Hmdb loader

Showing metabocard for Yayoisaponin B (HMDB0033402)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:07:18 UTC
Update Date2022-03-07 02:53:41 UTC
HMDB IDHMDB0033402
Secondary Accession Numbers
  • HMDB33402
Metabolite Identification
Common NameYayoisaponin B
DescriptionYayoisaponin B 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 B is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563862400
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033402 (Yayoisaponin B)


  Mrv0541 05061307062D          

 85 95  0  0  0  0            999 V2000
    4.3030   -3.2858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2076   -4.2801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4351   -3.9046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9810   -3.8035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6399   -3.7902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1573   -3.8514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3337   -3.8994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4540   -3.6564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4446   -1.6877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6640   -1.8929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5451   -2.2811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8046   -3.7555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2655    5.9244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8777    4.3540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8570   -1.2562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6560   -0.0694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4082   -2.3802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.7085    2.4300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1170   -3.1521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3319   -3.4645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0743   -2.4249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5276   -3.1142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2507   -2.4728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   12.6282   -3.7076    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 HMDB0033402 (Yayoisaponin B)

HMDB0033402
     RDKit          3D
Yayoisaponin B
175185  0  0  0  0  0  0  0  0999 V2000
   14.3149    2.3703   -2.4048 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5760    0.8865   -2.5906 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9362    0.2588   -1.2519 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6595    0.2559   -0.4129 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5112   -0.2974   -1.2024 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8842   -0.8232   -2.4148 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3626    0.2322   -3.2051 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5178    0.6932   -1.3447 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0183    0.8782   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4971    1.1431   -0.0836 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1342    0.5641    1.2353 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7049    0.5555    1.6337 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1218    1.8973    1.2750 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0864    1.8580    0.1729 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5177    3.1243    0.1048 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0513    0.9122    0.6958 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6848    1.0353    0.1235 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7483    0.3618    1.1408 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5359    0.0115    0.6083 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4642    0.7117    1.1721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2338    1.4396    0.2478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9084    0.6593   -0.6911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4669    1.6043   -1.7399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3339    2.4802   -1.0886 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.2079    0.2446   -0.4378 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.5012   -4.8516    1.1823 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2276   -3.6434    1.0708 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4476   -4.6366    2.2441 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.1758   -4.0470    2.3521 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1843   -1.0072   -0.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9953    0.1161   -0.1948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2699    0.5759    1.0698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6338    0.3467    1.3400 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9378    0.8894    2.6114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1696    0.2618    3.1455 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3108    0.4019    2.4072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8863    2.3716    2.5957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1232    2.9793    2.7818 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2293    2.8180    1.3080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0634    2.4420    0.2614 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4381    3.4929   -0.5450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8511    3.5743   -0.4971 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3039    2.2679   -0.6724 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7825    2.2464   -0.3169 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8888    2.6612    1.0258 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0606    1.8694   -2.0963 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2797    1.7639   -2.7950 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1958    2.8485   -2.8391 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8953    3.9875   -3.2458 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0033402 (Yayoisaponin B)


  Mrv0541 05061307062D          

 85 95  0  0  0  0            999 V2000
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   17.2377    2.2862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9329   -0.7107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6079    3.0234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3207    0.8596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4971    0.8117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5146    1.6448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1923   -2.1852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8018    3.8086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4140    2.2382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1268    0.0745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8804   -3.2101    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3512   -3.0662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7452   -2.8845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4419    5.8765    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0541    4.3061    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6807   -1.2082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.0263    0.6679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.6385   -0.9025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0815   -4.3969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.9854    1.7886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.2448    0.3142    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.9127    6.0203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5249    4.4499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5976    0.2183    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.8193    4.6417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2098   -1.3521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1017    0.1414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0788    3.1672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4693   -2.8265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.0096    1.9950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.8849    2.3820    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2223   -2.2464    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8221   -2.9224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.3485    4.4979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9607    2.9275    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5801   -0.6148    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.7390   -1.4959    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3032    0.0265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.4315    3.0713    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.6910    1.5969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0438    1.5010    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1155   -2.1473    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0  0  0  0
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M  END
> <DATABASE_ID>
HMDB0033402

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1C2C(CC3C4CC(O)C5CC(OC6OC(CO)C(OC7OC(CO)C(O)C(OC8OCC(O)C(O)C8O)C7OC7OC(CO)C(O)C(OC8OC(CO)C(O)C(O)C8O)C7O)C(O)C6O)C(=O)CC5(C)C4CCC23C)OC11CCC(C)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C56H90O29/c1-19-5-8-56(75-17-19)20(2)34-29(85-56)10-23-21-9-25(61)24-11-28(26(62)12-55(24,4)22(21)6-7-54(23,34)3)76-50-43(72)40(69)45(33(16-60)80-50)81-53-48(47(38(67)32(15-59)79-53)83-49-41(70)35(64)27(63)18-74-49)84-52-44(73)46(37(66)31(14-58)78-52)82-51-42(71)39(68)36(65)30(13-57)77-51/h19-25,27-53,57-61,63-73H,5-18H2,1-4H3

