Hmdb loader

Showing metabocard for Yayoisaponin C (HMDB0033401)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:07:11 UTC
Update Date2022-03-07 02:53:41 UTC
HMDB IDHMDB0033401
Secondary Accession Numbers
  • HMDB33401
Metabolite Identification
Common NameYayoisaponin C
DescriptionYayoisaponin C belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative. Yayoisaponin C is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563862400
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033401 (Yayoisaponin C)


  Mrv0541 02241209122D          

 76 85  0  0  0  0            999 V2000
    4.7093    5.2764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0411    4.7910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2877    5.1264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2011    5.9472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8693    6.4325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6227    6.0970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2894    6.5810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5190    2.3975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5190    3.2223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1946    3.6348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0188    3.3805    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 HMDB0033401 (Yayoisaponin C)

HMDB0033401
     RDKit          3D
Yayoisaponin C
160169  0  0  0  0  0  0  0  0999 V2000
   13.1881    1.0563    2.4954 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9073    0.9201    1.7121 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5920    2.3176    1.1652 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3448    2.1333    0.2992 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3686    1.2255    0.9563 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5941    1.1787    2.3293 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7886    0.5351    2.6225 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5745   -0.0735    0.4692 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9548   -0.1294   -0.7745 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2842   -1.4473   -1.0281 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8109   -1.1386   -0.8108 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9092   -2.1096   -1.4792 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7452   -3.3017   -0.5759 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5336   -3.2772    0.2617 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4633   -4.5135    0.9758 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3142   -3.1796   -0.5524 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1752   -2.6968    0.3171 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8237   -2.9567   -0.3859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1337   -2.0601   -0.0478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1021   -2.3709    0.8814 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2255   -2.8193    0.1101 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3560   -3.0014    0.9200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1822   -3.9900    2.0174 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8359   -5.2720    1.5360 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.4818    7.1703    3.6702 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8895    6.0567    1.6170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8124    7.3529    2.0869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5223    5.4132    1.6665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1016    5.2401    2.9807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6508    4.0588    0.9668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6399    4.3054   -0.3964 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6038    0.3184    0.0600 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.6702    0.4675   -2.0416 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.9710    0.9846   -4.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2522    0.4991   -4.6793 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8785    1.5419   -3.0334 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0421    2.6333   -2.9731 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8021   -0.5925    1.2340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6958   -0.0403   -0.0261 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4739   -1.1923    1.6965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3797   -1.2851    3.0535 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0389   -2.8973   -1.8735 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3380   -4.1239   -2.4296 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1300   -1.8854   -2.2230 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4699   -2.4683   -1.8271 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7294   -3.5207   -2.9206 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5832   -1.4567   -1.7979 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974   -0.2672   -0.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3751    0.8331   -1.3554 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7379    0.2632   -1.3727 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1209    0.1351   -2.8678 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8440    0.9347   -0.7364 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9197    1.4588    0.5862 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0033401 (Yayoisaponin C)


  Mrv0541 02241209122D          

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   -2.3322   -6.0160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8829   -6.5810    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1465   -5.5197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2894   -6.3322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 75 76  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033401

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1C2C(CC3C4CC(O)C5CC(OC6OC(CO)C(OC7OC(CO)C(O)C(OC8OC(CO)C(O)C(O)C8O)C7OC7OC(CO)C(O)C(O)C7O)C(O)C6O)C(O)CC5(C)C4CCC23C)OC11CCC(C)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C51H84O25/c1-18-5-8-51(67-17-18)19(2)32-27(76-51)10-22-20-9-24(56)23-11-26(25(57)12-50(23,4)21(20)6-7-49(22,32)3)68-45-41(66)38(63)42(31(16-55)72-45)73-48-44(75-47-40(65)37(62)34(59)29(14-53)70-47)43(35(60)30(15-54)71-48)74-46-39(64)36(61)33(58)28(13-52)69-46/h18-48,52-66H,5-17H2,1-4H3

> <INCHI_KEY>
IFCJNJJMBPXNRD-UHFFFAOYSA-N

> <FORMULA>
C51H84O25

> <MOLECULAR_WEIGHT>
1097.1977

> <EXACT_MASS>
1096.530168238

> <JCHEM_ACCEPTOR_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
113.36957351835026

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
15

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2-{[4,5-dihydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15',19'-dioloxy}oxan-3-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-4-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-1.23

> <JCHEM_LOGP>
-4.134126051333329

> <ALOGPS_LOGS>
-2.22

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
10

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.192816385216195

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.754279523599475

> <JCHEM_PKA_STRONGEST_BASIC>
-3.648377595760352

> <JCHEM_POLAR_SURFACE_AREA>
395.75000000000006

> <JCHEM_REFRACTIVITY>
252.02310000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.59e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2-{[4,5-dihydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15',19'-dioloxy}oxan-3-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-4-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0033401 (Yayoisaponin C)

