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Showing metabocard for Gynosaponin I (HMDB0039549)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:02:28 UTC
Update Date2022-03-07 02:56:15 UTC
HMDB IDHMDB0039549
Secondary Accession Numbers
  • HMDB39549
Metabolite Identification
Common NameGynosaponin I
DescriptionGynosaponin I, also known as gypenoside IX, belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Gynosaponin I is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563863395
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039549 (Gynosaponin I)


  Mrv0541 05061311132D          

 64 70  0  0  0  0            999 V2000
    2.4492    0.5172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8358   -0.0345    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0068   -0.8416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7913   -1.0970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5758   -1.3524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8364   -3.7815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7506   -2.9609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5351   -3.2163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0204   -2.5492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5359   -1.8815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7511   -2.1359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0369   -1.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3222   -2.1351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3217   -2.9601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0359   -3.3730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0431   -2.5793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0352   -0.8979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0352   -4.1976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3217   -4.6101    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3932   -4.1976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3932   -3.3726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3932   -2.5476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8916    1.8759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2781    1.3242    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4937    1.5796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.9653   -2.1352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6802   -1.7227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9653   -5.4350    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.6376   -5.2411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.0467   -0.3125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8538   -0.1415    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1092    0.6430    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9162    0.8141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1716    1.5985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6200    2.2119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.3862    4.5654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.3563   -1.5983    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4054   -0.7549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2125   -0.5838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4679    0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2750    0.3717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7449    4.1230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9379    3.9519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6825    3.1675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2341    2.5540    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7642   -1.1973    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 24  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4 10  1  0  0  0  0
  4 44  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  1  0  0  0  0
  7 15  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
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 12 13  1  0  0  0  0
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 13 14  1  0  0  0  0
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 50 51  1  0  0  0  0
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 60 61  1  0  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
M  END
Download

3D MOL for HMDB0039549 (Gynosaponin I)

HMDB0039549
     RDKit          3D
Gynosaponin I
144150  0  0  0  0  0  0  0  0999 V2000
    5.3524   -5.7570    2.1585 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6253   -4.9334    0.9370 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9168   -5.0473    0.2489 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6703   -4.0941    0.4913 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3913   -3.9465    1.1335 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9190   -2.7577    1.7831 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6977   -1.4258    1.2117 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1319   -0.5789    2.4052 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7911   -0.7610    0.8984 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8013   -0.6996    0.1637 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9384    0.5394   -0.4789 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0087    1.6309    0.3118 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7146    2.7363   -0.4794 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9805    2.3805   -0.8491 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6337    3.3827   -1.5598 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0307    2.9513   -2.8017 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1605    3.5999   -3.2315 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4136    3.1873   -2.4687 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0536    2.1263   -3.0930 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9624    2.8089   -1.0644 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9968    2.9520   -0.1312 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8533    3.7489   -0.7000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1416    5.0748   -0.9271 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5803    1.4557    1.6656 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4126    2.5732    1.9544 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3805    0.2324    1.9133 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7324    0.5617    2.0944 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1861   -0.8083    0.8785 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1205   -0.6108   -0.1356 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6917   -1.3200    0.1265 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6240    0.1224   -0.3212 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2041    0.3351   -0.8320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3274   -1.0576   -0.9481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3650   -1.5640   -2.2309 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.4722   -2.0032    1.3665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1505   -3.2699    1.4238 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6950   -1.0540    1.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5366   -1.4369    0.2385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9614   -1.0094    0.2658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8173   -2.1478    0.8684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1284    0.1519    1.1996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1949    1.1479    0.7859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3467    0.5926    0.0603 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1825    1.6421   -0.3133 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4127    1.6194    0.2981 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4193    1.4194   -0.6361 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6639    1.2634   -0.0652 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6417    0.9140   -1.1639 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7247    1.8936   -2.1462 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1056    2.4569    0.7355 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6128    2.0668    1.9781 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0147    3.4807    0.9013 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1165    4.4364   -0.1365 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6425    2.9156    0.9925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2191    2.8114    2.3366 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9670   -0.2908   -1.0747 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9959   -1.4331   -1.1588 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2419    0.5419   -2.3405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5773   -0.7941   -1.0858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7492    0.0489   -2.0069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3127    0.1075   -1.5970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7898   -1.2163   -1.0323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1845   -2.3651   -1.9769 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2705   -6.3648    2.4089 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4997   -6.4479    2.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1227   -5.0736    2.9931 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3625   -6.0485    0.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5796   -4.2401    0.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7564   -4.8512   -0.8456 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9471   -3.5674   -0.4073 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3656   -4.7729    1.9329 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6157   -4.4174    0.4130 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6089   -2.5992    2.7022 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9905   -3.0817    2.3820 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8619    0.1825    2.7489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9955   -1.2156    3.3046 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2479   -0.0143    2.1234 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9830   -1.3980   -0.6927 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9586    2.0372    0.4327 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7654    3.6807    0.1207 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1282    3.0029   -1.3842 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9886    4.2920   -1.6979 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3608    3.3199   -4.3082 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9844    4.6825   -3.2202 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0698    4.0830   -2.4277 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4041    1.4813   -2.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5796    1.7614   -1.0780 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3486    2.0295    0.0350 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5912    3.5756    0.3720 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8482    5.3391   -0.2985 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7712    1.5678    2.4497 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4851    2.6777    2.9327 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0039549 (Gynosaponin I)