> <INCHI_KEY>
JPQIKXKRKWQQOU-UHFFFAOYSA-N

> <FORMULA>
C56H90O29

> <MOLECULAR_WEIGHT>
1227.2964

> <EXACT_MASS>
1226.556776918

> <JCHEM_ACCEPTOR_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
126.29163977654173

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
16

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
16'-({5-[(3-{[3,5-dihydroxy-6-(hydroxymethyl)-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl)oxy]-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl}oxy)-19'-hydroxy-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15'-one

> <ALOGPS_LOGP>
-1.16

> <JCHEM_LOGP>
-4.863288266999995

> <ALOGPS_LOGS>
-1.87

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
11

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.08683464684267

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.676064456502589

> <JCHEM_PKA_STRONGEST_BASIC>
-3.655542356905616

> <JCHEM_POLAR_SURFACE_AREA>
451.5100000000002

> <JCHEM_REFRACTIVITY>
277.5765000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.67e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
16'-({5-[(3-{[3,5-dihydroxy-6-(hydroxymethyl)-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl)oxy]-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl}oxy)-19'-hydroxy-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15'-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0033402 (Yayoisaponin B)

HMDB0033402
     RDKit          3D
Yayoisaponin B
175185  0  0  0  0  0  0  0  0999 V2000
   14.3149    2.3703   -2.4048 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5760    0.8865   -2.5906 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9362    0.2588   -1.2519 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6595    0.2559   -0.4129 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5112   -0.2974   -1.2024 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8842   -0.8232   -2.4148 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3626    0.2322   -3.2051 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5178    0.6932   -1.3447 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0183    0.8782   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4971    1.1431   -0.0836 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1342    0.5641    1.2353 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7049    0.5555    1.6337 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1218    1.8973    1.2750 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0864    1.8580    0.1729 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5177    3.1243    0.1048 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0513    0.9122    0.6958 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6848    1.0353    0.1235 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7483    0.3618    1.1408 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5359    0.0115    0.6083 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4642    0.7117    1.1721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2338    1.4396    0.2478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9084    0.6593   -0.6911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4669    1.6043   -1.7399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3339    2.4802   -1.0886 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9388   -0.2218   -0.0726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2079    0.2446   -0.4378 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9635   -0.7045   -1.0645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4341   -0.2349   -2.2745 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9437   -1.2931   -3.0246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9723   -0.8644   -4.0362 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0628   -0.2507   -3.4265 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4201   -2.4543   -2.2268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3979   -3.1927   -2.9127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0134   -2.1123   -0.8809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0153   -3.2755   -0.1147 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2655   -3.7068    0.2442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5843   -4.9578   -0.2821 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9274   -5.2600   -0.1349 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5012   -4.8516    1.1823 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2276   -3.6434    1.0708 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4476   -4.6366    2.2441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0007   -4.2094    3.4337 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3769   -3.6835    1.7495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1758   -4.0470    2.3521 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1843   -1.0072   -0.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9953    0.1161   -0.1948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2699    0.5759    1.0698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6338    0.3467    1.3400 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9378    0.8894    2.6114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1696    0.2618    3.1455 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3108    0.4019    2.4072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8863    2.3716    2.5957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1232    2.9793    2.7818 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2293    2.8180    1.3080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0634    2.4420    0.2614 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4381    3.4929   -0.5450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8511    3.5743   -0.4971 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3039    2.2679   -0.6724 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7825    2.2464   -0.3169 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8888    2.6612    1.0258 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0606    1.8694   -2.0963 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2797    1.7639   -2.7950 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1958    2.8485   -2.8391 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8953    3.9875   -3.2458 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9992    3.2057   -1.9581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3451    4.3150   -2.5280 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9330    2.0338    1.1623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2283    2.5065    0.0410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8770   -0.2030    1.4422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4157   -1.4009    1.9095 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4548   -0.1632    1.9473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5227    0.2863    3.2645 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4740   -0.8037    1.6625 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1236   -1.2362    2.7519 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5958   -1.5051    0.9871 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6427   -0.4705    0.5071 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8080   -0.7116   -0.9469 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8831   -0.6346    1.3475 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5941   -1.8628    0.8448 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9773   -1.6672    0.3390 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8154   -0.7858    1.2105 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0033402 (Yayoisaponin B)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       8.032  -6.133   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.454  -7.990   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.746  -7.289   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      20.498  -7.100   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.528  -7.075   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.960  -7.189   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      17.423  -7.279   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.047  -6.825   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      19.497  -3.150   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      16.173  -3.533   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.418  -4.258   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      22.035  -7.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      34.096  11.059   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      29.638   8.127   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      33.333  -2.345   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      25.491  -0.130   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.095  -4.443   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      36.789   4.536   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.552  -5.884   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      13.686  -6.467   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      18.805  -4.526   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      19.652  -5.813   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      17.268  -4.616   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      21.880  -4.347   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      21.034  -3.061   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      23.573  -6.921   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      37.635   3.249   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      24.264  -5.545   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      14.805  -4.240   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      34.942   9.772   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      30.485   6.841   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      32.487  -1.058   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      26.337  -1.416   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      15.054  -5.760   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      36.944   1.873   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      36.479   9.862   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      32.022   6.930   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      33.178   0.318   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      37.325   8.575   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      28.721  -2.613   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      35.407   1.784   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      36.634   7.199   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      28.030  -3.989   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      32.177   4.268   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      27.875  -1.327   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      32.868   5.644   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      32.332   1.605   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      30.795   1.515   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      34.561   3.070   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      26.492  -4.079   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      35.097   7.109   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      30.639   4.178   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      30.103   0.139   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      16.577  -5.992   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      21.189  -5.724   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      12.591  -5.384   0.000  0.00  0.00           C+0
