.14e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0039944 (Notoginsenoside M)

HMDB0039944
     RDKit          3D
Notoginsenoside M
149155  0  0  0  0  0  0  0  0999 V2000
   -6.0666   -4.2146    4.4470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1635   -2.9686    5.2210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0004   -2.9378    6.4402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5223   -1.8740    4.8597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6384   -1.8144    3.6233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2088   -0.7961    2.7422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5568   -0.5123    1.4104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5058   -1.7784    0.6095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5071    0.2647    0.7339 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7226   -0.2840    0.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8932   -0.4680   -0.8658 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5220    0.4389   -1.6193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9155    0.7218   -2.9810 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7101    1.6898   -3.5853 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9403    1.7105   -0.8943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6567    2.5590   -1.6997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7709    1.1866    0.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7302    0.2804   -0.1603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7769    0.5124    1.1998 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1873    1.5758    1.9367 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3392    0.2952    1.5238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1973   -0.2760    2.3217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9531    0.4652    1.7851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2503    0.4296    0.3180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1163   -0.9667   -0.1600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6839    0.9384    0.3910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2845    1.0702   -0.9304 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3771    1.9809   -0.9240 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3496    1.8386   -1.8576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9574    1.2916   -1.8600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1592    1.7376   -3.0269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8060    1.0494   -4.2539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3841    3.2066   -3.2985 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4328    3.7848   -4.3997 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6606    3.0526   -4.7605 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5527    2.2968   -5.9246 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2492    2.2632   -3.6142 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3897    1.4535   -4.2649 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9293    3.1911   -2.6656 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2683    1.3010   -2.9901 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8105    0.8143   -1.7059 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2239   -0.5524   -1.7722 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5402   -0.7830   -1.6020 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8590   -1.3735   -0.3628 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2469   -1.2895   -0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5872   -1.1240    1.1964 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9651   -1.0437    1.3707 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3504   -0.8613    2.6862 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0400   -1.9772    3.1070 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4079   -1.8280    3.1016 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0626   -3.1950    3.0482 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6851   -3.9483    4.1691 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9324   -0.9879    1.9863 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6512   -1.4982    0.7307 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4432    0.4191    2.1819 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3697    1.2640    2.7473 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1159    0.4205    2.8923 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3513    0.5710    4.2543 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7806   -2.5499   -0.8820 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1590   -2.4943   -1.0607 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0477   -2.7351   -2.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2745   -3.8892   -2.0614 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2595   -1.5550   -2.6525 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3539   -2.0850   -3.6133 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0165    0.9087   -0.4710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3763    1.4013   -0.5057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3736    2.7726    0.0837 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0629   -4.6426    4.4525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7502   -5.0074    4.8670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4798   -4.0278    3.4254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9880   -2.4520    6.2547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1932   -3.9564    6.8403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4790   -2.3201    7.1980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5794   -0.9450    5.4151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6374   -2.8519    3.2405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6529   -1.5940    4.0559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0771    0.1968    3.3020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3028   -0.9037    2.7212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8097   -1.5722   -0.4252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5453   -2.2917    0.5995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2254   -2.5173    1.