HMDB0033401
     RDKit          3D
Yayoisaponin C
160169  0  0  0  0  0  0  0  0999 V2000
   13.1881    1.0563    2.4954 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9073    0.9201    1.7121 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5920    2.3176    1.1652 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3448    2.1333    0.2992 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3686    1.2255    0.9563 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5941    1.1787    2.3293 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7886    0.5351    2.6225 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5745   -0.0735    0.4692 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9548   -0.1294   -0.7745 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2842   -1.4473   -1.0281 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8109   -1.1386   -0.8108 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9092   -2.1096   -1.4792 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7452   -3.3017   -0.5759 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5336   -3.2772    0.2617 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4633   -4.5135    0.9758 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3142   -3.1796   -0.5524 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1752   -2.6968    0.3171 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8237   -2.9567   -0.3859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1337   -2.0601   -0.0478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1021   -2.3709    0.8814 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2255   -2.8193    0.1101 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3560   -3.0014    0.9200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1822   -3.9900    2.0174 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8359   -5.2720    1.5360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9003   -1.6726    1.3258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9147   -1.3418    0.4857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0227   -0.7533    0.9714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1416   -1.6383    1.1429 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9839   -1.0256    2.0319 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3250   -1.7920    1.9597 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2432   -1.2513    2.8644 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3073    0.4005    1.8177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4044    1.0531    3.0633 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4446    1.2064    0.8770 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6167    2.0271    1.6711 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8983    3.3709    1.4517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3699    3.9340    2.6439 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8534    5.2045    2.3960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0051    5.8703    3.7697 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4818    7.1703    3.6702 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8895    6.0567    1.6170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8124    7.3529    2.0869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5223    5.4132    1.6665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1016    5.2401    2.9807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6508    4.0588    0.9668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6399    4.3054   -0.3964 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6038    0.3184    0.0600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5899    0.8821   -0.6943 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6702    0.4675   -2.0416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6674   -0.4390   -2.3215 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7048   -1.0251   -3.5527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8835   -1.9747   -3.6083 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8149   -2.9391   -2.5982 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9129   -0.0220   -4.6671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7075    0.6516   -4.8402 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9710    0.9846   -4.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2522    0.4991   -4.6793 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8785    1.5419   -3.0334 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0421    2.6333   -2.9731 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8021   -0.5925    1.2340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6958   -0.0403   -0.0261 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4739   -1.1923    1.6965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3797   -1.2851    3.0535 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0389   -2.8973   -1.8735 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3380   -4.1239   -2.4296 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1300   -1.8854   -2.2230 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4699   -2.4683   -1.8271 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7294   -3.5207   -2.9206 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5832   -1.4567   -1.7979 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974   -0.2672   -0.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3751    0.8331   -1.3554 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7379    0.2632   -1.3727 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1209    0.1351   -2.8678 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8440    0.9347   -0.7364 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9197    1.4588    0.5862 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0989    0.9285    1.6969 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9528    1.1586    3.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7332    1.9877    2.2231 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.9114    0.2351    2.3283 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.0027    0.2549    0.8251 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3304    3.0115    1.9594 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.4293    2.6168    0.5272 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6899    1.6590   -0.6385 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9073    3.1039    0.0178 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.1163    0.6001    3.6553 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.5852   -0.5603    2.4393 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6690    0.0467   -1.6056 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5025   -1.9068   -1.9955 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5909   -2.1793   -0.2451 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6440   -1.1982    0.2736 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3385   -2.5267   -2.4189 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6249   -3.4229    0.1207 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7317   -4.2584   -1.1705 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6356   -2.5328    1.0913 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5588   -4.9241    0.8657 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0181   -4.2566   -0.8079 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2024   -3.1681    1.3051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2576   -1.6147    0.4271 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5775   -3.9608   -0.0529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8357   -3.2602    1.4410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1007   -3.4870    0.1968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2229   -4.1589    2.4401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4808   -3.7345    2.8001 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5623   -5.5766    0.9053 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2308   -1.6639    2.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8657   -0.4018    1.9911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6356   -1.1542    3.1020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7234   -1.4901    0.9496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2097   -2.8624    1.9858 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0536   -1.6322    3.7851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3647    0.4775    1.3805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9278    0.4895    3.6736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1172    1.8652    0.2560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7114    3.5235    0.6922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8366    5.2474    1.9271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9790    5.9379    4.1726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6713    5.2804    4.4340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0511    7.2980    2.8577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1564    6.1041    0.5233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9007    7.7504    1.9371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7721    5.9830    1.0987 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0883    4.3145    3.2749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7129    3.5092    1.2180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0858    5.1426   -0.5329 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3055   -0.2641   -0.6083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6155   -0.1760   -2.0662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7916   -1.5998   -3.8021 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8826   -2.5636   -4.5567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8646   -1.4844   -3.5464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5759   -2.7688   -1.9662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0618   -0.5769   -5.6474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9799    0.2857   -4.2287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8675    1.8733   -5.1222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3174    0.4312   -5.6836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9288    1.9591   -2.8210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1757    2.3703   -2.6327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0750    0.1920    1.9515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8321   -0.3261   -0.4474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7291   -0.3735    1.4078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4387   -1.3851    3.3527 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1144   -2.5157   -2.3441 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9547   -4.2469   -3.3337 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0954   -1.8300   -3.3252 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9254   -0.8926   -1.8169 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6413   -4.5574   -2.5339 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1161   -3.3384   -3.8199 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7777   -3.3777   -3.2418 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6718   -1.0890   -2.8520 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3996    0.2149   -1.0245 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5218   -0.4332    0.1587 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0069    1.1475   -2.3808 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2540    1.7410   -0.7360 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4833    0.8280   -3.4907 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1528    0.5143   -3.0561 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1224   -0.8940   -3.2172 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2161    1.7280   -1.4606 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7818    2.5881    0.5651 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0127    0.8522    1.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1847    1.6683    2.5481 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5548    0.0126    2.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
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M  END
Download