HETATM   57  O   UNK     0      32.558  10.969   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      28.101   8.038   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      34.871  -2.255   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      26.182   1.247   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      21.725  -1.685   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      24.419  -8.208   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      39.173   3.339   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      37.790   0.587   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      37.170  11.238   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      32.713   8.306   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0      34.716   0.407   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      38.863   8.665   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0      30.258  -2.524   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0      35.657   0.264   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0      37.480   5.912   0.000  0.00  0.00           O+0
HETATM   72  O   UNK     0      28.876  -5.276   0.000  0.00  0.00           O+0
HETATM   73  O   UNK     0      33.618   3.724   0.000  0.00  0.00           O+0
HETATM   74  O   UNK     0      35.252   4.446   0.000  0.00  0.00           O+0
HETATM   75  O   UNK     0      11.615  -4.193   0.000  0.00  0.00           O+0
HETATM   76  O   UNK     0      25.801  -5.455   0.000  0.00  0.00           O+0
HETATM   77  O   UNK     0      34.251   8.396   0.000  0.00  0.00           O+0
HETATM   78  O   UNK     0      29.793   5.465   0.000  0.00  0.00           O+0
HETATM   79  O   UNK     0      30.950  -1.148   0.000  0.00  0.00           O+0
HETATM   80  O   UNK     0      25.646  -2.792   0.000  0.00  0.00           O+0
HETATM   81  O   UNK     0      28.566   0.049   0.000  0.00  0.00           O+0
HETATM   82  O   UNK     0      34.405   5.733   0.000  0.00  0.00           O+0
HETATM   83  O   UNK     0      33.023   2.981   0.000  0.00  0.00           O+0
HETATM   84  O   UNK     0      29.948   2.802   0.000  0.00  0.00           O+0
HETATM   85  O   UNK     0      13.282  -4.008   0.000  0.00  0.00           O+0
CONECT    1   19                                                            
CONECT    2   20                                                            
CONECT    3   54                                                            
CONECT    4   55                                                            
CONECT    5    8   19                                                       
CONECT    6    7   22                                                       
CONECT    7    6   54                                                       
CONECT    8    5   56                                                       
CONECT    9   21   25                                                       
CONECT   10   23   29                                                       
CONECT   11   24   28                                                       
CONECT   12   26   55                                                       
CONECT   13   30   57                                                       
CONECT   14   31   58                                                       
CONECT   15   32   59                                                       
CONECT   16   33   60                                                       
CONECT   17   19   75                                                       
CONECT   18   27   74                                                       
CONECT   19    1    5   17                                                  
CONECT   20    2   34   56                                                  
CONECT   21    9   22   23                                                  
CONECT   22    6   21   55                                                  
CONECT   23   10   21   54                                                  
CONECT   24   11   25   55                                                  
CONECT   25    9   24   61                                                  
CONECT   26   12   28   62                                                  
CONECT   27   18   35   63                                                  
CONECT   28   11   26   76                                                  
CONECT   29   10   34   85                                                  
CONECT   30   13   36   77                                                  
CONECT   31   14   37   78                                                  
CONECT   32   15   38   79                                                  
CONECT   33   16   45   80                                                  
CONECT   34   20   29   54                                                  
CONECT   35   27   41   64                                                  
CONECT   36   30   39   65                                                  
CONECT   37   31   46   66                                                  
CONECT   38   32   47   67                                                  
CONECT   39   36   42   68                                                  
CONECT   40   43   45   69                                                  
CONECT   41   35   49   70                                                  
CONECT   42   39   51   71                                                  
CONECT   43   40   50   72                                                  
CONECT   44   46   52   73                                                  
CONECT   45   33   40   81                                                  
CONECT   46   37   44   82                                                  
CONECT   47   38   48   83                                                  
CONECT   48   47   53   84                                                  
CONECT   49   41   74   83                                                  
CONECT   50   43   76   80                                                  
CONECT   51   42   77   82                                                  
CONECT   52   44   78   84                                                  
CONECT   53   48   79   81                                                  
CONECT   54    3    7   23   34                                             
CONECT   55    4   12   22   24                                             
CONECT   56    8   20   75   85                                             
CONECT   57   13                                                            
CONECT   58   14                                                            
CONECT   59   15                                                            
CONECT   60   16                                                            
CONECT   61   25                                                            
CONECT   62   26                                                            
CONECT   63   27                                                            
CONECT   64   35                                                            
CONECT   65   36                                                            
CONECT   66   37                                                            
CONECT   67   38                                                            
CONECT   68   39                                                            
CONECT   69   40                                                            
CONECT   70   41                                                            
CONECT   71   42                                                            
CONECT   72   43                                                            
CONECT   73   44                                                            
CONECT   74   18   49                                                       
CONECT   75   17   56                                                       
CONECT   76   28   50                                                       
CONECT   77   30   51                                                       
CONECT   78   31   52                                                       
CONECT   79   32   53                                                       
CONECT   80   33   50                                                       
CONECT   81   45   53                                                       
CONECT   82   46   51                                                       
CONECT   83   47   49                                                       
CONECT   84   48   52                                                       
CONECT   85   29   56                                                       
MASTER        0    0    0    0    0    0    0    0   85    0  190    0
END
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3D PDB for HMDB0033402 (Yayoisaponin B)