  Mrv0541 05061311132D          

 64 70  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0039549

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCCC(C)(OC1OC(COC2OCC(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C

> <INCHI_IDENTIFIER>
InChI=1S/C47H80O17/c1-22(2)10-9-14-47(8,64-42-39(58)36(55)34(53)27(62-42)21-60-40-37(56)32(51)25(50)20-59-40)23-11-16-46(7)31(23)24(49)18-29-44(5)15-13-30(43(3,4)28(44)12-17-45(29,46)6)63-41-38(57)35(54)33(52)26(19-48)61-41/h10,23-42,48-58H,9,11-21H2,1-8H3

> <INCHI_KEY>
ZTQSADJAYQOCDD-UHFFFAOYSA-N

> <FORMULA>
C47H80O17

> <MOLECULAR_WEIGHT>
917.1279

> <EXACT_MASS>
916.539551134

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
100.35045156581721

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[2-(16-hydroxy-2,6,6,10,11-pentamethyl-5-{[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-trihydroxyoxan-2-yl)oxy]methyl}oxane-3,4,5-triol

> <ALOGPS_LOGP>
1.12

> <JCHEM_LOGP>
0.8497658100000014

> <ALOGPS_LOGS>
-3.69

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.20254607278125

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.757522801319347

> <JCHEM_PKA_STRONGEST_BASIC>
-3.648377536839617

> <JCHEM_POLAR_SURFACE_AREA>
277.90999999999997

> <JCHEM_REFRACTIVITY>
228.5133000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.89e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[2-(16-hydroxy-2,6,6,10,11-pentamethyl-5-{[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-trihydroxyoxan-2-yl)oxy]methyl}oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0039549 (Gynosaponin I)