PDB for HMDB0033401 (Yayoisaponin 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       8.791   9.849   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       7.543   8.943   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       6.137   9.569   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.975  11.101   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.223  12.007   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.629  11.381   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.874  12.285   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.969   4.475   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.969   6.015   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.363   6.785   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.363   8.325   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.969   9.095   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.303   8.325   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.465   9.857   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.303   6.785   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.768   6.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.672   7.555   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.768   8.799   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.672  10.047   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.197  11.509   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.698   7.555   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.698   6.015   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.029   6.785   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.364   6.015   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -5.698   6.785   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       6.137   8.030   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -5.698   3.705   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -4.364   4.475   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.029   3.705   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.698   4.475   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.363   3.705   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -0.363   2.166   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -5.698   2.166   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.364   1.396   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -4.364  -0.144   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -5.698  -0.914   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -7.030  -0.144   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -7.030   1.396   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      -8.365  -0.914   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -8.365  -2.453   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      -5.698  -2.453   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      -3.029  -0.914   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      -3.029   2.166   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      -4.364  -3.223   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0      -3.029  -2.453   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0      -1.698  -3.223   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -1.698  -4.763   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -3.029  -5.533   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -4.364  -4.763   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -0.363  -2.453   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       0.969  -3.223   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      -0.363  -5.533   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      -3.029  -7.073   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      -6.099  -5.764   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0      -1.297  -8.073   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0       0.037  -7.304   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0       1.369  -8.073   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       1.369  -9.613   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0       0.037 -10.383   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      -1.297  -9.613   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       2.703  -7.304   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0       4.038  -8.073   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0       2.703 -10.383   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       0.037 -11.923   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      -2.631 -10.383   0.000  0.00  0.00           O+0
HETATM   66  C   UNK     0      -6.445  -7.735   0.000  0.00  0.00           C+0
HETATM   67  O   UNK     0      -7.892  -8.261   0.000  0.00  0.00           O+0
HETATM   68  C   UNK     0      -8.159  -9.777   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      -6.979 -10.768   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      -5.534 -10.242   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0      -5.265  -8.725   0.000  0.00  0.00           C+0
HETATM   72  O   UNK     0      -3.820  -8.199   0.000  0.00  0.00           O+0
HETATM   73  O   UNK     0      -4.353 -11.230   0.000  0.00  0.00           O+0
HETATM   74  O   UNK     0      -7.248 -12.285   0.000  0.00  0.00           O+0
HETATM   75  C   UNK     0      -9.607 -10.303   0.000  0.00  0.00           C+0
HETATM   76  O   UNK     0      -9.874 -11.820   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   19   26                                             
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    5    7                                                  
CONECT    7    6                                                            
CONECT    8    9   31                                                       
CONECT    9    8   10   15                                                  
CONECT   10    9   11   22                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15   18                                             
CONECT   14   13                                                            
CONECT   15    9   13   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   26                                                  
CONECT   18   13   17   19                                                  
CONECT   19    3   18   20                                                  
CONECT   20   19                                                            
CONECT   21   22                                                            
CONECT   22   10   21   23   30                                             
CONECT   23   22   24                                                       
CONECT   24   23   25   28                                                  
CONECT   25   24                                                            
CONECT   26    3   17                                                       
CONECT   27   28   33                                                       
CONECT   28   24   27   29                                                  
CONECT   29   28   30                                                       
CONECT   30   22   29   31                                                  
CONECT   31    8   30   32                                                  
CONECT   32   31                                                            
CONECT   33   27   34   38                                                  
CONECT   34   33   35   43                                                  
CONECT   35   34   36   42                                                  
CONECT   36   35   37   41                                                  
CONECT   37   36   38   39                                                  
CONECT   38   33   37                                                       
CONECT   39   37   40                                                       
CONECT   40   39                                                            
CONECT   41   36   44                                                       
CONECT   42   35                                                            
CONECT   43   34                                                            
CONECT   44   41   45   49                                                  
CONECT   45   44   46                                                       
CONECT   46   45   47   50                                                  
CONECT   47   46   48   52                                                  
CONECT   48   47   49   53                                                  
CONECT   49   44   48   54                                                  
CONECT   50   46   51                                                       
CONECT   51   50                                                            
CONECT   52   47                                                            
CONECT   53   48   55                                                       
CONECT   54   49   66                                                       
CONECT   55   53   56   60                                                  
CONECT   56   55   57                                                       
CONECT   57   56   58   61                                                  
CONECT   58   57   59   63                                                  
CONECT   59   58   60   64                                                  
CONECT   60   55   59   65                                                  
CONECT   61   57   62                                                       
CONECT   62   61                                                            
CONECT   63   58                                                            
CONECT   64   59                                                            
CONECT   65   60                                                            
CONECT   66   54   67   71                                                  
CONECT   67   66   68                                                       
CONECT   68   67   69   75                                                  
CONECT   69   68   70   74                                                  
CONECT   70   69   71   73                                                  
CONECT   71   66   70   72                                                  
CONECT   72   71                                                            
CONECT   73   70                                                            
CONECT   74   69                                                            
CONECT   75   68   76                                                       
CONECT   76   75                                                            
MASTER        0    0    0    0    0    0    0    0   76    0  170    0
END
Download