COMPND    HMDB0033402
HETATM    1  C1  UNL     1      14.315   2.370  -2.405  1.00  0.00           C  
HETATM    2  C2  UNL     1      14.576   0.887  -2.591  1.00  0.00           C  
HETATM    3  C3  UNL     1      14.936   0.259  -1.252  1.00  0.00           C  
HETATM    4  C4  UNL     1      13.660   0.256  -0.413  1.00  0.00           C  
HETATM    5  C5  UNL     1      12.511  -0.297  -1.202  1.00  0.00           C  
HETATM    6  O1  UNL     1      12.884  -0.823  -2.415  1.00  0.00           O  
HETATM    7  C6  UNL     1      13.363   0.232  -3.205  1.00  0.00           C  
HETATM    8  O2  UNL     1      11.518   0.693  -1.345  1.00  0.00           O  
HETATM    9  C7  UNL     1      11.018   0.878  -0.081  1.00  0.00           C  
HETATM   10  C8  UNL     1       9.497   1.143  -0.084  1.00  0.00           C  
HETATM   11  C9  UNL     1       9.134   0.564   1.235  1.00  0.00           C  
HETATM   12  C10 UNL     1       7.705   0.556   1.634  1.00  0.00           C  
HETATM   13  C11 UNL     1       7.122   1.897   1.275  1.00  0.00           C  
HETATM   14  C12 UNL     1       6.086   1.858   0.173  1.00  0.00           C  
HETATM   15  O3  UNL     1       5.518   3.124   0.105  1.00  0.00           O  
HETATM   16  C13 UNL     1       5.051   0.912   0.696  1.00  0.00           C  
HETATM   17  C14 UNL     1       3.685   1.035   0.124  1.00  0.00           C  
HETATM   18  C15 UNL     1       2.748   0.362   1.141  1.00  0.00           C  
HETATM   19  O4  UNL     1       1.536   0.011   0.608  1.00  0.00           O  
HETATM   20  C16 UNL     1       0.464   0.712   1.172  1.00  0.00           C  
HETATM   21  O5  UNL     1      -0.234   1.440   0.248  1.00  0.00           O  
HETATM   22  C17 UNL     1      -0.908   0.659  -0.691  1.00  0.00           C  
HETATM   23  C18 UNL     1      -1.467   1.604  -1.740  1.00  0.00           C  
HETATM   24  O6  UNL     1      -2.334   2.480  -1.089  1.00  0.00           O  
HETATM   25  C19 UNL     1      -1.939  -0.222  -0.073  1.00  0.00           C  
HETATM   26  O7  UNL     1      -3.208   0.245  -0.438  1.00  0.00           O  
HETATM   27  C20 UNL     1      -3.963  -0.705  -1.064  1.00  0.00           C  
HETATM   28  O8  UNL     1      -4.434  -0.235  -2.274  1.00  0.00           O  
HETATM   29  C21 UNL     1      -4.944  -1.293  -3.025  1.00  0.00           C  
HETATM   30  C22 UNL     1      -5.972  -0.864  -4.036  1.00  0.00           C  
HETATM   31  O9  UNL     1      -7.063  -0.251  -3.427  1.00  0.00           O  
HETATM   32  C23 UNL     1      -5.420  -2.454  -2.227  1.00  0.00           C  
HETATM   33  O10 UNL     1      -6.398  -3.193  -2.913  1.00  0.00           O  
HETATM   34  C24 UNL     1      -6.013  -2.112  -0.881  1.00  0.00           C  
HETATM   35  O11 UNL     1      -6.015  -3.276  -0.115  1.00  0.00           O  
HETATM   36  C25 UNL     1      -7.265  -3.707   0.244  1.00  0.00           C  
HETATM   37  O12 UNL     1      -7.584  -4.958  -0.282  1.00  0.00           O  
HETATM   38  C26 UNL     1      -8.927  -5.260  -0.135  1.00  0.00           C  
HETATM   39  C27 UNL     1      -9.501  -4.852   1.182  1.00  0.00           C  
HETATM   40  O13 UNL     1     -10.228  -3.643   1.071  1.00  0.00           O  
HETATM   41  C28 UNL     1      -8.448  -4.637   2.244  1.00  0.00           C  
HETATM   42  O14 UNL     1      -9.001  -4.209   3.434  1.00  0.00           O  
HETATM   43  C29 UNL     1      -7.377  -3.683   1.750  1.00  0.00           C  
HETATM   44  O15 UNL     1      -6.176  -4.047   2.352  1.00  0.00           O  
HETATM   45  C30 UNL     1      -5.184  -1.007  -0.210  1.00  0.00           C  
HETATM   46  O16 UNL     1      -5.995   0.116  -0.195  1.00  0.00           O  
HETATM   47  C31 UNL     1      -6.270   0.576   1.070  1.00  0.00           C  
HETATM   48  O17 UNL     1      -7.634   0.347   1.340  1.00  0.00           O  
HETATM   49  C32 UNL     1      -7.938   0.889   2.611  1.00  0.00           C  
HETATM   50  C33 UNL     1      -9.170   0.262   3.145  1.00  0.00           C  
