Hmdb loader

Showing metabocard for Centellasaponin C (HMDB0039946)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:29:38 UTC
Update Date2022-03-07 02:56:24 UTC
HMDB IDHMDB0039946
Secondary Accession Numbers
  • HMDB39946
Metabolite Identification
Common NameCentellasaponin C
DescriptionCentellasaponin C belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton. Based on a literature review a small amount of articles have been published on Centellasaponin C.
Structure
Data?1563863465
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039946 (Centellasaponin C)


  Mrv0541 02241207532D          

 67 74  0  0  0  0            999 V2000
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   -2.8554    1.9914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8266    2.8163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8829    1.1679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1845    0.7307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2134   -0.0942    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1006    2.3626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0992    3.2026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3693    3.5903    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6708    3.1531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0039946 (Centellasaponin C)

HMDB0039946
     RDKit          3D
Centellasaponin C
145152  0  0  0  0  0  0  0  0999 V2000
   -0.3808    4.0636   -0.9801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5908    2.6089   -0.6011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5116    2.4665    0.8634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1885    1.3298    1.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0082    0.5410    0.4826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9659   -0.2036   -0.1833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8939   -0.3463   -1.4015 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0850   -0.8515    0.5171 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0650   -1.5793   -0.2010 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3052   -0.9380   -0.0774 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6297   -0.6481    1.2239 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0756   -0.1147    1.1573 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8052   -1.1705    0.6126 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1466   -0.8223    0.4209 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5144   -0.9420   -0.8954 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7431   -0.3863   -1.1409 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7199    1.1288   -1.0869 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8070    1.5506   -2.0618 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8387   -0.9653   -0.3038 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9804   -0.2155   -0.4332 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0742   -0.9715   -0.8478 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0354   -0.9165    0.1603 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6388    0.3119    0.2523 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.2227   -2.4787    0.9864 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.0815   -0.1345   -1.1707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1337    0.1462   -2.7133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7418    1.6357   -0.2286 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8865    2.1770   -1.2790 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6225    3.4064   -1.8695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4188    4.2586   -2.0561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9733    4.7666   -0.3699 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6892    4.2844   -0.6830 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2670    2.0793   -1.0881 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.1222    0.7672    0.4934 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2481    0.2356    0.7512 H   0  0  0  0  0  0  0  0  0  0  0  0
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    8.7359    1.5137   -1.3773 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5290    1.5312   -0.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1239    1.1871   -2.9282 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9755   -2.0313   -0.5732 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7186   -2.0222   -0.9659 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7352    0.2808    0.0425 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0039946 (Centellasaponin C)


  Mrv0541 02241207532D          

 67 74  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0039946

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1CCC2(CCC3(C)C(=CCC4C5(C)CC(O)C(O)C(C)(C)C5C(O)CC34C)C2C1C)C(=O)OC1OC(COC2OC(CO)C(OC3OC(C)C(O)C(O)C3O)C(O)C2O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C48H78O19/c1-19-11-12-48(14-13-46(7)22(28(48)20(19)2)9-10-27-45(6)15-24(51)39(60)44(4,5)38(45)23(50)16-47(27,46)8)43(61)67-42-35(58)32(55)30(53)26(65-42)18-62-40-36(59)33(56)37(25(17-49)64-40)66-41-34(57)31(54)29(52)21(3)63-41/h9,19-21,23-42,49-60H,10-18H2,1-8H3

> <INCHI_KEY>
SOOVZDUBVGGAAJ-UHFFFAOYSA-N

> <FORMULA>
C48H78O19

> <MOLECULAR_WEIGHT>
959.1215

> <EXACT_MASS>
958.513730314

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
102.11544770749566

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-({[3,4-dihydroxy-6-(hydroxymethyl)-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 8,10,11-trihydroxy-1,2,6a,6b,9,9,12a-heptamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylate

> <ALOGPS_LOGP>
0.64

> <JCHEM_LOGP>
-0.5646924123333316

> <ALOGPS_LOGS>
-3.01

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.201051911554664

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.754330014941177

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6121826089009508

> <JCHEM_POLAR_SURFACE_AREA>
315.21

> <JCHEM_REFRACTIVITY>
232.36610000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.31e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-({[3,4-dihydroxy-6-(hydroxymethyl)-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 8,10,11-trihydroxy-1,2,6a,6b,9,9,12a-heptamethyl-2,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydro-1H-picene-4a-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0039946 (Centellasaponin C)