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8423   -1.3339    0.8764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5325   -0.0262   -1.8891 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8520    0.9232   -2.9813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0779   -0.2076   -3.6087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5978    1.2620   -3.7460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0499    2.1596   -0.4630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2643    3.1427   -1.1718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1942    2.0695    0.7837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3863   -0.6402   -0.1440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3861   -0.0992    1.9095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6699    2.4122    1.8560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6777    1.1496    2.2319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1959    0.0019    3.3989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0968   -1.3502    2.2759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0344    1.4504    2.2660 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0343   -0.0832    2.0617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9968   -1.7218    0.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0115   -1.1730   -0.8190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2706   -1.1870   -0.8448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4857    2.0291    0.6735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5481    0.1271   -1.4495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4969    2.4499   -1.7625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3334    2.9116   -1.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7609    1.6321   -2.8948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1342    0.1798   -2.0460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0558    0.4028   -4.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6089    0.3465   -3.9552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2156    1.7315   -4.9814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4256    3.8508   -2.4049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4612    3.2666   -3.6724 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015    4.8363   -4.0801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1458    3.9580   -5.3554 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4674    3.8107   -5.0091 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8481    1.3781   -5.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7633    1.9530   -5.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2619    1.3721   -3.5912 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0680    0.4505   -4.5403 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2087    4.1171   -3.2476 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9355    2.8001   -2.3299 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3893    3.5094   -1.7897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3456    0.3943   -3.6810 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8116    1.3128   -1.5156 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0526    0.2228   -1.5056 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6269   -0.4571   -0.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0434   -0.2963    1.6714 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2518   -2.0518    1.7248 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4333   -0.8082    3.3067 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7015   -1.3181    4.0587 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.1562   -3.0637    3.0223 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7195   -3.7585    2.1580 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1697   -3.6452    4.9821 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0427   -0.9551    2.0704 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4467   -1.6062    0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2421    0.8288    1.1480 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2022    2.2149    2.4905 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4572    1.2570    2.5870 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5479    1.4931    4.5283 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5709   -3.3688   -0.1599 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5897   -2.9709   -0.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8112   -2.9702   -2.9563 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9771   -4.0203   -1.1260 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9527   -0.9229   -3.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4535   -1.9499   -3.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5935    1.6047    0.2382 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1205   -0.0634    0.0893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0623    2.6982    1.1563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2128    3.4194   -0.0916 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5242    3.3076   -0.3578 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 95  1  0