HETATM   51  O18 UNL     1     -10.311   0.402   2.407  1.00  0.00           O  
HETATM   52  C34 UNL     1      -7.886   2.372   2.596  1.00  0.00           C  
HETATM   53  O19 UNL     1      -9.123   2.979   2.782  1.00  0.00           O  
HETATM   54  C35 UNL     1      -7.229   2.818   1.308  1.00  0.00           C  
HETATM   55  O20 UNL     1      -8.063   2.442   0.261  1.00  0.00           O  
HETATM   56  C36 UNL     1      -8.438   3.493  -0.545  1.00  0.00           C  
HETATM   57  O21 UNL     1      -9.851   3.574  -0.497  1.00  0.00           O  
HETATM   58  C37 UNL     1     -10.304   2.268  -0.672  1.00  0.00           C  
HETATM   59  C38 UNL     1     -11.783   2.246  -0.317  1.00  0.00           C  
HETATM   60  O22 UNL     1     -11.889   2.661   1.026  1.00  0.00           O  
HETATM   61  C39 UNL     1     -10.061   1.869  -2.096  1.00  0.00           C  
HETATM   62  O23 UNL     1     -11.280   1.764  -2.795  1.00  0.00           O  
HETATM   63  C40 UNL     1      -9.196   2.849  -2.839  1.00  0.00           C  
HETATM   64  O24 UNL     1      -9.895   3.988  -3.246  1.00  0.00           O  
HETATM   65  C41 UNL     1      -7.999   3.206  -1.958  1.00  0.00           C  
HETATM   66  O25 UNL     1      -7.345   4.315  -2.528  1.00  0.00           O  
HETATM   67  C42 UNL     1      -5.933   2.034   1.162  1.00  0.00           C  
HETATM   68  O26 UNL     1      -5.228   2.506   0.041  1.00  0.00           O  
HETATM   69  C43 UNL     1      -1.877  -0.203   1.442  1.00  0.00           C  
HETATM   70  O27 UNL     1      -2.416  -1.401   1.910  1.00  0.00           O  
HETATM   71  C44 UNL     1      -0.455  -0.163   1.947  1.00  0.00           C  
HETATM   72  O28 UNL     1      -0.523   0.286   3.265  1.00  0.00           O  
HETATM   73  C45 UNL     1       3.474  -0.804   1.663  1.00  0.00           C  
HETATM   74  O29 UNL     1       3.124  -1.236   2.752  1.00  0.00           O  
HETATM   75  C46 UNL     1       4.596  -1.505   0.987  1.00  0.00           C  
HETATM   76  C47 UNL     1       5.643  -0.471   0.507  1.00  0.00           C  
HETATM   77  C48 UNL     1       5.808  -0.712  -0.947  1.00  0.00           C  
HETATM   78  C49 UNL     1       6.883  -0.635   1.348  1.00  0.00           C  
HETATM   79  C50 UNL     1       7.594  -1.863   0.845  1.00  0.00           C  
HETATM   80  C51 UNL     1       8.977  -1.667   0.339  1.00  0.00           C  
HETATM   81  C52 UNL     1       9.815  -0.786   1.210  1.00  0.00           C  
HETATM   82  C53 UNL     1       9.896  -1.397   2.605  1.00  0.00           C  
HETATM   83  C54 UNL     1      11.147  -0.451   0.669  1.00  0.00           C  
HETATM   84  C55 UNL     1      11.707  -1.332  -0.395  1.00  0.00           C  
HETATM   85  C56 UNL     1      12.629  -2.405   0.130  1.00  0.00           C  
HETATM   86  H1  UNL     1      14.398   2.679  -1.331  1.00  0.00           H  
HETATM   87  H2  UNL     1      13.275   2.648  -2.719  1.00  0.00           H  
HETATM   88  H3  UNL     1      15.031   2.975  -3.034  1.00  0.00           H  
HETATM   89  H4  UNL     1      15.482   0.722  -3.241  1.00  0.00           H  
HETATM   90  H5  UNL     1      15.343  -0.760  -1.414  1.00  0.00           H  
HETATM   91  H6  UNL     1      15.651   0.902  -0.715  1.00  0.00           H  
HETATM   92  H7  UNL     1      13.466   1.314  -0.134  1.00  0.00           H  
HETATM   93  H8  UNL     1      13.832  -0.287   0.540  1.00  0.00           H  
HETATM   94  H9  UNL     1      12.541   0.987  -3.368  1.00  0.00           H  
HETATM   95  H10 UNL     1      13.623  -0.170  -4.204  1.00  0.00           H  
HETATM   96  H11 UNL     1      11.557   1.631   0.505  1.00  0.00           H  
HETATM   97  H12 UNL     1       9.058   0.678  -0.964  1.00  0.00           H  
HETATM   98  H13 UNL     1       9.421   2.233  -0.183  1.00  0.00           H  
HETATM   99  H14 UNL     1       9.759   1.160   1.977  1.00  0.00           H  
HETATM  100  H15 UNL     1       7.781   0.639   2.779  1.00  0.00           H  