HMDB0039946
     RDKit          3D
Centellasaponin C
145152  0  0  0  0  0  0  0  0999 V2000
   -0.3808    4.0636   -0.9801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5908    2.6089   -0.6011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5116    2.4665    0.8634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1885    1.3298    1.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0082    0.5410    0.4826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9659   -0.2036   -0.1833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8939   -0.3463   -1.4015 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0850   -0.8515    0.5171 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0650   -1.5793   -0.2010 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3052   -0.9380   -0.0774 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6297   -0.6481    1.2239 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0756   -0.1147    1.1573 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8052   -1.1705    0.6126 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1466   -0.8223    0.4209 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5144   -0.9420   -0.8954 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7431   -0.3863   -1.1409 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7199    1.1288   -1.0869 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8070    1.5506   -2.0618 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8387   -0.9653   -0.3038 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9804   -0.2155   -0.4332 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0742   -0.9715   -0.8478 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0354   -0.9165    0.1603 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6388    0.3119    0.2523 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5131    0.7515    1.7168 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0229    1.3950   -0.5724 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9135    2.4986   -0.4986 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8163    1.0566   -2.0126 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9076    1.4635   -2.7952 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5687   -0.4197   -2.1561 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5964   -0.6628   -3.1289 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4470   -0.9849    1.1742 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4787    0.2827    1.7234 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0658   -1.6211    1.3082 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6980   -1.4824    2.6499 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6665   -1.8765    2.1017 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7097   -1.4587    3.4274 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4101   -2.7106    1.9273 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5259   -3.9005    2.6027 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1917   -2.9357    0.4331 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2645   -3.6645   -0.0924 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0557   -0.2907    1.1531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1059   -0.8969    0.2978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6174   -0.0412   -0.8416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9167   -0.6109   -2.0819 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1695    1.3203   -0.4604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0654    2.2392   -0.2525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5409    2.2172   -0.3162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0045    0.8455   -0.5889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0651    0.3144    0.3826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5559    0.2371    1.7566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2182    1.3074    0.3941 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3979    0.8452    1.2043 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3464    1.8674    1.1508 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.9746   -0.3239    0.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5461    0.1666   -0.7481 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9683   -1.3903    0.1748 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5408   -2.1706   -1.0362 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0546   -2.3782    1.3045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6313   -0.9374   -0.2257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5999   -1.9903   -0.2510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2227   -2.4787    0.9864 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4334   -1.5831   -1.0414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0815   -0.1345   -1.1707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1337    0.1462   -2.7133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7418    1.6357   -0.2286 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8865    2.1770   -1.2790 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6225    3.4064   -1.8695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4188    4.2586   -2.0561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9733    4.7666   -0.3699 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6892    4.2844   -0.6830 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2670    2.0793   -1.0881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9191    3.4097    1.3314 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5608    2.4585    1.1520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9156    1.6254    2.3178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5113    0.5916    1.9922 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8159   -1.6094   -1.2928 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9882    0.1566    1.5911 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3692    0.1035    2.1928 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1222    0.7672    0.4934 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2481    0.2356    0.7512 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0020   -0.6286   -2.2121 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7359    1.5137   -1.3773 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5290    1.5312   -0.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1239    1.1871   -2.9282 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9755   -2.0313   -0.5732 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7186   -2.0222   -0.9659 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7352    0.2808    0.0425 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.3005    0.3184    2.3401 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.4626    1.8526    1.7972 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.5325    0.3786    2.1368 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0892    1.7977   -0.0805 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8579    2.1633   -0.5563 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8825    1.5669   -2.3869 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5320    1.5354   -3.7287 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5186   -0.9492   -2.4382 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2930   -1.6056   -3.0426 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1731   -1.6326    1.6934 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7958    0.3498    2.4517 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1211   -2.6791    1.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3321   -2.0760    3.1613 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5604   -2.4611    1.8441 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5456   -0.4854    3.5345 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5690   -2.1163    2.2938 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3983   -3.9836    3.0183 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2814   -3.5605    0.2900 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8516   -3.0357   -0.6050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5105    0.3304    1.9541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5312   -1.1182    1.6920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8822   -1.2579    0.9903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6575   -1.8565   -0.1014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6050   -1.1564   -2.7670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3838    0.1169   -2.6710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2582   -1.5015   -1.7990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6236    3.2506    0.0360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9899    2.7039    0.5779 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.8933    1.1554    2.3263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9327   -0.6061    2.3668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4605    0.2427    1.8881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5806    1.3294   -0.6775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8865    2.3089    0.6366 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1848    0.6504    2.2514 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4127    2.1220    0.1875 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.6604    3.0301   -2.1155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7544    4.2013   -1.1211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2032    3.7173   -2.8262 H   0  0  0  0  0  0  0  0  0  0  0  0
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 53124  1  0
 54125  1  0
 55126  1  0
 57127  1  0
 57128  1  0
 57129  1  0
 58130  1  0
 58131  1  0
 58132  1  0
 59133  1  0
 60134  1  0
 61135  1  0
 62136  1  0
 62137  1  0
 64138  1  0
 64139  1  0
 64140  1  0
 65141  1  0
 66142  1  0
 67143  1  0
 67144  1  0
 67145  1  0
M  END
Download