 23 96  1  0
 23 97  1  0
 25 98  1  0
 25 99  1  0
 25100  1  0
 26101  1  0
 27102  1  0
 28103  1  0
 29104  1  0
 29105  1  0
 30106  1  0
 32107  1  0
 32108  1  0
 32109  1  0
 33110  1  0
 33111  1  0
 34112  1  0
 34113  1  0
 35114  1  0
 36115  1  0
 38116  1  0
 38117  1  0
 38118  1  0
 39119  1  0
 39120  1  0
 39121  1  0
 40122  1  0
 41123  1  0
 43124  1  0
 45125  1  0
 46126  1  0
 46127  1  0
 48128  1  0
 50129  1  0
 51130  1  0
 51131  1  0
 52132  1  0
 53133  1  0
 54134  1  0
 55135  1  0
 56136  1  0
 57137  1  0
 58138  1  0
 59139  1  0
 60140  1  0
 61141  1  0
 62142  1  0
 63143  1  0
 64144  1  0
 65145  1  0
 65146  1  0
 67147  1  0
 67148  1  0
 67149  1  0
M  END
Download

PDB for HMDB0039944 (Notoginsenoside M)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -0.060   7.130   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.060   5.590   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.274   4.820   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.274   3.280   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.242   3.547   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.666  -0.200   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.797  -0.675   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.703   0.570   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.797   1.817   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.666   1.340   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.001   2.110   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -2.001   3.650   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -3.335   1.340   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -3.335  -0.200   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.001  -0.970   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.666  -1.740   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -3.333  -4.820   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -3.333  -3.280   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.001  -2.510   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.668  -2.510   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -4.668  -0.970   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -4.668   0.570   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.607   7.130   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.274   7.900   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.274   9.440   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -6.002  -0.200   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -7.334  -0.970   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -7.334  -2.510   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -8.669  -3.280   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -6.990  -4.458   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -6.002  -3.280   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -5.011  -4.458   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       2.607   2.510   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       3.941   3.280   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       3.941   4.820   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       5.276   5.590   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       6.608   4.820   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       6.608   3.280   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       5.276   2.510   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       5.276   7.130   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       6.608   7.900   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       7.943   5.590   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       7.943   2.510   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0       5.276   0.970   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -2.001  -5.590   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -2.001  -7.130   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -0.666  -7.900   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       0.666  -7.130   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       0.666  -5.590   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0      -0.666  -4.820   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -3.333  -7.900   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      -0.666  -9.440   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       2.001  -7.900   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0       2.001  -4.820   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0       3.336  -5.590   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0       4.668  -4.820   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       4.668  -3.280   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       6.002  -2.510   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0       7.335  -3.280   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       7.335  -4.820   0.000  0.00  0.00           C+0
HETATM   61  O   UNK     0       6.002  -5.590   0.000  0.00  0.00           O+0
HETATM   62  C   UNK     0       8.669  -5.590   0.000  0.00  0.00           C+0