3D PDB for HMDB0033401 (Yayoisaponin C)

COMPND    HMDB0033401
HETATM    1  C1  UNL     1      13.188   1.056   2.495  1.00  0.00           C  
HETATM    2  C2  UNL     1      11.907   0.920   1.712  1.00  0.00           C  
HETATM    3  C3  UNL     1      11.592   2.318   1.165  1.00  0.00           C  
HETATM    4  C4  UNL     1      10.345   2.133   0.299  1.00  0.00           C  
HETATM    5  C5  UNL     1       9.369   1.225   0.956  1.00  0.00           C  
HETATM    6  O1  UNL     1       9.594   1.179   2.329  1.00  0.00           O  
HETATM    7  C6  UNL     1      10.789   0.535   2.623  1.00  0.00           C  
HETATM    8  O2  UNL     1       9.574  -0.074   0.469  1.00  0.00           O  
HETATM    9  C7  UNL     1       8.955  -0.129  -0.774  1.00  0.00           C  
HETATM   10  C8  UNL     1       8.284  -1.447  -1.028  1.00  0.00           C  
HETATM   11  C9  UNL     1       6.811  -1.139  -0.811  1.00  0.00           C  
HETATM   12  C10 UNL     1       5.909  -2.110  -1.479  1.00  0.00           C  
HETATM   13  C11 UNL     1       5.745  -3.302  -0.576  1.00  0.00           C  
HETATM   14  C12 UNL     1       4.534  -3.277   0.262  1.00  0.00           C  
HETATM   15  O3  UNL     1       4.463  -4.513   0.976  1.00  0.00           O  
HETATM   16  C13 UNL     1       3.314  -3.180  -0.552  1.00  0.00           C  
HETATM   17  C14 UNL     1       2.175  -2.697   0.317  1.00  0.00           C  
HETATM   18  C15 UNL     1       0.824  -2.957  -0.386  1.00  0.00           C  
HETATM   19  O4  UNL     1      -0.134  -2.060  -0.048  1.00  0.00           O  
HETATM   20  C16 UNL     1      -1.102  -2.371   0.881  1.00  0.00           C  
HETATM   21  O5  UNL     1      -2.226  -2.819   0.110  1.00  0.00           O  
HETATM   22  C17 UNL     1      -3.356  -3.001   0.920  1.00  0.00           C  
HETATM   23  C18 UNL     1      -3.182  -3.990   2.017  1.00  0.00           C  
HETATM   24  O6  UNL     1      -2.836  -5.272   1.536  1.00  0.00           O  
HETATM   25  C19 UNL     1      -3.900  -1.673   1.326  1.00  0.00           C  
HETATM   26  O7  UNL     1      -4.915  -1.342   0.486  1.00  0.00           O  
HETATM   27  C20 UNL     1      -6.023  -0.753   0.971  1.00  0.00           C  
HETATM   28  O8  UNL     1      -7.142  -1.638   1.143  1.00  0.00           O  
HETATM   29  C21 UNL     1      -7.984  -1.026   2.032  1.00  0.00           C  
HETATM   30  C22 UNL     1      -9.325  -1.792   1.960  1.00  0.00           C  
HETATM   31  O9  UNL     1     -10.243  -1.251   2.864  1.00  0.00           O  
HETATM   32  C23 UNL     1      -8.307   0.400   1.818  1.00  0.00           C  
HETATM   33  O10 UNL     1      -8.404   1.053   3.063  1.00  0.00           O  
HETATM   34  C24 UNL     1      -7.445   1.206   0.877  1.00  0.00           C  
HETATM   35  O11 UNL     1      -6.617   2.027   1.671  1.00  0.00           O  
HETATM   36  C25 UNL     1      -6.898   3.371   1.452  1.00  0.00           C  
HETATM   37  O12 UNL     1      -7.370   3.934   2.644  1.00  0.00           O  
HETATM   38  C26 UNL     1      -7.853   5.205   2.396  1.00  0.00           C  
HETATM   39  C27 UNL     1      -8.005   5.870   3.770  1.00  0.00           C  
HETATM   40  O13 UNL     1      -8.482   7.170   3.670  1.00  0.00           O  
HETATM   41  C28 UNL     1      -6.889   6.057   1.617  1.00  0.00           C  
HETATM   42  O14 UNL     1      -6.812   7.353   2.087  1.00  0.00           O  
HETATM   43  C29 UNL     1      -5.522   5.413   1.666  1.00  0.00           C  
HETATM   44  O15 UNL     1      -5.102   5.240   2.981  1.00  0.00           O  
HETATM   45  C30 UNL     1      -5.651   4.059   0.967  1.00  0.00           C  