PDB for HMDB0039946 (Centellasaponin C)

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      -6.637   4.533   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.330   3.717   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.276   5.257   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.381   2.180   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.078   1.364   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.132  -0.176   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.921   4.410   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.919   5.978   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.556   6.702   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.252   5.886   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.108   6.609   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.159   8.147   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.144   8.963   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.854   2.098   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.666   3.625   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.840   2.301   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -7.773   0.312   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.744   1.456   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.795   0.243   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.360   2.809   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.306   4.346   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000   3.530   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.360   4.254   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.414   5.793   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.772   6.514   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.828   8.054   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.522   8.870   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.573  10.408   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.666   3.438   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       2.718   4.977   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.078   5.698   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -9.300   4.628   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -7.994   3.812   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -8.050   2.272   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -9.408   1.549   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       5.384   4.882   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       5.328   3.348   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       6.634   2.532   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       7.994   3.253   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       8.048   4.792   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       6.742   5.609   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       6.583   0.992   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0       5.220   0.268   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0       9.298   2.437   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0       9.408   5.514   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0       6.798   7.143   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0       5.168  -1.269   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       3.808  -1.993   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       3.757  -3.530   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       5.061  -4.346   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0       6.418  -3.625   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0       6.472  -2.085   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0       7.725  -4.441   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0       7.671  -5.978   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       5.004  -5.886   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0       2.395  -4.254   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       2.502  -1.177   0.000  0.00  0.00           O+0
HETATM   58  C   UNK     0       3.647  -6.609   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0       2.343  -5.793   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0       0.983  -6.515   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       0.932  -8.052   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       2.235  -8.868   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       3.593  -8.147   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      -0.323  -5.698   0.000  0.00  0.00           C+0
HETATM   65  O   UNK     0      -0.428  -8.776   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       2.181 -10.408   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0       4.899  -8.963   0.000  0.00  0.00           O+0
CONECT    1    2   33                                                       
CONECT    2    1    3    4    7                                             
CONECT    3    2                                                            
CONECT    4    2    5   18                                                  
CONECT    5    4    6   14                                                  
CONECT    6    5                                                            
CONECT    7    2    8   15                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   21                                                  
CONECT   11   10   12   24                                                  
CONECT   12   11   13   27                                                  
CONECT   13   12                                                            
CONECT   14    5   15                                                       
CONECT   15    7   14   16   21                                             
CONECT   16   15                                                            
CONECT   17   18                                                            
CONECT   18    4   17   19   34                                             
CONECT   19   18                                                            
CONECT   20   21                                                            
CONECT   21   10   15   20   22                                             
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   11   23   25   30                                             
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   12   26   28                                                  
CONECT   28   27                                                            
CONECT   29   30                                                            
CONECT   30   24   29   31                                                  
CONECT   31   30   36                                                       
CONECT   32   33                                                            
CONECT   33    1   32   34                                                  
CONECT   34   18   33   35                                                  
CONECT   35   34                                                            
CONECT   36   31   37   41                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39   42                                                  
CONECT   39   38   40   44                                                  
CONECT   40   39   41   45                                                  
CONECT   41   36   40   46                                                  
CONECT   42   38   43                                                       
CONECT   43   42   47                                                       
CONECT   44   39                                                            
CONECT   45   40                                                            
CONECT   46   41                                                            
CONECT   47   43   48   52                                                  
CONECT   48   47   49   57                                                  
CONECT   49   48   50   56                                                  
CONECT   50   49   51   55                                                  
CONECT   51   50   52   53                                                  
CONECT   52   47   51                                                       
CONECT   53   51   54                                                       
CONECT   54   53                                                            
CONECT   55   50   58                                                       
CONECT   56   49                                                            
CONECT   57   48                                                            
CONECT   58   55   59   63                                                  
CONECT   59   58   60                                                       
CONECT   60   59   61   64                                                  
CONECT   61   60   62   65                                                  
CONECT   62   61   63   66                                                  
CONECT   63   58   62   67                                                  
CONECT   64   60                                                            
CONECT   65   61                                                            
CONECT   66   62                                                            
CONECT   67   63                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  148    0
END
Download