HMDB0039549
     RDKit          3D
Gynosaponin I
144150  0  0  0  0  0  0  0  0999 V2000
    5.3524   -5.7570    2.1585 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6253   -4.9334    0.9370 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9168   -5.0473    0.2489 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6703   -4.0941    0.4913 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3913   -3.9465    1.1335 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9190   -2.7577    1.7831 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6977   -1.4258    1.2117 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1319   -0.5789    2.4052 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7911   -0.7610    0.8984 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8013   -0.6996    0.1637 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9384    0.5394   -0.4789 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0087    1.6309    0.3118 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7146    2.7363   -0.4794 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9805    2.3805   -0.8491 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6337    3.3827   -1.5598 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0307    2.9513   -2.8017 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1605    3.5999   -3.2315 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4136    3.1873   -2.4687 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0536    2.1263   -3.0930 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9624    2.8089   -1.0644 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9968    2.9520   -0.1312 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8533    3.7489   -0.7000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1416    5.0748   -0.9271 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5803    1.4557    1.6656 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4126    2.5732    1.9544 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3805    0.2324    1.9133 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7324    0.5617    2.0944 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1861   -0.8083    0.8785 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1205   -0.6108   -0.1356 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6917   -1.3200    0.1265 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6240    0.1224   -0.3212 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2041    0.3351   -0.8320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3274   -1.0576   -0.9481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3650   -1.5640   -2.2309 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3542   -1.8748    0.1766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4722   -2.0032    1.3665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1505   -3.2699    1.4238 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6950   -1.0540    1.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5366   -1.4369    0.2385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9614   -1.0094    0.2658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8173   -2.1478    0.8684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1284    0.1519    1.1996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1949    1.1479    0.7859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3467    0.5926    0.0603 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1825    1.6421   -0.3133 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4127    1.6194    0.2981 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4193    1.4194   -0.6361 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6639    1.2634   -0.0652 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6417    0.9140   -1.1639 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7247    1.8936   -2.1462 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1056    2.4569    0.7355 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6128    2.0668    1.9781 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0147    3.4807    0.9013 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1165    4.4364   -0.1365 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6425    2.9156    0.9925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2191    2.8114    2.3366 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9670   -0.2908   -1.0747 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9959   -1.4331   -1.1588 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2419    0.5419   -2.3405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5773   -0.7941   -1.0858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7492    0.0489   -2.0069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3127    0.1075   -1.5970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7898   -1.2163   -1.0323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1845   -2.3651   -1.9769 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2705   -6.3648    2.4089 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4997   -6.4479    2.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1227   -5.0736    2.9931 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3625   -6.0485    0.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5796   -4.2401    0.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7564   -4.8512   -0.8456 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9471   -3.5674   -0.4073 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3656   -4.7729    1.9329 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6157   -4.4174    0.4130 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6089   -2.5992    2.7022 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9905   -3.0817    2.3820 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8619    0.1825    2.7489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9955   -1.2156    3.3046 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2479   -0.0143    2.1234 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9830   -1.3980   -0.6927 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9586    2.0372    0.4327 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7654    3.6807    0.1207 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1282    3.0029   -1.3842 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9886    4.2920   -1.6979 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3608    3.3199   -4.3082 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9844    4.6825   -3.2202 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0698    4.0830   -2.4277 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4041    1.4813   -2.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5796    1.7614   -1.0780 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3486    2.0295    0.0350 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5912    3.5756    0.3720 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8482    5.3391   -0.2985 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7712    1.5678    2.4497 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.3361   -1.8465    1.2336 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0039549 (Gynosaponin I)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.572   0.965   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.427  -0.064   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.746  -1.571   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.210  -2.048   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.675  -2.524   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.428  -7.059   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.268  -5.527   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.732  -6.004   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.638  -4.759   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.734  -3.512   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.269  -3.987   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.936  -3.216   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.601  -3.986   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.601  -5.526   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.934  -6.296   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.947  -4.815   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       1.932  -1.676   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.932  -7.836   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.601  -8.606   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.734  -7.836   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.734  -6.296   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.734  -4.756   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.398   3.502   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.252   2.472   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.788   2.949   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.069  -5.526   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -3.401  -6.296   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -3.401  -7.836   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -4.735  -8.606   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -6.067  -7.836   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -6.067  -6.296   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -7.402  -5.526   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -7.402  -3.986   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -8.736  -3.216   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -7.402 -10.145   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -7.402  -8.606   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -8.736  -7.836   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -8.736  -6.296   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0     -10.068  -5.526   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0     -10.068  -8.606   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      -3.057  -9.783   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -2.069  -8.606   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -1.078  -9.783   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0       5.687  -0.583   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0       7.194  -0.264   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0       7.671   1.200   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0       9.177   1.520   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       9.654   2.984   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0       8.624   4.129   0.000  0.00  0.00           O+0
HETATM   50  C   UNK     0       9.101   5.593   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       8.071   6.738   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0       8.548   8.203   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      10.054   8.522   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      10.531   9.986   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       8.132  -2.983   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0       8.223  -1.409   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       9.730  -1.090   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      10.207   0.374   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0      11.713   0.694   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      12.590   7.696   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0      11.084   7.377   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      10.607   5.913   0.000  0.00  0.00           C+0
HETATM   63  O   UNK     0      11.637   4.767   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      10.760  -2.235   0.000  0.00  0.00           O+0
CONECT    1    2   24                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10   44                                             
CONECT    5    4                                                            
CONECT    6    7                                                            
CONECT    7    6    8   11   15                                             
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    4    9   11                                                  
CONECT   11    7   10   12                                                  
CONECT   12   11   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   21                                                  
CONECT   15    7   14   16   18                                             
CONECT   16   15                                                            
CONECT   17   12                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   42                                                  
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   42                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   36                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   38                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   36                                                            
CONECT   36   30   35   37                                                  
CONECT   37   36   38   40                                                  
CONECT   38   32   37   39                                                  
CONECT   39   38                                                            
CONECT   40   37                                                            
CONECT   41   42                                                            
CONECT   42   20   28   41   43                                             
CONECT   43   42                                                            
CONECT   44    4   45                                                       
CONECT   45   44   46   56                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48   58                                                  
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51   62                                                  
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54   61                                                  
CONECT   54   53                                                            
CONECT   55   56                                                            
CONECT   56   45   55   57                                                  
CONECT   57   56   58   64                                                  
CONECT   58   47   57   59                                                  
CONECT   59   58                                                            
CONECT   60   61                                                            
CONECT   61   53   60   62                                                  
CONECT   62   50   61   63                                                  
CONECT   63   62                                                            
CONECT   64   57                                                            
MASTER        0    0    0    0    0    0    0    0   64    0  140    0
END
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3D PDB for HMDB0039549 (Gynosaponin I)