HETATM  101  H16 UNL     1       6.561   2.376   2.138  1.00  0.00           H  
HETATM  102  H17 UNL     1       7.870   2.661   0.998  1.00  0.00           H  
HETATM  103  H18 UNL     1       6.512   1.544  -0.788  1.00  0.00           H  
HETATM  104  H19 UNL     1       5.324   3.392   1.049  1.00  0.00           H  
HETATM  105  H20 UNL     1       4.951   1.032   1.815  1.00  0.00           H  
HETATM  106  H21 UNL     1       3.492   0.539  -0.823  1.00  0.00           H  
HETATM  107  H22 UNL     1       3.444   2.113   0.031  1.00  0.00           H  
HETATM  108  H23 UNL     1       2.669   1.120   1.957  1.00  0.00           H  
HETATM  109  H24 UNL     1       0.928   1.430   1.900  1.00  0.00           H  
HETATM  110  H25 UNL     1      -0.113   0.047  -1.202  1.00  0.00           H  
HETATM  111  H26 UNL     1      -2.040   1.082  -2.517  1.00  0.00           H  
HETATM  112  H27 UNL     1      -0.648   2.161  -2.245  1.00  0.00           H  
HETATM  113  H28 UNL     1      -1.934   2.767  -0.211  1.00  0.00           H  
HETATM  114  H29 UNL     1      -1.878  -1.269  -0.427  1.00  0.00           H  
HETATM  115  H30 UNL     1      -3.438  -1.686  -1.169  1.00  0.00           H  
HETATM  116  H31 UNL     1      -4.052  -1.663  -3.620  1.00  0.00           H  
HETATM  117  H32 UNL     1      -6.371  -1.759  -4.576  1.00  0.00           H  
HETATM  118  H33 UNL     1      -5.513  -0.219  -4.832  1.00  0.00           H  
HETATM  119  H34 UNL     1      -7.071   0.698  -3.775  1.00  0.00           H  
HETATM  120  H35 UNL     1      -4.585  -3.171  -2.035  1.00  0.00           H  
HETATM  121  H36 UNL     1      -6.035  -3.596  -3.754  1.00  0.00           H  
HETATM  122  H37 UNL     1      -7.070  -1.794  -1.032  1.00  0.00           H  
HETATM  123  H38 UNL     1      -8.020  -3.008  -0.159  1.00  0.00           H  
HETATM  124  H39 UNL     1      -9.083  -6.323  -0.394  1.00  0.00           H  
HETATM  125  H40 UNL     1      -9.476  -4.686  -0.933  1.00  0.00           H  
HETATM  126  H41 UNL     1     -10.203  -5.627   1.522  1.00  0.00           H  
HETATM  127  H42 UNL     1     -11.149  -3.818   0.740  1.00  0.00           H  
HETATM  128  H43 UNL     1      -7.976  -5.628   2.442  1.00  0.00           H  
HETATM  129  H44 UNL     1      -9.045  -3.227   3.409  1.00  0.00           H  
HETATM  130  H45 UNL     1      -7.634  -2.662   2.125  1.00  0.00           H  
HETATM  131  H46 UNL     1      -5.564  -3.288   2.310  1.00  0.00           H  
HETATM  132  H47 UNL     1      -4.895  -1.378   0.775  1.00  0.00           H  
HETATM  133  H48 UNL     1      -5.735  -0.023   1.844  1.00  0.00           H  
HETATM  134  H49 UNL     1      -7.085   0.512   3.256  1.00  0.00           H  
HETATM  135  H50 UNL     1      -9.401   0.626   4.187  1.00  0.00           H  
HETATM  136  H51 UNL     1      -9.014  -0.842   3.289  1.00  0.00           H  
HETATM  137  H52 UNL     1     -10.920  -0.378   2.435  1.00  0.00           H  
HETATM  138  H53 UNL     1      -7.237   2.752   3.433  1.00  0.00           H  
HETATM  139  H54 UNL     1      -9.167   3.759   2.177  1.00  0.00           H  
HETATM  140  H55 UNL     1      -7.029   3.914   1.299  1.00  0.00           H  
HETATM  141  H56 UNL     1      -8.001   4.467  -0.240  1.00  0.00           H  
HETATM  142  H57 UNL     1      -9.762   1.587   0.017  1.00  0.00           H  
HETATM  143  H58 UNL     1     -12.259   3.069  -0.903  1.00  0.00           H  
HETATM  144  H59 UNL     1     -12.237   1.270  -0.484  1.00  0.00           H  
HETATM  145  H60 UNL     1     -11.568   3.603   1.051  1.00  0.00           H  
HETATM  146  H61 UNL     1      -9.538   0.874  -2.090  1.00  0.00           H  
HETATM  147  H62 UNL     1     -11.487   2.662  -3.130  1.00  0.00           H  
HETATM  148  H63 UNL     1      -8.803   2.353  -3.736  1.00  0.00           H  
HETATM  149  H64 UNL     1     -10.238   3.905  -4.152  1.00  0.00           H  
HETATM  150  H65 UNL     1      -7.291   2.355  -2.039  1.00  0.00           H  