3D PDB for HMDB0039946 (Centellasaponin C)

COMPND    HMDB0039946
HETATM    1  C1  UNL     1      -0.381   4.064  -0.980  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.591   2.609  -0.601  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.512   2.467   0.863  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.189   1.330   1.529  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.008   0.541   0.483  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.966  -0.204  -0.183  1.00  0.00           C  
HETATM    7  O1  UNL     1      -0.894  -0.346  -1.402  1.00  0.00           O  
HETATM    8  O2  UNL     1       0.085  -0.851   0.517  1.00  0.00           O  
HETATM    9  C7  UNL     1       1.065  -1.579  -0.201  1.00  0.00           C  
HETATM   10  O3  UNL     1       2.305  -0.938  -0.077  1.00  0.00           O  
HETATM   11  C8  UNL     1       2.630  -0.648   1.224  1.00  0.00           C  
HETATM   12  C9  UNL     1       4.076  -0.115   1.157  1.00  0.00           C  
HETATM   13  O4  UNL     1       4.805  -1.171   0.613  1.00  0.00           O  
HETATM   14  C10 UNL     1       6.147  -0.822   0.421  1.00  0.00           C  
HETATM   15  O5  UNL     1       6.514  -0.942  -0.895  1.00  0.00           O  
HETATM   16  C11 UNL     1       7.743  -0.386  -1.141  1.00  0.00           C  
HETATM   17  C12 UNL     1       7.720   1.129  -1.087  1.00  0.00           C  
HETATM   18  O6  UNL     1       6.807   1.551  -2.062  1.00  0.00           O  
HETATM   19  C13 UNL     1       8.839  -0.965  -0.304  1.00  0.00           C  
HETATM   20  O7  UNL     1       9.980  -0.215  -0.433  1.00  0.00           O  
HETATM   21  C14 UNL     1      11.074  -0.971  -0.848  1.00  0.00           C  
HETATM   22  O8  UNL     1      12.035  -0.917   0.160  1.00  0.00           O  
HETATM   23  C15 UNL     1      12.639   0.312   0.252  1.00  0.00           C  
HETATM   24  C16 UNL     1      12.513   0.752   1.717  1.00  0.00           C  
HETATM   25  C17 UNL     1      12.023   1.395  -0.572  1.00  0.00           C  
HETATM   26  O9  UNL     1      12.913   2.499  -0.499  1.00  0.00           O  
HETATM   27  C18 UNL     1      11.816   1.057  -2.013  1.00  0.00           C  
HETATM   28  O10 UNL     1      12.908   1.464  -2.795  1.00  0.00           O  
HETATM   29  C19 UNL     1      11.569  -0.420  -2.156  1.00  0.00           C  
HETATM   30  O11 UNL     1      10.596  -0.663  -3.129  1.00  0.00           O  
HETATM   31  C20 UNL     1       8.447  -0.985   1.174  1.00  0.00           C  
HETATM   32  O12 UNL     1       8.479   0.283   1.723  1.00  0.00           O  
HETATM   33  C21 UNL     1       7.066  -1.621   1.308  1.00  0.00           C  
HETATM   34  O13 UNL     1       6.698  -1.482   2.650  1.00  0.00           O  
HETATM   35  C22 UNL     1       2.667  -1.876   2.102  1.00  0.00           C  
HETATM   36  O14 UNL     1       2.710  -1.459   3.427  1.00  0.00           O  
HETATM   37  C23 UNL     1       1.410  -2.711   1.927  1.00  0.00           C  
HETATM   38  O15 UNL     1       1.526  -3.901   2.603  1.00  0.00           O  
HETATM   39  C24 UNL     1       1.192  -2.936   0.433  1.00  0.00           C  
HETATM   40  O16 UNL     1       2.265  -3.664  -0.092  1.00  0.00           O  
HETATM   41  C25 UNL     1      -3.056  -0.291   1.153  1.00  0.00           C  
HETATM   42  C26 UNL     1      -4.106  -0.897   0.298  1.00  0.00           C  
HETATM   43  C27 UNL     1      -4.617  -0.041  -0.842  1.00  0.00           C  
HETATM   44  C28 UNL     1      -3.917  -0.611  -2.082  1.00  0.00           C  
HETATM   45  C29 UNL     1      -4.170   1.320  -0.460  1.00  0.00           C  
HETATM   46  C30 UNL     1      -5.065   2.239  -0.253  1.00  0.00           C  
HETATM   47  C31 UNL     1      -6.541   2.217  -0.316  1.00  0.00           C  
HETATM   48  C32 UNL     1      -7.004   0.845  -0.589  1.00  0.00           C  
HETATM   49  C33 UNL     1      -8.065   0.314   0.383  1.00  0.00           C  
HETATM   50  C34 UNL     1      -7.556   0.237   1.757  1.00  0.00           C  
HETATM   51  C35 UNL     1      -9.218   1.307   0.394  1.00  0.00           C  
HETATM   52  C36 UNL     1     -10.398   0.845   1.204  1.00  0.00           C  
HETATM   53  O17 UNL     1     -11.346   1.867   1.151  1.00  0.00           O  
HETATM   54  C37 UNL     1     -10.975  -0.324   0.441  1.00  0.00           C  
HETATM   55  O18 UNL     1     -11.546   0.167  -0.748  1.00  0.00           O  