COMPND    HMDB0039549
HETATM    1  C1  UNL     1       5.352  -5.757   2.158  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.625  -4.933   0.937  1.00  0.00           C  
HETATM    3  C3  UNL     1       6.917  -5.047   0.249  1.00  0.00           C  
HETATM    4  C4  UNL     1       4.670  -4.094   0.491  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.391  -3.947   1.133  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.919  -2.758   1.783  1.00  0.00           C  
HETATM    7  C7  UNL     1       2.698  -1.426   1.212  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.132  -0.579   2.405  1.00  0.00           C  
HETATM    9  O1  UNL     1       3.791  -0.761   0.898  1.00  0.00           O  
HETATM   10  C9  UNL     1       4.801  -0.700   0.164  1.00  0.00           C  
HETATM   11  O2  UNL     1       4.938   0.539  -0.479  1.00  0.00           O  
HETATM   12  C10 UNL     1       5.009   1.631   0.312  1.00  0.00           C  
HETATM   13  C11 UNL     1       5.715   2.736  -0.479  1.00  0.00           C  
HETATM   14  O3  UNL     1       6.980   2.381  -0.849  1.00  0.00           O  
HETATM   15  C12 UNL     1       7.634   3.383  -1.560  1.00  0.00           C  
HETATM   16  O4  UNL     1       8.031   2.951  -2.802  1.00  0.00           O  
HETATM   17  C13 UNL     1       9.161   3.600  -3.231  1.00  0.00           C  
HETATM   18  C14 UNL     1      10.414   3.187  -2.469  1.00  0.00           C  
HETATM   19  O5  UNL     1      11.054   2.126  -3.093  1.00  0.00           O  
HETATM   20  C15 UNL     1       9.962   2.809  -1.064  1.00  0.00           C  
HETATM   21  O6  UNL     1      10.997   2.952  -0.131  1.00  0.00           O  
HETATM   22  C16 UNL     1       8.853   3.749  -0.700  1.00  0.00           C  
HETATM   23  O7  UNL     1       9.142   5.075  -0.927  1.00  0.00           O  
HETATM   24  C17 UNL     1       5.580   1.456   1.666  1.00  0.00           C  
HETATM   25  O8  UNL     1       6.413   2.573   1.954  1.00  0.00           O  
HETATM   26  C18 UNL     1       6.381   0.232   1.913  1.00  0.00           C  
HETATM   27  O9  UNL     1       7.732   0.562   2.094  1.00  0.00           O  
HETATM   28  C19 UNL     1       6.186  -0.808   0.879  1.00  0.00           C  
HETATM   29  O10 UNL     1       7.121  -0.611  -0.136  1.00  0.00           O  
HETATM   30  C20 UNL     1       1.692  -1.320   0.127  1.00  0.00           C  
HETATM   31  C21 UNL     1       1.624   0.122  -0.321  1.00  0.00           C  
HETATM   32  C22 UNL     1       0.204   0.335  -0.832  1.00  0.00           C  
HETATM   33  C23 UNL     1      -0.327  -1.058  -0.948  1.00  0.00           C  
HETATM   34  C24 UNL     1       0.365  -1.564  -2.231  1.00  0.00           C  
HETATM   35  C25 UNL     1       0.354  -1.875   0.177  1.00  0.00           C  
HETATM   36  C26 UNL     1      -0.472  -2.003   1.366  1.00  0.00           C  
HETATM   37  O11 UNL     1      -1.150  -3.270   1.424  1.00  0.00           O  
HETATM   38  C27 UNL     1      -1.695  -1.054   1.408  1.00  0.00           C  
HETATM   39  C28 UNL     1      -2.537  -1.437   0.239  1.00  0.00           C  
HETATM   40  C29 UNL     1      -3.961  -1.009   0.266  1.00  0.00           C  
HETATM   41  C30 UNL     1      -4.817  -2.148   0.868  1.00  0.00           C  