HETATM   63  O   UNK     0       8.669  -7.130   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       8.669  -2.510   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       6.002  -0.970   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       3.336  -2.510   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0       0.104  -1.535   0.000  0.00  0.00           C+0
CONECT    1    2   24                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9   33                                             
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   21                                                  
CONECT   15    6   14   16   19                                             
CONECT   16   15                                                            
CONECT   17   18   45                                                       
CONECT   18   17   19   20                                                  
CONECT   19   15   18                                                       
CONECT   20   18   21   31                                                  
CONECT   21   14   20   22   26                                             
CONECT   22   21                                                            
CONECT   23   24                                                            
CONECT   24    1   23   25                                                  
CONECT   25   24                                                            
CONECT   26   21   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   31                                                  
CONECT   29   28                                                            
CONECT   30   31                                                            
CONECT   31   20   28   30   32                                             
CONECT   32   31                                                            
CONECT   33    4   34                                                       
CONECT   34   33   35   39                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37   40                                                  
CONECT   37   36   38   42                                                  
CONECT   38   37   39   43                                                  
CONECT   39   34   38   44                                                  
CONECT   40   36   41                                                       
CONECT   41   40                                                            
CONECT   42   37                                                            
CONECT   43   38                                                            
CONECT   44   39                                                            
CONECT   45   17   46   50                                                  
CONECT   46   45   47   51                                                  
CONECT   47   46   48   52                                                  
CONECT   48   47   49   53                                                  
CONECT   49   48   50   54                                                  
CONECT   50   45   49                                                       
CONECT   51   46                                                            
CONECT   52   47                                                            
CONECT   53   48                                                            
CONECT   54   49   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57   61                                                  
CONECT   57   56   58   66                                                  
CONECT   58   57   59   65                                                  
CONECT   59   58   60   64                                                  
CONECT   60   59   61   62                                                  
CONECT   61   56   60                                                       
CONECT   62   60   63                                                       
CONECT   63   62                                                            
CONECT   64   59                                                            
CONECT   65   58                                                            
CONECT   66   57                                                            
CONECT   67    6                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  146    0
END
Download

3D PDB for HMDB0039944 (Notoginsenoside M)

COMPND    HMDB0039944
HETATM    1  C1  UNL     1      -6.067  -4.215   4.447  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.164  -2.969   5.221  1.00  0.00           C  
HETATM    3  C3  UNL     1      -7.000  -2.938   6.440  1.00  0.00           C  
HETATM    4  C4  UNL     1      -5.522  -1.874   4.860  1.00  0.00           C  
HETATM    5  C5  UNL     1      -4.638  -1.814   3.623  1.00  0.00           C  
HETATM    6  C6  UNL     1      -5.209  -0.796   2.742  1.00  0.00           C  
HETATM    7  C7  UNL     1      -4.557  -0.512   1.410  1.00  0.00           C  
HETATM    8  C8  UNL     1      -4.506  -1.778   0.609  1.00  0.00           C  
HETATM    9  O1  UNL     1      -5.507   0.265   0.734  1.00  0.00           O  
HETATM   10  C9  UNL     1      -6.723  -0.284   0.487  1.00  0.00           C  
HETATM   11  O2  UNL     1      -6.893  -0.468  -0.866  1.00  0.00           O  
HETATM   12  C10 UNL     1      -7.522   0.439  -1.619  1.00  0.00           C  
HETATM   13  C11 UNL     1      -6.915   0.722  -2.981  1.00  0.00           C  
HETATM   14  O3  UNL     1      -7.710   1.690  -3.585  1.00  0.00           O  