HETATM   46  O16 UNL     1      -5.640   4.305  -0.396  1.00  0.00           O  
HETATM   47  C31 UNL     1      -6.604   0.318   0.060  1.00  0.00           C  
HETATM   48  O17 UNL     1      -5.590   0.882  -0.694  1.00  0.00           O  
HETATM   49  C32 UNL     1      -5.670   0.468  -2.042  1.00  0.00           C  
HETATM   50  O18 UNL     1      -4.667  -0.439  -2.321  1.00  0.00           O  
HETATM   51  C33 UNL     1      -4.705  -1.025  -3.553  1.00  0.00           C  
HETATM   52  C34 UNL     1      -5.884  -1.975  -3.608  1.00  0.00           C  
HETATM   53  O19 UNL     1      -5.815  -2.939  -2.598  1.00  0.00           O  
HETATM   54  C35 UNL     1      -4.913  -0.022  -4.667  1.00  0.00           C  
HETATM   55  O20 UNL     1      -3.708   0.652  -4.840  1.00  0.00           O  
HETATM   56  C36 UNL     1      -5.971   0.985  -4.421  1.00  0.00           C  
HETATM   57  O21 UNL     1      -7.252   0.499  -4.679  1.00  0.00           O  
HETATM   58  C37 UNL     1      -5.879   1.542  -3.033  1.00  0.00           C  
HETATM   59  O22 UNL     1      -5.042   2.633  -2.973  1.00  0.00           O  
HETATM   60  C38 UNL     1      -2.802  -0.593   1.234  1.00  0.00           C  
HETATM   61  O23 UNL     1      -2.696  -0.040  -0.026  1.00  0.00           O  
HETATM   62  C39 UNL     1      -1.474  -1.192   1.696  1.00  0.00           C  
HETATM   63  O24 UNL     1      -1.380  -1.285   3.054  1.00  0.00           O  
HETATM   64  C40 UNL     1       1.039  -2.897  -1.873  1.00  0.00           C  
HETATM   65  O25 UNL     1       1.338  -4.124  -2.430  1.00  0.00           O  
HETATM   66  C41 UNL     1       2.130  -1.885  -2.223  1.00  0.00           C  
HETATM   67  C42 UNL     1       3.470  -2.468  -1.827  1.00  0.00           C  
HETATM   68  C43 UNL     1       3.729  -3.521  -2.921  1.00  0.00           C  
HETATM   69  C44 UNL     1       4.583  -1.457  -1.798  1.00  0.00           C  
HETATM   70  C45 UNL     1       4.397  -0.267  -0.951  1.00  0.00           C  
HETATM   71  C46 UNL     1       5.375   0.833  -1.355  1.00  0.00           C  
HETATM   72  C47 UNL     1       6.738   0.263  -1.373  1.00  0.00           C  
HETATM   73  C48 UNL     1       7.121   0.135  -2.868  1.00  0.00           C  
HETATM   74  C49 UNL     1       7.844   0.935  -0.736  1.00  0.00           C  
HETATM   75  C50 UNL     1       7.920   1.459   0.586  1.00  0.00           C  
HETATM   76  C51 UNL     1       7.099   0.929   1.697  1.00  0.00           C  
HETATM   77  H1  UNL     1      12.953   1.159   3.593  1.00  0.00           H  
HETATM   78  H2  UNL     1      13.733   1.988   2.223  1.00  0.00           H  
HETATM   79  H3  UNL     1      13.911   0.235   2.328  1.00  0.00           H  
HETATM   80  H4  UNL     1      12.003   0.255   0.825  1.00  0.00           H  
HETATM   81  H5  UNL     1      11.330   3.012   1.959  1.00  0.00           H  
HETATM   82  H6  UNL     1      12.429   2.617   0.527  1.00  0.00           H  
HETATM   83  H7  UNL     1      10.690   1.659  -0.638  1.00  0.00           H  
HETATM   84  H8  UNL     1       9.907   3.104   0.018  1.00  0.00           H  
HETATM   85  H9  UNL     1      11.116   0.600   3.655  1.00  0.00           H  
HETATM   86  H10 UNL     1      10.585  -0.560   2.439  1.00  0.00           H  
HETATM   87  H11 UNL     1       9.669   0.047  -1.606  1.00  0.00           H  
HETATM   88  H12 UNL     1       8.503  -1.907  -1.995  1.00  0.00           H  
HETATM   89  H13 UNL     1       8.591  -2.179  -0.245  1.00  0.00           H  
HETATM   90  H14 UNL     1       6.644  -1.198   0.274  1.00  0.00           H  
HETATM   91  H15 UNL     1       6.338  -2.527  -2.419  1.00  0.00           H  