HETATM   42  C31 UNL     1      -4.128   0.152   1.200  1.00  0.00           C  
HETATM   43  C32 UNL     1      -5.195   1.148   0.786  1.00  0.00           C  
HETATM   44  C33 UNL     1      -6.347   0.593   0.060  1.00  0.00           C  
HETATM   45  O12 UNL     1      -7.182   1.642  -0.313  1.00  0.00           O  
HETATM   46  C34 UNL     1      -8.413   1.619   0.298  1.00  0.00           C  
HETATM   47  O13 UNL     1      -9.419   1.419  -0.636  1.00  0.00           O  
HETATM   48  C35 UNL     1     -10.664   1.263  -0.065  1.00  0.00           C  
HETATM   49  C36 UNL     1     -11.642   0.914  -1.164  1.00  0.00           C  
HETATM   50  O14 UNL     1     -11.725   1.894  -2.146  1.00  0.00           O  
HETATM   51  C37 UNL     1     -11.106   2.457   0.736  1.00  0.00           C  
HETATM   52  O15 UNL     1     -11.613   2.067   1.978  1.00  0.00           O  
HETATM   53  C38 UNL     1     -10.015   3.481   0.901  1.00  0.00           C  
HETATM   54  O16 UNL     1     -10.116   4.436  -0.136  1.00  0.00           O  
HETATM   55  C39 UNL     1      -8.642   2.916   0.992  1.00  0.00           C  
HETATM   56  O17 UNL     1      -8.219   2.811   2.337  1.00  0.00           O  
HETATM   57  C40 UNL     1      -5.967  -0.291  -1.075  1.00  0.00           C  
HETATM   58  C41 UNL     1      -6.996  -1.433  -1.159  1.00  0.00           C  
HETATM   59  C42 UNL     1      -6.242   0.542  -2.341  1.00  0.00           C  
HETATM   60  C43 UNL     1      -4.577  -0.794  -1.086  1.00  0.00           C  
HETATM   61  C44 UNL     1      -3.749   0.049  -2.007  1.00  0.00           C  
HETATM   62  C45 UNL     1      -2.313   0.107  -1.597  1.00  0.00           C  
HETATM   63  C46 UNL     1      -1.790  -1.216  -1.032  1.00  0.00           C  
HETATM   64  C47 UNL     1      -2.185  -2.365  -1.977  1.00  0.00           C  
HETATM   65  H1  UNL     1       6.270  -6.365   2.409  1.00  0.00           H  
HETATM   66  H2  UNL     1       4.500  -6.448   2.035  1.00  0.00           H  
HETATM   67  H3  UNL     1       5.123  -5.074   2.993  1.00  0.00           H  
HETATM   68  H4  UNL     1       7.362  -6.048   0.335  1.00  0.00           H  
HETATM   69  H5  UNL     1       7.580  -4.240   0.655  1.00  0.00           H  
HETATM   70  H6  UNL     1       6.756  -4.851  -0.846  1.00  0.00           H  
HETATM   71  H7  UNL     1       4.947  -3.567  -0.407  1.00  0.00           H  
HETATM   72  H8  UNL     1       3.366  -4.773   1.933  1.00  0.00           H  
HETATM   73  H9  UNL     1       2.616  -4.417   0.413  1.00  0.00           H  
HETATM   74  H10 UNL     1       3.609  -2.599   2.702  1.00  0.00           H  
HETATM   75  H11 UNL     1       1.991  -3.082   2.382  1.00  0.00           H  
HETATM   76  H12 UNL     1       2.862   0.183   2.749  1.00  0.00           H  
HETATM   77  H13 UNL     1       1.996  -1.216   3.305  1.00  0.00           H  
HETATM   78  H14 UNL     1       1.248  -0.014   2.123  1.00  0.00           H  
HETATM   79  H15 UNL     1       4.983  -1.398  -0.693  1.00  0.00           H  
HETATM   80  H16 UNL     1       3.959   2.037   0.433  1.00  0.00           H  
HETATM   81  H17 UNL     1       5.765   3.681   0.121  1.00  0.00           H  
HETATM   82  H18 UNL     1       5.128   3.003  -1.384  1.00  0.00           H  