HETATM   15  C12 UNL     1      -7.940   1.711  -0.894  1.00  0.00           C  
HETATM   16  O4  UNL     1      -8.657   2.559  -1.700  1.00  0.00           O  
HETATM   17  C13 UNL     1      -8.771   1.187   0.289  1.00  0.00           C  
HETATM   18  O5  UNL     1      -9.730   0.280  -0.160  1.00  0.00           O  
HETATM   19  C14 UNL     1      -7.777   0.512   1.200  1.00  0.00           C  
HETATM   20  O6  UNL     1      -7.187   1.576   1.937  1.00  0.00           O  
HETATM   21  C15 UNL     1      -3.339   0.295   1.524  1.00  0.00           C  
HETATM   22  C16 UNL     1      -2.197  -0.276   2.322  1.00  0.00           C  
HETATM   23  C17 UNL     1      -0.953   0.465   1.785  1.00  0.00           C  
HETATM   24  C18 UNL     1      -1.250   0.430   0.318  1.00  0.00           C  
HETATM   25  C19 UNL     1      -1.116  -0.967  -0.160  1.00  0.00           C  
HETATM   26  C20 UNL     1      -2.684   0.938   0.391  1.00  0.00           C  
HETATM   27  C21 UNL     1      -3.285   1.070  -0.930  1.00  0.00           C  
HETATM   28  O7  UNL     1      -4.377   1.981  -0.924  1.00  0.00           O  
HETATM   29  C22 UNL     1      -2.350   1.839  -1.858  1.00  0.00           C  
HETATM   30  C23 UNL     1      -0.957   1.292  -1.860  1.00  0.00           C  
HETATM   31  C24 UNL     1      -0.159   1.738  -3.027  1.00  0.00           C  
HETATM   32  C25 UNL     1      -0.806   1.049  -4.254  1.00  0.00           C  
HETATM   33  C26 UNL     1      -0.384   3.207  -3.299  1.00  0.00           C  
HETATM   34  C27 UNL     1       0.433   3.785  -4.400  1.00  0.00           C  
HETATM   35  C28 UNL     1       1.661   3.053  -4.760  1.00  0.00           C  
HETATM   36  O8  UNL     1       1.553   2.297  -5.925  1.00  0.00           O  
HETATM   37  C29 UNL     1       2.249   2.263  -3.614  1.00  0.00           C  
HETATM   38  C30 UNL     1       3.390   1.453  -4.265  1.00  0.00           C  
HETATM   39  C31 UNL     1       2.929   3.191  -2.666  1.00  0.00           C  
HETATM   40  C32 UNL     1       1.268   1.301  -2.990  1.00  0.00           C  
HETATM   41  C33 UNL     1       1.810   0.814  -1.706  1.00  0.00           C  
HETATM   42  O9  UNL     1       2.224  -0.552  -1.772  1.00  0.00           O  
HETATM   43  C34 UNL     1       3.540  -0.783  -1.602  1.00  0.00           C  
HETATM   44  O10 UNL     1       3.859  -1.374  -0.363  1.00  0.00           O  
HETATM   45  C35 UNL     1       5.247  -1.290  -0.247  1.00  0.00           C  
HETATM   46  C36 UNL     1       5.587  -1.124   1.196  1.00  0.00           C  
HETATM   47  O11 UNL     1       6.965  -1.044   1.371  1.00  0.00           O  
HETATM   48  C37 UNL     1       7.350  -0.861   2.686  1.00  0.00           C  
HETATM   49  O12 UNL     1       8.040  -1.977   3.107  1.00  0.00           O  
HETATM   50  C38 UNL     1       9.408  -1.828   3.102  1.00  0.00           C  
HETATM   51  C39 UNL     1      10.063  -3.195   3.048  1.00  0.00           C  
HETATM   52  O13 UNL     1       9.685  -3.948   4.169  1.00  0.00           O  
HETATM   53  C40 UNL     1       9.932  -0.988   1.986  1.00  0.00           C  
HETATM   54  O14 UNL     1       9.651  -1.498   0.731  1.00  0.00           O  
HETATM   55  C41 UNL     1       9.443   0.419   2.182  1.00  0.00           C  
HETATM   56  O15 UNL     1      10.370   1.264   2.747  1.00  0.00           O  
HETATM   57  C42 UNL     1       8.116   0.421   2.892  1.00  0.00           C  
HETATM   58  O16 UNL     1       8.351   0.571   4.254  1.00  0.00           O  
HETATM   59  C43 UNL     1       5.781  -2.550  -0.882  1.00  0.00           C  
HETATM   60  O17 UNL     1       7.159  -2.494  -1.061  1.00  0.00           O  
HETATM   61  C44 UNL     1       5.048  -2.735  -2.177  1.00  0.00           C  
HETATM   62  O18 UNL     1       4.275  -3.889  -2.061  1.00  0.00           O  
HETATM   63  C45 UNL     1       4.259  -1.555  -2.652  1.00  0.00           C  
HETATM   64  O19 UNL     1       3.354  -2.085  -3.613  1.00  0.00           O  
HETATM   65  C46 UNL     1       1.017   0.909  -0.471  1.00  0.00           C  
HETATM   66  C47 UNL     1      -0.376   1.401  -0.506  1.00  0.00           C  
HETATM   67  C48 UNL     1      -0.374   2.773   0.084  1.00  0.00           C  
HETATM   68  H1  UNL     1      -5.063  -4.643   4.453  1.00  0.00           H  
HETATM   69  H2  UNL     1      -6.750  -5.007   4.867  1.00  0.00           H  
HETATM   70  H3  UNL     1      -6.480  -4.028   3.425  1.00  0.00           H  
HETATM   71  H4  UNL     1      -7.988  -2.452   6.255  1.00  0.00           H  
HETATM   72  H5  UNL     1      -7.193  -3.956   6.840  1.00  0.00           H  
HETATM   73  H6  UNL     1      -6.479  -2.320   7.198  1.00  0.00           H  
HETATM   74  H7  UNL     1      -5.579  -0.945   5.415  1.00  0.00           H  
HETATM   75  H8  UNL     1      -4.637  -2.852   3.240  1.00  0.00           H  
HETATM   76  H9  UNL     1      -3.653  -1.594   4.056  1.00  0.00           H  
HETATM   77  H10 UNL     1      -5.077   0.197   3.302  1.00  0.00           H  
HETATM   78  H11 UNL     1      -6.303  -0.904   2.721  1.00  0.00           H  
HETATM   79  H12 UNL     1      -4.810  -1.572  -0.425  1.00  0.00           H  
HETATM   80  H13 UNL     1      -3.545  -2.292   0.600  1.00  0.00           H  
HETATM   81  H14 UNL     1      -5.225  -2.517   1.012  1.00  0.00           H  
HETATM   82  H15 UNL     1      -6.842  -1.334   0.876  1.00  0.00           H  
HETATM   83  H16 UNL     1      -8.532  -0.026  -1.889  1.00  0.00           H  
HETATM   84  H17 UNL     1      -5.852   0.923  -2.981  1.00  0.00           H  