HETATM  151  H66 UNL     1      -8.005   4.917  -3.001  1.00  0.00           H  
HETATM  152  H67 UNL     1      -5.348   2.237   2.100  1.00  0.00           H  
HETATM  153  H68 UNL     1      -5.419   3.475  -0.012  1.00  0.00           H  
HETATM  154  H69 UNL     1      -2.500   0.627   1.817  1.00  0.00           H  
HETATM  155  H70 UNL     1      -2.298  -2.155   1.299  1.00  0.00           H  
HETATM  156  H71 UNL     1      -0.028  -1.208   2.026  1.00  0.00           H  
HETATM  157  H72 UNL     1       0.203  -0.032   3.837  1.00  0.00           H  
HETATM  158  H73 UNL     1       5.064  -2.240   1.667  1.00  0.00           H  
HETATM  159  H74 UNL     1       4.168  -2.071   0.136  1.00  0.00           H  
HETATM  160  H75 UNL     1       6.832  -0.778  -1.316  1.00  0.00           H  
HETATM  161  H76 UNL     1       5.297  -1.653  -1.315  1.00  0.00           H  
HETATM  162  H77 UNL     1       5.322   0.090  -1.583  1.00  0.00           H  
HETATM  163  H78 UNL     1       6.435  -0.972   2.344  1.00  0.00           H  
HETATM  164  H79 UNL     1       7.645  -2.678   1.629  1.00  0.00           H  
HETATM  165  H80 UNL     1       7.023  -2.360   0.014  1.00  0.00           H  
HETATM  166  H81 UNL     1       9.067  -1.328  -0.700  1.00  0.00           H  
HETATM  167  H82 UNL     1       9.477  -2.683   0.341  1.00  0.00           H  
HETATM  168  H83 UNL     1      10.220  -2.435   2.487  1.00  0.00           H  
HETATM  169  H84 UNL     1       8.858  -1.416   3.020  1.00  0.00           H  
HETATM  170  H85 UNL     1      10.597  -0.828   3.245  1.00  0.00           H  
HETATM  171  H86 UNL     1      11.873  -0.383   1.515  1.00  0.00           H  
HETATM  172  H87 UNL     1      11.008  -1.775  -1.095  1.00  0.00           H  
HETATM  173  H88 UNL     1      12.785  -2.309   1.226  1.00  0.00           H  
HETATM  174  H89 UNL     1      13.598  -2.310  -0.361  1.00  0.00           H  
HETATM  175  H90 UNL     1      12.193  -3.391  -0.083  1.00  0.00           H  
CONECT    1    2   86   87   88
CONECT    2    3    7   89
CONECT    3    4   90   91
CONECT    4    5   92   93
CONECT    5    6    8   84
CONECT    6    7
CONECT    7   94   95
CONECT    8    9
CONECT    9   10   83   96
CONECT   10   11   97   98
CONECT   11   12   81   99
CONECT   12   13   78  100
CONECT   13   14  101  102
CONECT   14   15   16  103
CONECT   15  104
CONECT   16   17   76  105
CONECT   17   18  106  107
CONECT   18   19   73  108
CONECT   19   20
CONECT   20   21   71  109
CONECT   21   22
CONECT   22   23   25  110
CONECT   23   24  111  112
CONECT   24  113
CONECT   25   26   69  114
CONECT   26   27
CONECT   27   28   45  115
CONECT   28   29
CONECT   29   30   32  116
CONECT   30   31  117  118
CONECT   31  119
CONECT   32   33   34  120
CONECT   33  121
CONECT   34   35   45  122
CONECT   35   36
CONECT   36   37   43  123
CONECT   37   38
CONECT   38   39  124  125
CONECT   39   40   41  126
CONECT   40  127
CONECT   41   42   43  128
CONECT   42  129
CONECT   43   44  130
CONECT   44  131
CONECT   45   46  132
CONECT   46   47
CONECT   47   48   67  133
CONECT   48   49
CONECT   49   50   52  134
CONECT   50   51  135  136
CONECT   51  137
CONECT   52   53   54  138
CONECT   53  139
CONECT   54   55   67  140
CONECT   55   56
CONECT   56   57   65  141
CONECT   57   58
CONECT   58   59   61  142
CONECT   59   60  143  144
CONECT   60  145
CONECT   61   62   63  146
CONECT   62  147
CONECT   63   64   65  148
CONECT   64  149
CONECT   65   66  150
CONECT   66  151
CONECT   67   68  152
CONECT   68  153
CONECT   69   70   71  154
CONECT   70  155
CONECT   71   72  156
CONECT   72  157
CONECT   73   74   74   75
CONECT   75   76  158  159
CONECT   76   77   78
CONECT   77  160  161  162
CONECT   78   79  163
CONECT   79   80  164  165
CONECT   80   81  166  167
CONECT   81   82   83
CONECT   82  168  169  170
CONECT   83   84  171
CONECT   84   85  172
CONECT   85  173  174  175
END
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SMILES for HMDB0033402 (Yayoisaponin B)