HETATM   92  H16 UNL     1       6.625  -3.423   0.121  1.00  0.00           H  
HETATM   93  H17 UNL     1       5.732  -4.258  -1.171  1.00  0.00           H  
HETATM   94  H18 UNL     1       4.636  -2.533   1.091  1.00  0.00           H  
HETATM   95  H19 UNL     1       3.559  -4.924   0.866  1.00  0.00           H  
HETATM   96  H20 UNL     1       3.018  -4.257  -0.808  1.00  0.00           H  
HETATM   97  H21 UNL     1       2.202  -3.168   1.305  1.00  0.00           H  
HETATM   98  H22 UNL     1       2.258  -1.615   0.427  1.00  0.00           H  
HETATM   99  H23 UNL     1       0.578  -3.961  -0.053  1.00  0.00           H  
HETATM  100  H24 UNL     1      -0.836  -3.260   1.441  1.00  0.00           H  
HETATM  101  H25 UNL     1      -4.101  -3.487   0.197  1.00  0.00           H  
HETATM  102  H26 UNL     1      -4.223  -4.159   2.440  1.00  0.00           H  
HETATM  103  H27 UNL     1      -2.481  -3.734   2.800  1.00  0.00           H  
HETATM  104  H28 UNL     1      -3.562  -5.577   0.905  1.00  0.00           H  
HETATM  105  H29 UNL     1      -4.231  -1.664   2.384  1.00  0.00           H  
HETATM  106  H30 UNL     1      -5.866  -0.402   1.991  1.00  0.00           H  
HETATM  107  H31 UNL     1      -7.636  -1.154   3.102  1.00  0.00           H  
HETATM  108  H32 UNL     1      -9.723  -1.490   0.950  1.00  0.00           H  
HETATM  109  H33 UNL     1      -9.210  -2.862   1.986  1.00  0.00           H  
HETATM  110  H34 UNL     1     -10.054  -1.632   3.785  1.00  0.00           H  
HETATM  111  H35 UNL     1      -9.365   0.477   1.381  1.00  0.00           H  
HETATM  112  H36 UNL     1      -8.928   0.490   3.674  1.00  0.00           H  
HETATM  113  H37 UNL     1      -8.117   1.865   0.256  1.00  0.00           H  
HETATM  114  H38 UNL     1      -7.711   3.523   0.692  1.00  0.00           H  
HETATM  115  H39 UNL     1      -8.837   5.247   1.927  1.00  0.00           H  
HETATM  116  H40 UNL     1      -6.979   5.938   4.173  1.00  0.00           H  
HETATM  117  H41 UNL     1      -8.671   5.280   4.434  1.00  0.00           H  
HETATM  118  H42 UNL     1      -9.051   7.298   2.858  1.00  0.00           H  
HETATM  119  H43 UNL     1      -7.156   6.104   0.523  1.00  0.00           H  
HETATM  120  H44 UNL     1      -5.901   7.750   1.937  1.00  0.00           H  
HETATM  121  H45 UNL     1      -4.772   5.983   1.099  1.00  0.00           H  
HETATM  122  H46 UNL     1      -5.088   4.314   3.275  1.00  0.00           H  
HETATM  123  H47 UNL     1      -4.713   3.509   1.218  1.00  0.00           H  
HETATM  124  H48 UNL     1      -5.086   5.143  -0.533  1.00  0.00           H  
HETATM  125  H49 UNL     1      -7.305  -0.264  -0.608  1.00  0.00           H  
HETATM  126  H50 UNL     1      -6.615  -0.176  -2.066  1.00  0.00           H  
HETATM  127  H51 UNL     1      -3.792  -1.600  -3.802  1.00  0.00           H  
HETATM  128  H52 UNL     1      -5.883  -2.564  -4.557  1.00  0.00           H  
HETATM  129  H53 UNL     1      -6.865  -1.484  -3.546  1.00  0.00           H  
HETATM  130  H54 UNL     1      -6.576  -2.769  -1.966  1.00  0.00           H  
HETATM  131  H55 UNL     1      -5.062  -0.577  -5.647  1.00  0.00           H  
HETATM  132  H56 UNL     1      -2.980   0.286  -4.229  1.00  0.00           H  
HETATM  133  H57 UNL     1      -5.868   1.873  -5.122  1.00  0.00           H  
HETATM  134  H58 UNL     1      -7.317   0.431  -5.684  1.00  0.00           H  
HETATM  135  H59 UNL     1      -6.929   1.959  -2.821  1.00  0.00           H  
HETATM  136  H60 UNL     1      -4.176   2.370  -2.633  1.00  0.00           H  
HETATM  137  H61 UNL     1      -3.075   0.192   1.951  1.00  0.00           H  