HETATM   85  H18 UNL     1      -7.078  -0.208  -3.609  1.00  0.00           H  
HETATM   86  H19 UNL     1      -8.598   1.262  -3.746  1.00  0.00           H  
HETATM   87  H20 UNL     1      -7.050   2.160  -0.463  1.00  0.00           H  
HETATM   88  H21 UNL     1      -9.264   3.143  -1.172  1.00  0.00           H  
HETATM   89  H22 UNL     1      -9.194   2.070   0.784  1.00  0.00           H  
HETATM   90  H23 UNL     1      -9.386  -0.640  -0.144  1.00  0.00           H  
HETATM   91  H24 UNL     1      -8.386  -0.099   1.910  1.00  0.00           H  
HETATM   92  H25 UNL     1      -7.670   2.412   1.856  1.00  0.00           H  
HETATM   93  H26 UNL     1      -3.678   1.150   2.232  1.00  0.00           H  
HETATM   94  H27 UNL     1      -2.196   0.002   3.399  1.00  0.00           H  
HETATM   95  H28 UNL     1      -2.097  -1.350   2.276  1.00  0.00           H  
HETATM   96  H29 UNL     1      -1.034   1.450   2.266  1.00  0.00           H  
HETATM   97  H30 UNL     1      -0.034  -0.083   2.062  1.00  0.00           H  
HETATM   98  H31 UNL     1      -0.997  -1.722   0.645  1.00  0.00           H  
HETATM   99  H32 UNL     1      -2.012  -1.173  -0.819  1.00  0.00           H  
HETATM  100  H33 UNL     1      -0.271  -1.187  -0.845  1.00  0.00           H  
HETATM  101  H34 UNL     1      -2.486   2.029   0.673  1.00  0.00           H  
HETATM  102  H35 UNL     1      -3.548   0.127  -1.449  1.00  0.00           H  
HETATM  103  H36 UNL     1      -4.497   2.450  -1.763  1.00  0.00           H  
HETATM  104  H37 UNL     1      -2.333   2.912  -1.670  1.00  0.00           H  
HETATM  105  H38 UNL     1      -2.761   1.632  -2.895  1.00  0.00           H  
HETATM  106  H39 UNL     1      -1.134   0.180  -2.046  1.00  0.00           H  
HETATM  107  H40 UNL     1      -0.056   0.403  -4.779  1.00  0.00           H  
HETATM  108  H41 UNL     1      -1.609   0.346  -3.955  1.00  0.00           H  
HETATM  109  H42 UNL     1      -1.216   1.732  -4.981  1.00  0.00           H  
HETATM  110  H43 UNL     1      -0.426   3.851  -2.405  1.00  0.00           H  
HETATM  111  H44 UNL     1      -1.461   3.267  -3.672  1.00  0.00           H  
HETATM  112  H45 UNL     1       0.702   4.836  -4.080  1.00  0.00           H  
HETATM  113  H46 UNL     1      -0.146   3.958  -5.355  1.00  0.00           H  
HETATM  114  H47 UNL     1       2.467   3.811  -5.009  1.00  0.00           H  
HETATM  115  H48 UNL     1       1.848   1.378  -5.862  1.00  0.00           H  
HETATM  116  H49 UNL     1       3.763   1.953  -5.185  1.00  0.00           H  
HETATM  117  H50 UNL     1       4.262   1.372  -3.591  1.00  0.00           H  
HETATM  118  H51 UNL     1       3.068   0.451  -4.540  1.00  0.00           H  
HETATM  119  H52 UNL     1       3.209   4.117  -3.248  1.00  0.00           H  
HETATM  120  H53 UNL     1       3.935   2.800  -2.330  1.00  0.00           H  
HETATM  121  H54 UNL     1       2.389   3.509  -1.790  1.00  0.00           H  
HETATM  122  H55 UNL     1       1.346   0.394  -3.681  1.00  0.00           H  
HETATM  123  H56 UNL     1       2.812   1.313  -1.516  1.00  0.00           H  
HETATM  124  H57 UNL     1       4.053   0.223  -1.506  1.00  0.00           H  
HETATM  125  H58 UNL     1       5.627  -0.457  -0.881  1.00  0.00           H  
HETATM  126  H59 UNL     1       5.043  -0.296   1.671  1.00  0.00           H  
HETATM  127  H60 UNL     1       5.252  -2.052   1.725  1.00  0.00           H  
HETATM  128  H61 UNL     1       6.433  -0.808   3.307  1.00  0.00           H  
HETATM  129  H62 UNL     1       9.701  -1.318   4.059  1.00  0.00           H  
HETATM  130  H63 UNL     1      11.156  -3.064   3.022  1.00  0.00           H  
HETATM  131  H64 UNL     1       9.719  -3.759   2.158  1.00  0.00           H  
HETATM  132  H65 UNL     1      10.170  -3.645   4.982  1.00  0.00           H  
HETATM  133  H66 UNL     1      11.043  -0.955   2.070  1.00  0.00           H  
HETATM  134  H67 UNL     1      10.447  -1.606   0.158  1.00  0.00           H  
HETATM  135  H68 UNL     1       9.242   0.829   1.148  1.00  0.00           H  
HETATM  136  H69 UNL     1      10.202   2.215   2.490  1.00  0.00           H  
HETATM  137  H70 UNL     1       7.457   1.257   2.587  1.00  0.00           H  
HETATM  138  H71 UNL     1       8.548   1.493   4.528  1.00  0.00           H  
HETATM  139  H72 UNL     1       5.571  -3.369  -0.160  1.00  0.00           H  
HETATM  140  H73 UNL     1       7.590  -2.971  -0.315  1.00  0.00           H  
HETATM  141  H74 UNL     1       5.811  -2.970  -2.956  1.00  0.00           H  
HETATM  142  H75 UNL     1       3.977  -4.020  -1.126  1.00  0.00           H  
HETATM  143  H76 UNL     1       4.953  -0.923  -3.271  1.00  0.00           H  
HETATM  144  H77 UNL     1       2.453  -1.950  -3.238  1.00  0.00           H  
HETATM  145  H78 UNL     1       1.594   1.605   0.238  1.00  0.00           H  
HETATM  146  H79 UNL     1       1.121  -0.063   0.089  1.00  0.00           H  
HETATM  147  H80 UNL     1      -0.062   2.698   1.156  1.00  0.00           H  
HETATM  148  H81 UNL     1      -1.213   3.419  -0.092  1.00  0.00           H  
HETATM  149  H82 UNL     1       0.524   3.308  -0.358  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   21
CONECT    8   79   80   81
CONECT    9   10
CONECT   10   11   19   82
CONECT   11   12
CONECT   12   13   15   83
CONECT   13   14   84   85
CONECT   14   86
CONECT   15   16   17   87
CONECT   16   88
CONECT   17   18   19   89
CONECT   18   90
CONECT   19   20   91
CONECT   20   92
CONECT   21   22   26   93
CONECT   22   23   94   95
CONECT   23   24   96   97
CONECT   24   25   26   66