HETATM   56  C38 UNL     1      -9.968  -1.390   0.175  1.00  0.00           C  
HETATM   57  C39 UNL     1     -10.541  -2.171  -1.036  1.00  0.00           C  
HETATM   58  C40 UNL     1     -10.055  -2.378   1.305  1.00  0.00           C  
HETATM   59  C41 UNL     1      -8.631  -0.937  -0.226  1.00  0.00           C  
HETATM   60  C42 UNL     1      -7.600  -1.990  -0.251  1.00  0.00           C  
HETATM   61  O19 UNL     1      -7.223  -2.479   0.986  1.00  0.00           O  
HETATM   62  C43 UNL     1      -6.433  -1.583  -1.041  1.00  0.00           C  
HETATM   63  C44 UNL     1      -6.081  -0.134  -1.171  1.00  0.00           C  
HETATM   64  C45 UNL     1      -6.134   0.146  -2.713  1.00  0.00           C  
HETATM   65  C46 UNL     1      -2.742   1.636  -0.229  1.00  0.00           C  
HETATM   66  C47 UNL     1      -1.887   2.177  -1.279  1.00  0.00           C  
HETATM   67  C48 UNL     1      -2.623   3.406  -1.870  1.00  0.00           C  
HETATM   68  H1  UNL     1      -0.419   4.259  -2.056  1.00  0.00           H  
HETATM   69  H2  UNL     1      -0.973   4.767  -0.370  1.00  0.00           H  
HETATM   70  H3  UNL     1       0.689   4.284  -0.683  1.00  0.00           H  
HETATM   71  H4  UNL     1       0.267   2.079  -1.088  1.00  0.00           H  
HETATM   72  H5  UNL     1      -0.919   3.410   1.331  1.00  0.00           H  
HETATM   73  H6  UNL     1       0.561   2.459   1.152  1.00  0.00           H  
HETATM   74  H7  UNL     1      -1.916   1.625   2.318  1.00  0.00           H  
HETATM   75  H8  UNL     1      -0.511   0.592   1.992  1.00  0.00           H  
HETATM   76  H9  UNL     1       0.816  -1.609  -1.293  1.00  0.00           H  
HETATM   77  H10 UNL     1       1.988   0.157   1.591  1.00  0.00           H  
HETATM   78  H11 UNL     1       4.369   0.104   2.193  1.00  0.00           H  
HETATM   79  H12 UNL     1       4.122   0.767   0.493  1.00  0.00           H  
HETATM   80  H13 UNL     1       6.248   0.236   0.751  1.00  0.00           H  
HETATM   81  H14 UNL     1       8.002  -0.629  -2.212  1.00  0.00           H  
HETATM   82  H15 UNL     1       8.736   1.514  -1.377  1.00  0.00           H  
HETATM   83  H16 UNL     1       7.529   1.531  -0.096  1.00  0.00           H  
HETATM   84  H17 UNL     1       7.124   1.187  -2.928  1.00  0.00           H  
HETATM   85  H18 UNL     1       8.975  -2.031  -0.573  1.00  0.00           H  
HETATM   86  H19 UNL     1      10.719  -2.022  -0.966  1.00  0.00           H  
HETATM   87  H20 UNL     1      13.735   0.281   0.043  1.00  0.00           H  
HETATM   88  H21 UNL     1      13.300   0.318   2.340  1.00  0.00           H  
HETATM   89  H22 UNL     1      12.463   1.853   1.797  1.00  0.00           H  
HETATM   90  H23 UNL     1      11.533   0.379   2.137  1.00  0.00           H  
HETATM   91  H24 UNL     1      11.089   1.798  -0.080  1.00  0.00           H  
HETATM   92  H25 UNL     1      13.858   2.163  -0.556  1.00  0.00           H  
HETATM   93  H26 UNL     1      10.882   1.567  -2.387  1.00  0.00           H  
HETATM   94  H27 UNL     1      12.532   1.535  -3.729  1.00  0.00           H  
HETATM   95  H28 UNL     1      12.519  -0.949  -2.438  1.00  0.00           H  
HETATM   96  H29 UNL     1      10.293  -1.606  -3.043  1.00  0.00           H  
HETATM   97  H30 UNL     1       9.173  -1.633   1.693  1.00  0.00           H  
HETATM   98  H31 UNL     1       7.796   0.350   2.452  1.00  0.00           H  
HETATM   99  H32 UNL     1       7.121  -2.679   1.057  1.00  0.00           H  
HETATM  100  H33 UNL     1       7.332  -2.076   3.161  1.00  0.00           H  
HETATM  101  H34 UNL     1       3.560  -2.461   1.844  1.00  0.00           H  
HETATM  102  H35 UNL     1       2.546  -0.485   3.535  1.00  0.00           H  
HETATM  103  H36 UNL     1       0.569  -2.116   2.294  1.00  0.00           H  
HETATM  104  H37 UNL     1       2.398  -3.984   3.018  1.00  0.00           H  
HETATM  105  H38 UNL     1       0.281  -3.560   0.290  1.00  0.00           H  
HETATM  106  H39 UNL     1       2.852  -3.036  -0.605  1.00  0.00           H  
HETATM  107  H40 UNL     1      -3.510   0.330   1.954  1.00  0.00           H  
HETATM  108  H41 UNL     1      -2.531  -1.118   1.692  1.00  0.00           H  
HETATM  109  H42 UNL     1      -4.882  -1.258   0.990  1.00  0.00           H  
HETATM  110  H43 UNL     1      -3.658  -1.857  -0.101  1.00  0.00           H  