HETATM  138  H62 UNL     1      -1.832  -0.326  -0.447  1.00  0.00           H  
HETATM  139  H63 UNL     1      -0.729  -0.373   1.408  1.00  0.00           H  
HETATM  140  H64 UNL     1      -0.439  -1.385   3.353  1.00  0.00           H  
HETATM  141  H65 UNL     1       0.114  -2.516  -2.344  1.00  0.00           H  
HETATM  142  H66 UNL     1       0.955  -4.247  -3.334  1.00  0.00           H  
HETATM  143  H67 UNL     1       2.095  -1.830  -3.325  1.00  0.00           H  
HETATM  144  H68 UNL     1       1.925  -0.893  -1.817  1.00  0.00           H  
HETATM  145  H69 UNL     1       3.641  -4.557  -2.534  1.00  0.00           H  
HETATM  146  H70 UNL     1       3.116  -3.338  -3.820  1.00  0.00           H  
HETATM  147  H71 UNL     1       4.778  -3.378  -3.242  1.00  0.00           H  
HETATM  148  H72 UNL     1       4.672  -1.089  -2.852  1.00  0.00           H  
HETATM  149  H73 UNL     1       3.400   0.215  -1.024  1.00  0.00           H  
HETATM  150  H74 UNL     1       4.522  -0.433   0.159  1.00  0.00           H  
HETATM  151  H75 UNL     1       5.007   1.148  -2.381  1.00  0.00           H  
HETATM  152  H76 UNL     1       5.254   1.741  -0.736  1.00  0.00           H  
HETATM  153  H77 UNL     1       6.483   0.828  -3.491  1.00  0.00           H  
HETATM  154  H78 UNL     1       8.153   0.514  -3.056  1.00  0.00           H  
HETATM  155  H79 UNL     1       7.122  -0.894  -3.217  1.00  0.00           H  
HETATM  156  H80 UNL     1       8.216   1.728  -1.461  1.00  0.00           H  
HETATM  157  H81 UNL     1       7.782   2.588   0.565  1.00  0.00           H  
HETATM  158  H82 UNL     1       6.013   0.852   1.524  1.00  0.00           H  
HETATM  159  H83 UNL     1       7.185   1.668   2.548  1.00  0.00           H  
HETATM  160  H84 UNL     1       7.555   0.013   2.136  1.00  0.00           H  
CONECT    1    2   77   78   79
CONECT    2    3    7   80
CONECT    3    4   81   82
CONECT    4    5   83   84
CONECT    5    6    8   75
CONECT    6    7
CONECT    7   85   86
CONECT    8    9
CONECT    9   10   74   87
CONECT   10   11   88   89
CONECT   11   12   72   90
CONECT   12   13   69   91
CONECT   13   14   92   93
CONECT   14   15   16   94
CONECT   15   95
CONECT   16   17   67   96
CONECT   17   18   97   98
CONECT   18   19   64   99
CONECT   19   20
CONECT   20   21   62  100
CONECT   21   22
CONECT   22   23   25  101
CONECT   23   24  102  103
CONECT   24  104
CONECT   25   26   60  105
CONECT   26   27
CONECT   27   28   47  106
CONECT   28   29
CONECT   29   30   32  107
CONECT   30   31  108  109
CONECT   31  110
CONECT   32   33   34  111
CONECT   33  112
CONECT   34   35   47  113
CONECT   35   36
CONECT   36   37   45  114
CONECT   37   38
CONECT   38   39   41  115
CONECT   39   40  116  117
CONECT   40  118
CONECT   41   42   43  119
CONECT   42  120
CONECT   43   44   45  121
CONECT   44  122
CONECT   45   46  123
CONECT   46  124
CONECT   47   48  125
CONECT   48   49
CONECT   49   50   58  126
CONECT   50   51
CONECT   51   52   54  127
CONECT   52   53  128  129
CONECT   53  130
CONECT   54   55   56  131
CONECT   55  132
CONECT   56   57   58  133
CONECT   57  134
CONECT   58   59  135
CONECT   59  136
CONECT   60   61   62  137
CONECT   61  138
CONECT   62   63  139
CONECT   63  140
CONECT   64   65   66  141
CONECT   65  142
CONECT   66   67  143  144
CONECT   67   68   69
CONECT   68  145  146  147
CONECT   69   70  148
CONECT   70   71  149  150
CONECT   71   72  151  152
CONECT   72   73   74
CONECT   73  153  154  155
CONECT   74   75  156
CONECT   75   76  157
CONECT   76  158  159  160
END
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SMILES for HMDB0033401 (Yayoisaponin C)