HETATM   83  H19 UNL     1       6.989   4.292  -1.698  1.00  0.00           H  
HETATM   84  H20 UNL     1       9.361   3.320  -4.308  1.00  0.00           H  
HETATM   85  H21 UNL     1       8.984   4.682  -3.220  1.00  0.00           H  
HETATM   86  H22 UNL     1      11.070   4.083  -2.428  1.00  0.00           H  
HETATM   87  H23 UNL     1      11.404   1.481  -2.404  1.00  0.00           H  
HETATM   88  H24 UNL     1       9.580   1.761  -1.078  1.00  0.00           H  
HETATM   89  H25 UNL     1      11.349   2.029   0.035  1.00  0.00           H  
HETATM   90  H26 UNL     1       8.591   3.576   0.372  1.00  0.00           H  
HETATM   91  H27 UNL     1       9.848   5.339  -0.299  1.00  0.00           H  
HETATM   92  H28 UNL     1       4.771   1.568   2.450  1.00  0.00           H  
HETATM   93  H29 UNL     1       6.485   2.678   2.933  1.00  0.00           H  
HETATM   94  H30 UNL     1       6.074  -0.180   2.925  1.00  0.00           H  
HETATM   95  H31 UNL     1       7.849   1.111   2.909  1.00  0.00           H  
HETATM   96  H32 UNL     1       6.336  -1.847   1.234  1.00  0.00           H  
HETATM   97  H33 UNL     1       7.967  -0.352   0.306  1.00  0.00           H  
HETATM   98  H34 UNL     1       2.208  -1.825  -0.765  1.00  0.00           H  
HETATM   99  H35 UNL     1       1.890   0.862   0.455  1.00  0.00           H  
HETATM  100  H36 UNL     1       2.363   0.351  -1.151  1.00  0.00           H  
HETATM  101  H37 UNL     1      -0.278   1.035  -0.185  1.00  0.00           H  
HETATM  102  H38 UNL     1       0.334   0.810  -1.855  1.00  0.00           H  
HETATM  103  H39 UNL     1       1.332  -1.021  -2.411  1.00  0.00           H  
HETATM  104  H40 UNL     1       0.713  -2.624  -2.095  1.00  0.00           H  
HETATM  105  H41 UNL     1      -0.228  -1.387  -3.126  1.00  0.00           H  
HETATM  106  H42 UNL     1       0.371  -2.923  -0.282  1.00  0.00           H  
HETATM  107  H43 UNL     1      -0.048  -1.960   2.360  1.00  0.00           H  
HETATM  108  H44 UNL     1      -0.520  -3.900   1.012  1.00  0.00           H  
HETATM  109  H45 UNL     1      -1.410  -0.033   1.541  1.00  0.00           H  
HETATM  110  H46 UNL     1      -2.170  -1.359   2.392  1.00  0.00           H  
HETATM  111  H47 UNL     1      -2.565  -2.584   0.319  1.00  0.00           H  
HETATM  112  H48 UNL     1      -5.548  -1.786   1.584  1.00  0.00           H  
HETATM  113  H49 UNL     1      -4.108  -2.795   1.467  1.00  0.00           H  
HETATM  114  H50 UNL     1      -5.199  -2.818   0.082  1.00  0.00           H  
HETATM  115  H51 UNL     1      -4.558  -0.231   2.175  1.00  0.00           H  
HETATM  116  H52 UNL     1      -3.197   0.727   1.396  1.00  0.00           H  
HETATM  117  H53 UNL     1      -4.665   1.882   0.110  1.00  0.00           H  
HETATM  118  H54 UNL     1      -5.553   1.747   1.639  1.00  0.00           H  
HETATM  119  H55 UNL     1      -6.935  -0.017   0.779  1.00  0.00           H  
HETATM  120  H56 UNL     1      -8.470   0.738   0.999  1.00  0.00           H  
HETATM  121  H57 UNL     1     -10.613   0.383   0.610  1.00  0.00           H  
HETATM  122  H58 UNL     1     -12.667   0.752  -0.770  1.00  0.00           H  
HETATM  123  H59 UNL     1     -11.328  -0.051  -1.620  1.00  0.00           H  