HETATM  111  H44 UNL     1      -4.605  -1.156  -2.767  1.00  0.00           H  
HETATM  112  H45 UNL     1      -3.384   0.117  -2.671  1.00  0.00           H  
HETATM  113  H46 UNL     1      -3.258  -1.502  -1.799  1.00  0.00           H  
HETATM  114  H47 UNL     1      -4.624   3.251   0.036  1.00  0.00           H  
HETATM  115  H48 UNL     1      -6.990   2.704   0.578  1.00  0.00           H  
HETATM  116  H49 UNL     1      -6.809   2.925  -1.151  1.00  0.00           H  
HETATM  117  H50 UNL     1      -7.740   1.078  -1.485  1.00  0.00           H  
HETATM  118  H51 UNL     1      -7.893   1.155   2.326  1.00  0.00           H  
HETATM  119  H52 UNL     1      -7.933  -0.606   2.367  1.00  0.00           H  
HETATM  120  H53 UNL     1      -6.460   0.243   1.888  1.00  0.00           H  
HETATM  121  H54 UNL     1      -9.581   1.329  -0.678  1.00  0.00           H  
HETATM  122  H55 UNL     1      -8.886   2.309   0.637  1.00  0.00           H  
HETATM  123  H56 UNL     1     -10.185   0.650   2.251  1.00  0.00           H  
HETATM  124  H57 UNL     1     -11.413   2.122   0.187  1.00  0.00           H  
HETATM  125  H58 UNL     1     -11.806  -0.731   1.042  1.00  0.00           H  
HETATM  126  H59 UNL     1     -12.394  -0.258  -0.959  1.00  0.00           H  
HETATM  127  H60 UNL     1     -10.356  -1.602  -1.969  1.00  0.00           H  
HETATM  128  H61 UNL     1     -10.130  -3.189  -1.062  1.00  0.00           H  
HETATM  129  H62 UNL     1     -11.635  -2.265  -0.869  1.00  0.00           H  
HETATM  130  H63 UNL     1      -9.390  -3.229   1.261  1.00  0.00           H  
HETATM  131  H64 UNL     1      -9.945  -1.885   2.291  1.00  0.00           H  
HETATM  132  H65 UNL     1     -11.094  -2.827   1.357  1.00  0.00           H  
HETATM  133  H66 UNL     1      -8.741  -0.630  -1.323  1.00  0.00           H  
HETATM  134  H67 UNL     1      -8.100  -2.895  -0.744  1.00  0.00           H  
HETATM  135  H68 UNL     1      -6.769  -3.344   0.830  1.00  0.00           H  
HETATM  136  H69 UNL     1      -6.560  -2.065  -2.072  1.00  0.00           H  
HETATM  137  H70 UNL     1      -5.566  -2.218  -0.659  1.00  0.00           H  
HETATM  138  H71 UNL     1      -6.980   0.877  -2.925  1.00  0.00           H  
HETATM  139  H72 UNL     1      -5.257   0.705  -3.047  1.00  0.00           H  
HETATM  140  H73 UNL     1      -6.437  -0.728  -3.281  1.00  0.00           H  
HETATM  141  H74 UNL     1      -2.733   2.550   0.519  1.00  0.00           H  
HETATM  142  H75 UNL     1      -1.609   1.571  -2.134  1.00  0.00           H  
HETATM  143  H76 UNL     1      -3.660   3.030  -2.116  1.00  0.00           H  
HETATM  144  H77 UNL     1      -2.754   4.201  -1.121  1.00  0.00           H  
HETATM  145  H78 UNL     1      -2.203   3.717  -2.826  1.00  0.00           H  
CONECT    1    2   68   69   70
CONECT    2    3   66   71
CONECT    3    4   72   73
CONECT    4    5   74   75
CONECT    5    6   41   65
CONECT    6    7    7    8
CONECT    8    9
CONECT    9   10   39   76
CONECT   10   11
CONECT   11   12   35   77
CONECT   12   13   78   79
CONECT   13   14
CONECT   14   15   33   80
CONECT   15   16
CONECT   16   17   19   81
CONECT   17   18   82   83
CONECT   18   84
CONECT   19   20   31   85
CONECT   20   21
CONECT   21   22   29   86
CONECT   22   23
CONECT   23   24   25   87
CONECT   24   88   89   90
CONECT   25   26   27   91
CONECT   26   92
CONECT   27   28   29   93
CONECT   28   94
CONECT   29   30   95
CONECT   30   96
CONECT   31   32   33   97
CONECT   32   98
CONECT   33   34   99
CONECT   34  100
CONECT   35   36   37  101
CONECT   36  102
CONECT   37   38   39  103
CONECT   38  104
CONECT   39   40  105
CONECT   40  106
CONECT   41   42  107  108
CONECT   42   43  109  110
CONECT   43   44   45   63
CONECT   44  111  112  113
CONECT   45   46   46   65
CONECT   46   47  114
CONECT   47   48  115  116
CONECT   48   49   63  117
CONECT   49   50   51   59
CONECT   50  118  119  120
CONECT   51   52  121  122
CONECT   52   53   54  123
CONECT   53  124
CONECT   54   55   56  125
CONECT   55  126
CONECT   56   57   58   59
CONECT   57  127  128  129
CONECT   58  130  131  132
CONECT   59   60  133
CONECT   60   61   62  134
CONECT   61  135
CONECT   62   63  136  137
CONECT   63   64
CONECT   64  138  139  140
CONECT   65   66  141
CONECT   66   67  142
CONECT   67  143  144  145
END
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SMILES for HMDB0039946 (Centellasaponin C)