CC1C2C(CC3C4CC(O)C5CC(OC6OC(CO)C(OC7OC(CO)C(O)C(OC8OC(CO)C(O)C(O)C8O)C7OC7OC(CO)C(O)C(O)C7O)C(O)C6O)C(O)CC5(C)C4CCC23C)OC11CCC(C)CO1
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INCHI for HMDB0033401 (Yayoisaponin C)

InChI=1S/C51H84O25/c1-18-5-8-51(67-17-18)19(2)32-27(76-51)10-22-20-9-24(56)23-11-26(25(57)12-50(23,4)21(20)6-7-49(22,32)3)68-45-41(66)38(63)42(31(16-55)72-45)73-48-44(75-47-40(65)37(62)34(59)29(14-53)70-47)43(35(60)30(15-54)71-48)74-46-39(64)36(61)33(58)28(13-52)69-46/h18-48,52-66H,5-17H2,1-4H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Yayoisaponin CMeSH
Chemical FormulaC51H84O25
Average Molecular Weight1097.1977
Monoisotopic Molecular Weight1096.530168238
IUPAC Name2-[(2-{[4,5-dihydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15',19'-dioloxy}oxan-3-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-4-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Name2-[(2-{[4,5-dihydroxy-2-(hydroxymethyl)-6-{5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15',19'-dioloxy}oxan-3-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-4-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol
CAS Registry Number218934-75-9
SMILES
CC1C2C(CC3C4CC(O)C5CC(OC6OC(CO)C(OC7OC(CO)C(O)C(OC8OC(CO)C(O)C(O)C8O)C7OC7OC(CO)C(O)C(O)C7O)C(O)C6O)C(O)CC5(C)C4CCC23C)OC11CCC(C)CO1
InChI Identifier
InChI=1S/C51H84O25/c1-18-5-8-51(67-17-18)19(2)32-27(76-51)10-22-20-9-24(56)23-11-26(25(57)12-50(23,4)21(20)6-7-49(22,32)3)68-45-41(66)38(63)42(31(16-55)72-45)73-48-44(75-47-40(65)37(62)34(59)29(14-53)70-47)43(35(60)30(15-54)71-48)74-46-39(64)36(61)33(58)28(13-52)69-46/h18-48,52-66H,5-17H2,1-4H3
InChI KeyIFCJNJJMBPXNRD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSteroids and steroid derivatives
Sub ClassSteroidal glycosides
Direct ParentSteroidal saponins
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
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility6.59 g/LALOGPS
logP-1.2ALOGPS
logP-4.1ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)11.75ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count25ChemAxon
Hydrogen Donor Count15ChemAxon
Polar Surface Area395.75 ŲChemAxon
Rotatable Bond Count12ChemAxon
Refractivity252.02 m³·mol⁻¹ChemAxon
Polarizability113.37 ųChemAxon
Number of Rings10ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+302.832859911
AllCCS[M+H-H2O]+303.632859911
AllCCS[M+NH4]+302.132859911
AllCCS[M+Na]+301.932859911
AllCCS[M-H]-309.032859911
AllCCS[M+Na-2H]-315.132859911
AllCCS[M+HCOO]-321.832859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 10V, Positive-QTOFsplash10-016s-7000622109-79b528436c8337464c6f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 20V, Positive-QTOFsplash10-01c4-2101932407-f29e36173908dd226fe32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 40V, Positive-QTOFsplash10-02ft-6201912504-8e9162469d3d150648202016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 10V, Negative-QTOFsplash10-00os-9100321005-78723a783fcc85c034372016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 20V, Negative-QTOFsplash10-004i-9401722115-2f2046f87a1533927efa2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 40V, Negative-QTOFsplash10-004j-5702902101-6adb5f47428541be3b902016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 10V, Positive-QTOFsplash10-002b-9000200003-07ffcac81d9e67bc68992021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 20V, Positive-QTOFsplash10-0002-9104521007-1083fda1a93e65b7ce542021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 40V, Positive-QTOFsplash10-0a4j-9002300003-2f1d3f22c3cdde1b71372021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 10V, Negative-QTOFsplash10-0002-9000000000-1b096c8c672f882a2e622021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 20V, Negative-QTOFsplash10-0005-9000000001-a0a9710edfd7f6f734b92021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin C 40V, Negative-QTOFsplash10-0a4i-9002201103-16f916ef6979a0d8e4ce2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB011435
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound85125467
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.