HETATM  124  H60 UNL     1     -12.658   2.143  -2.366  1.00  0.00           H  
HETATM  125  H61 UNL     1     -11.939   2.943   0.188  1.00  0.00           H  
HETATM  126  H62 UNL     1     -10.859   2.146   2.622  1.00  0.00           H  
HETATM  127  H63 UNL     1     -10.223   4.044   1.834  1.00  0.00           H  
HETATM  128  H64 UNL     1     -10.469   4.031  -0.961  1.00  0.00           H  
HETATM  129  H65 UNL     1      -7.941   3.680   0.545  1.00  0.00           H  
HETATM  130  H66 UNL     1      -8.240   3.725   2.731  1.00  0.00           H  
HETATM  131  H67 UNL     1      -7.909  -1.061  -1.669  1.00  0.00           H  
HETATM  132  H68 UNL     1      -6.619  -2.269  -1.771  1.00  0.00           H  
HETATM  133  H69 UNL     1      -7.328  -1.746  -0.148  1.00  0.00           H  
HETATM  134  H70 UNL     1      -5.747   0.137  -3.220  1.00  0.00           H  
HETATM  135  H71 UNL     1      -6.057   1.627  -2.151  1.00  0.00           H  
HETATM  136  H72 UNL     1      -7.350   0.498  -2.569  1.00  0.00           H  
HETATM  137  H73 UNL     1      -4.650  -1.796  -1.574  1.00  0.00           H  
HETATM  138  H74 UNL     1      -3.770  -0.319  -3.073  1.00  0.00           H  
HETATM  139  H75 UNL     1      -4.097   1.107  -2.087  1.00  0.00           H  
HETATM  140  H76 UNL     1      -1.728   0.416  -2.486  1.00  0.00           H  
HETATM  141  H77 UNL     1      -2.246   0.844  -0.772  1.00  0.00           H  
HETATM  142  H78 UNL     1      -2.731  -3.178  -1.423  1.00  0.00           H  
HETATM  143  H79 UNL     1      -1.270  -2.928  -2.330  1.00  0.00           H  
HETATM  144  H80 UNL     1      -2.671  -2.022  -2.886  1.00  0.00           H  
CONECT    1    2   65   66   67
CONECT    2    3    4    4
CONECT    3   68   69   70
CONECT    4    5   71
CONECT    5    6   72   73
CONECT    6    7   74   75
CONECT    7    8    9   30
CONECT    8   76   77   78
CONECT    9   10
CONECT   10   11   28   79
CONECT   11   12
CONECT   12   13   24   80
CONECT   13   14   81   82
CONECT   14   15
CONECT   15   16   22   83
CONECT   16   17
CONECT   17   18   84   85
CONECT   18   19   20   86
CONECT   19   87
CONECT   20   21   22   88
CONECT   21   89
CONECT   22   23   90
CONECT   23   91
CONECT   24   25   26   92
CONECT   25   93
CONECT   26   27   28   94
CONECT   27   95
CONECT   28   29   96
CONECT   29   97
CONECT   30   31   35   98
CONECT   31   32   99  100
CONECT   32   33  101  102
CONECT   33   34   35   63
CONECT   34  103  104  105
CONECT   35   36  106
CONECT   36   37   38  107
CONECT   37  108
CONECT   38   39  109  110
CONECT   39   40   63  111
CONECT   40   41   42   60
CONECT   41  112  113  114
CONECT   42   43  115  116
CONECT   43   44  117  118
CONECT   44   45   57  119
CONECT   45   46
CONECT   46   47   55  120
CONECT   47   48
CONECT   48   49   51  121
CONECT   49   50  122  123
CONECT   50  124
CONECT   51   52   53  125
CONECT   52  126
CONECT   53   54   55  127
CONECT   54  128
CONECT   55   56  129
CONECT   56  130
CONECT   57   58   59   60
CONECT   58  131  132  133
CONECT   59  134  135  136
CONECT   60   61  137
CONECT   61   62  138  139
CONECT   62   63  140  141
CONECT   63   64
CONECT   64  142  143  144
END
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SMILES for HMDB0039549 (Gynosaponin I)