CC1C2C(CC3C4CC(O)C5CC(OC6OC(CO)C(OC7OC(CO)C(O)C(OC8OCC(O)C(O)C8O)C7OC7OC(CO)C(O)C(OC8OC(CO)C(O)C(O)C8O)C7O)C(O)C6O)C(=O)CC5(C)C4CCC23C)OC11CCC(C)CO1
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INCHI for HMDB0033402 (Yayoisaponin B)

InChI=1S/C56H90O29/c1-19-5-8-56(75-17-19)20(2)34-29(85-56)10-23-21-9-25(61)24-11-28(26(62)12-55(24,4)22(21)6-7-54(23,34)3)76-50-43(72)40(69)45(33(16-60)80-50)81-53-48(47(38(67)32(15-59)79-53)83-49-41(70)35(64)27(63)18-74-49)84-52-44(73)46(37(66)31(14-58)78-52)82-51-42(71)39(68)36(65)30(13-57)77-51/h19-25,27-53,57-61,63-73H,5-18H2,1-4H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Yayoisaponin bMeSH
Chemical FormulaC56H90O29
Average Molecular Weight1227.2964
Monoisotopic Molecular Weight1226.556776918
IUPAC Name16'-({5-[(3-{[3,5-dihydroxy-6-(hydroxymethyl)-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl)oxy]-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl}oxy)-19'-hydroxy-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15'-one
Traditional Name16'-({5-[(3-{[3,5-dihydroxy-6-(hydroxymethyl)-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl)oxy]-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl}oxy)-19'-hydroxy-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-15'-one
CAS Registry Number218934-74-8
SMILES
CC1C2C(CC3C4CC(O)C5CC(OC6OC(CO)C(OC7OC(CO)C(O)C(OC8OCC(O)C(O)C8O)C7OC7OC(CO)C(O)C(OC8OC(CO)C(O)C(O)C8O)C7O)C(O)C6O)C(=O)CC5(C)C4CCC23C)OC11CCC(C)CO1
InChI Identifier
InChI=1S/C56H90O29/c1-19-5-8-56(75-17-19)20(2)34-29(85-56)10-23-21-9-25(61)24-11-28(26(62)12-55(24,4)22(21)6-7-54(23,34)3)76-50-43(72)40(69)45(33(16-60)80-50)81-53-48(47(38(67)32(15-59)79-53)83-49-41(70)35(64)27(63)18-74-49)84-52-44(73)46(37(66)31(14-58)78-52)82-51-42(71)39(68)36(65)30(13-57)77-51/h19-25,27-53,57-61,63-73H,5-18H2,1-4H3
InChI KeyJPQIKXKRKWQQOU-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 Solubility16.7 g/LALOGPS
logP-1.2ALOGPS
logP-4.9ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)11.68ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count29ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area451.51 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity277.58 m³·mol⁻¹ChemAxon
Polarizability126.29 ųChemAxon
Number of Rings11ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 10V, Positive-QTOFsplash10-0a6s-9260622132-41986147bb504392ab9d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 20V, Positive-QTOFsplash10-054k-5221923323-bc92daf6cccdd6eeee5d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 40V, Positive-QTOFsplash10-05mk-9520812404-d3f420766f71a16f85ae2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 10V, Negative-QTOFsplash10-0a4j-9582311121-c1e64595f31202ae5ef82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 20V, Negative-QTOFsplash10-0a4j-4962521021-86015d70e6e5b9b543f32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 40V, Negative-QTOFsplash10-002e-5903602101-eed22d201c46b5abee842016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 10V, Negative-QTOFsplash10-004i-0290001000-3a57847e4b362cf71fb12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 20V, Negative-QTOFsplash10-0kdl-7930000000-b59c39194e94036333ec2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 40V, Negative-QTOFsplash10-0a4i-9510501203-7112f208757018358e172021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 10V, Positive-QTOFsplash10-056r-3190101000-0a55364bf4609e4a10372021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 20V, Positive-QTOFsplash10-004j-9580631002-b2c406fc66203a914a782021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yayoisaponin B 40V, Positive-QTOFsplash10-004r-7460911000-0fb2e95d02bc7295a6132021-09-22Wishart 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 IDFDB011436
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131751416
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.