CC1CCC2(CCC3(C)C(=CCC4C5(C)CC(O)C(O)C(C)(C)C5C(O)CC34C)C2C1C)C(=O)OC1OC(COC2OC(CO)C(OC3OC(C)C(O)C(O)C3O)C(O)C2O)C(O)C(O)C1O
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INCHI for HMDB0039946 (Centellasaponin C)

InChI=1S/C48H78O19/c1-19-11-12-48(14-13-46(7)22(28(48)20(19)2)9-10-27-45(6)15-24(51)39(60)44(4,5)38(45)23(50)16-47(27,46)8)43(61)67-42-35(58)32(55)30(53)26(65-42)18-62-40-36(59)33(56)37(25(17-49)64-40)66-41-34(57)31(54)29(52)21(3)63-41/h9,19-21,23-42,49-60H,10-18H2,1-8H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(+)-Centellasaponin CHMDB
6-({[3,4-dihydroxy-6-(hydroxymethyl)-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 8,10,11-trihydroxy-1,2,6a,6b,9,9,12a-heptamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acidGenerator
Centellasaponin CMeSH
Chemical FormulaC48H78O19
Average Molecular Weight959.1215
Monoisotopic Molecular Weight958.513730314
IUPAC Name6-({[3,4-dihydroxy-6-(hydroxymethyl)-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 8,10,11-trihydroxy-1,2,6a,6b,9,9,12a-heptamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylate
Traditional Name6-({[3,4-dihydroxy-6-(hydroxymethyl)-5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 8,10,11-trihydroxy-1,2,6a,6b,9,9,12a-heptamethyl-2,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydro-1H-picene-4a-carboxylate
CAS Registry Number386223-76-3
SMILES
CC1CCC2(CCC3(C)C(=CCC4C5(C)CC(O)C(O)C(C)(C)C5C(O)CC34C)C2C1C)C(=O)OC1OC(COC2OC(CO)C(OC3OC(C)C(O)C(O)C3O)C(O)C2O)C(O)C(O)C1O
InChI Identifier
InChI=1S/C48H78O19/c1-19-11-12-48(14-13-46(7)22(28(48)20(19)2)9-10-27-45(6)15-24(51)39(60)44(4,5)38(45)23(50)16-47(27,46)8)43(61)67-42-35(58)32(55)30(53)26(65-42)18-62-40-36(59)33(56)37(25(17-49)64-40)66-41-34(57)31(54)29(52)21(3)63-41/h9,19-21,23-42,49-60H,10-18H2,1-8H3
InChI KeySOOVZDUBVGGAAJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene glycosides
Direct ParentTriterpene saponins
Alternative Parents
Substituents
  • Triterpene saponin
  • Triterpenoid
  • Oligosaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • Oxane
  • Cyclic alcohol
  • Carboxylic acid ester
  • Secondary alcohol
  • Polyol
  • Organoheterocyclic compound
  • Oxacycle
  • Monocarboxylic acid or derivatives
  • Acetal
  • Carboxylic acid derivative
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Carbonyl group
  • Primary alcohol
  • 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 Point209 - 210 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.93 g/LALOGPS
logP0.64ALOGPS
logP-0.56ChemAxon
logS-3ALOGPS
pKa (Strongest Acidic)11.75ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area315.21 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity232.37 m³·mol⁻¹ChemAxon
Polarizability102.12 ųChemAxon
Number of Rings8ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-327.45730932474
DeepCCS[M+Na]+301.37830932474
AllCCS[M+H]+296.932859911
AllCCS[M+H-H2O]+297.432859911
AllCCS[M+NH4]+296.532859911
AllCCS[M+Na]+296.332859911
AllCCS[M-H]-268.532859911
AllCCS[M+Na-2H]-274.732859911
AllCCS[M+HCOO]-281.532859911