CC(C)=CCCC(C)(OC1OC(COC2OCC(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C
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INCHI for HMDB0039549 (Gynosaponin I)

InChI=1S/C47H80O17/c1-22(2)10-9-14-47(8,64-42-39(58)36(55)34(53)27(62-42)21-60-40-37(56)32(51)25(50)20-59-40)23-11-16-46(7)31(23)24(49)18-29-44(5)15-13-30(43(3,4)28(44)12-17-45(29,46)6)63-41-38(57)35(54)33(52)26(19-48)61-41/h10,23-42,48-58H,9,11-21H2,1-8H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Gypenoside IXHMDB
Notoginsenoside FDHMDB
Chemical FormulaC47H80O17
Average Molecular Weight917.1279
Monoisotopic Molecular Weight916.539551134
IUPAC Name2-{[2-(16-hydroxy-2,6,6,10,11-pentamethyl-5-{[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-trihydroxyoxan-2-yl)oxy]methyl}oxane-3,4,5-triol
Traditional Name2-{[2-(16-hydroxy-2,6,6,10,11-pentamethyl-5-{[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-trihydroxyoxan-2-yl)oxy]methyl}oxane-3,4,5-triol
CAS Registry Number80321-63-7
SMILES
CC(C)=CCCC(C)(OC1OC(COC2OCC(O)C(O)C2O)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4O)C(C)(C)C3CCC21C
InChI Identifier
InChI=1S/C47H80O17/c1-22(2)10-9-14-47(8,64-42-39(58)36(55)34(53)27(62-42)21-60-40-37(56)32(51)25(50)20-59-40)23-11-16-46(7)31(23)24(49)18-29-44(5)15-13-30(43(3,4)28(44)12-17-45(29,46)6)63-41-38(57)35(54)33(52)26(19-48)61-41/h10,23-42,48-58H,9,11-21H2,1-8H3
InChI KeyZTQSADJAYQOCDD-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 ParentsNot Available
SubstituentsNot Available
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 Point183 - 185 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.19 g/LALOGPS
logP1.12ALOGPS
logP0.85ChemAxon
logS-3.7ALOGPS
pKa (Strongest Acidic)11.76ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area277.91 ŲChemAxon
Rotatable Bond Count12ChemAxon
Refractivity228.51 m³·mol⁻¹ChemAxon
Polarizability100.35 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]-316.2530932474
DeepCCS[M+Na]+290.02630932474
AllCCS[M+H]+297.532859911
AllCCS[M+H-H2O]+297.632859911
AllCCS[M+NH4]+297.432859911
AllCCS[M+Na]+297.332859911
AllCCS[M-H]-252.132859911
AllCCS[M+Na-2H]-258.832859911
AllCCS[M+HCOO]-266.232859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 10V, Positive-QTOFsplash10-0a4s-0100307961-6195571fd5eafb6d2dd02015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 20V, Positive-QTOFsplash10-0a4i-0200908610-55b29c44894ad495da152015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 40V, Positive-QTOFsplash10-0a4i-2310902110-31c2c234f3f53db9886d2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 10V, Negative-QTOFsplash10-0v4j-1820118956-f425573a4e36d606c1b32015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 20V, Negative-QTOFsplash10-0ula-2910416620-af786eac401e09a19b5f2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 40V, Negative-QTOFsplash10-0pbc-7410933100-1640cfd7025671af84052015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 10V, Negative-QTOFsplash10-014i-0000000029-1a8187a1793f208795d82021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 20V, Negative-QTOFsplash10-05nf-9400002781-5c8ca5ed3c217f60e8d52021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 40V, Negative-QTOFsplash10-0a4l-9200001130-fd5da8124dfd4f6495a32021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 10V, Positive-QTOFsplash10-056r-0101947112-4d0743bfbc9ce1eca9c52021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 20V, Positive-QTOFsplash10-0699-1800915523-1f2a39710c41cc0e60632021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gynosaponin I 40V, Positive-QTOFsplash10-00kb-3900102100-ca360be7d213263d4c802021-09-22Wishart 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 IDFDB019168
KNApSAcK IDC00030445
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound15574810
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.