CONECT   25   98   99  100
CONECT   26   27  101
CONECT   27   28   29  102
CONECT   28  103
CONECT   29   30  104  105
CONECT   30   31   66  106
CONECT   31   32   33   40
CONECT   32  107  108  109
CONECT   33   34  110  111
CONECT   34   35  112  113
CONECT   35   36   37  114
CONECT   36  115
CONECT   37   38   39   40
CONECT   38  116  117  118
CONECT   39  119  120  121
CONECT   40   41  122
CONECT   41   42   65  123
CONECT   42   43
CONECT   43   44   63  124
CONECT   44   45
CONECT   45   46   59  125
CONECT   46   47  126  127
CONECT   47   48
CONECT   48   49   57  128
CONECT   49   50
CONECT   50   51   53  129
CONECT   51   52  130  131
CONECT   52  132
CONECT   53   54   55  133
CONECT   54  134
CONECT   55   56   57  135
CONECT   56  136
CONECT   57   58  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 HMDB0039944 (Notoginsenoside M)

CC(C)=CCCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(O)C(C)(C)C3C(CC21C)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O
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INCHI for HMDB0039944 (Notoginsenoside M)

InChI=1S/C48H82O19/c1-21(2)10-9-13-48(8,67-43-39(61)35(57)32(54)26(19-50)65-43)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)36(58)33(55)27(66-42)20-62-41-37(59)34(56)31(53)25(18-49)64-41/h10,22-43,49-61H,9,11-20H2,1-8H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(+)-Centellasaponin CHMDB
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-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-6-methylhept-5-en-2-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Name2-{[2-(5,16-dihydroxy-2,6,6,10,11-pentamethyl-8-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl)-6-methylhept-5-en-2-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
CAS Registry Number394246-74-3
SMILES
CC(C)=CCCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(O)C(C)(C)C3C(CC21C)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O
InChI Identifier
InChI=1S/C48H82O19/c1-21(2)10-9-13-48(8,67-43-39(61)35(57)32(54)26(19-50)65-43)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)36(58)33(55)27(66-42)20-62-41-37(59)34(56)31(53)25(18-49)64-41/h10,22-43,49-61H,9,11-20H2,1-8H3
InChI KeySXNNDEIXKBANEP-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
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point187 - 189 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.14 g/LALOGPS
logP0.19ALOGPS
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
Polarizability103.73 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]-326.34130932474
DeepCCS[M+Na]+300.17830932474
AllCCS[M+H]+298.332859911
AllCCS[M+H-H2O]+298.532859911
AllCCS[M+NH4]+298.032859911
AllCCS[M+Na]+298.032859911
AllCCS[M-H]-265.432859911
AllCCS[M+Na-2H]-272.232859911
AllCCS[M+HCOO]-279.632859911

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, 2022.5.75 minutes32390414
Predicted by Siyang on May 30, 202214.7473 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.07 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid262.6 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3334.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid164.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid177.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid208.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid171.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid476.4 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 Acid628.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)554.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1017.2 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid567.9 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1416.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid381.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid398.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate344.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA366.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water38.8 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 10V, Positive-QTOFsplash10-0fgk-0000207619-8c6fda5c07b5d8eff40e2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 20V, Positive-QTOFsplash10-00c9-0100709511-8eb89ad4db1e50e189a62015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 40V, Positive-QTOFsplash10-004i-1200903101-d4d8634765bd826191a52015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 10V, Negative-QTOFsplash10-03ym-0110016509-9dd3d01536d2f9e63d402015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 20V, Negative-QTOFsplash10-06a4-2401409704-4d63e1c85174f4f7eadc2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 40V, Negative-QTOFsplash10-00bi-4510946100-31465394cbc9424df6c92015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 10V, Positive-QTOFsplash10-00lr-0100003912-782f9de3f8e9940ed0812021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 20V, Positive-QTOFsplash10-0h9r-3500415559-3cfe6a4b846c3380525c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 40V, Positive-QTOFsplash10-01ox-9300002140-3efb53ea78ed440461a82021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 10V, Negative-QTOFsplash10-03di-0000000019-cf89be48f22fa5cc14d02021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 20V, Negative-QTOFsplash10-0a4j-9100000546-c34601dea539c19d7e8d2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Notoginsenoside M 40V, Negative-QTOFsplash10-0a4i-9200000611-6a73a02ffa53036df44d2021-09-23Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB019606
KNApSAcK IDC00032806
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound85316219
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.