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, 2022.5.6 minutes32390414
Predicted by Siyang on May 30, 202215.0999 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.85 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid201.2 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3331.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid154.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid175.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid197.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid172.6 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid466.8 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 Acid676.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)433.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1031.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid632.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1646.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid403.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid429.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate314.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA318.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water44.7 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 10V, Positive-QTOFsplash10-00dl-0001900204-975b66d72c077ebec80e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 20V, Positive-QTOFsplash10-0fdk-0101902401-e170a4efd5ffb4aff00d2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 40V, Positive-QTOFsplash10-00bm-1304900311-694eb35ef7c20ad7ae122017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 10V, Negative-QTOFsplash10-05n0-1111901116-ffb1ba65dd121dbfc2bd2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 20V, Negative-QTOFsplash10-000i-2413900313-d474093be5524b8525552017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 40V, Negative-QTOFsplash10-01pc-5631900010-dde4c3f8d476b7e7e3382017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 10V, Negative-QTOFsplash10-0a4i-0000400019-f336c0ed0a64478570d92021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 20V, Negative-QTOFsplash10-0a4i-2500201229-49eed6b526ea621eedc12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 40V, Negative-QTOFsplash10-014r-1200900010-c27f6e9711aec91772312021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 10V, Positive-QTOFsplash10-0adj-0600501219-7c86ca6fd9f2141172432021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 20V, Positive-QTOFsplash10-0002-2901502743-e371381cafaf856226d22021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Centellasaponin C 40V, Positive-QTOFsplash10-0a4r-7900400001-049c094e61327a0013992021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB019608
KNApSAcK IDC00032806
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound85348461
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1880931
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.