Hmdb loader

Showing metabocard for TR-Saponin B (HMDB0035342)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 20:18:26 UTC
Update Date2022-03-07 02:54:28 UTC
HMDB IDHMDB0035342
Secondary Accession Numbers
  • HMDB35342
Metabolite Identification
Common NameTR-Saponin B
DescriptionTR-Saponin B belongs to the class of organic compounds known as cucurbitacin glycosides. These are polycyclic compounds containing a carbohydrate derivative glycosidically linked to a curcubitane nucleus. Based on a literature review a small amount of articles have been published on TR-Saponin B.
Structure
Data?1563862704
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035342 (TR-Saponin B)


  Mrv0541 05061308232D          

 72 78  0  0  0  0            999 V2000
    0.2693    4.2858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0390    1.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1679    2.4427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2285    2.4427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2706   -0.2517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8559   -0.3449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4548   -2.9462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1526   -1.5753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 72 40  1  0  0  0  0
 72 43  1  0  0  0  0
M  END
Download

3D MOL for HMDB0035342 (TR-Saponin B)

HMDB0035342
     RDKit          3D
TR-Saponin B
152158  0  0  0  0  0  0  0  0999 V2000
   -7.4445    3.6679    2.7219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1501    2.6005    3.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8875    1.3092    3.3437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6633    0.3347    4.1547 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8567    0.9015    2.4286 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2150    1.7592    1.7717 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4674   -0.4108    2.1738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4448   -0.7381    1.2606 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9530   -1.4704    0.0444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1688   -1.0549   -0.4441 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2713   -1.8959   -0.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0865   -3.0479    0.0803 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6092   -1.5614   -0.9042 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0679   -0.3076   -0.1596 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5703   -2.6582   -0.4321 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5838   -2.7435    1.0755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8175   -1.4766   -1.0053 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0079   -2.7830   -1.7156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9102   -3.9004   -0.8852 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5174   -1.3729   -0.3395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4091   -2.1827    0.8879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3363   -1.4827    1.9117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4740   -0.4829    2.6525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7767   -2.5258    2.9034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3955   -1.3230   -1.2801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3768   -2.1566   -1.2944 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3289   -1.8801   -2.3499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0548   -0.4104   -2.1315 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3288    0.0926   -2.2947 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.2853    2.1222    1.0279 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5961    1.8124    2.3491 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5676    2.7555    2.9147 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9902    2.6505    4.0958 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0242    3.7919    2.1040 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0757    0.3920    2.5172 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0241    0.4133    3.5681 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8116   -0.1185    1.3108 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1464    0.2824    1.2993 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0117   -0.8070    1.3062 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7269   -0.8946    2.5124 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8193   -1.7540    2.3353 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9340   -0.9745    1.6637 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8967   -1.8164    1.1394 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2954   -0.1247    0.5887 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1036    0.0246   -0.5260 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9669   -0.7107    0.1403 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4124    0.1508   -0.7973 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0948    0.2211    0.0026 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8105   -0.9184   -0.7277 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7705    1.7062   -0.9168 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3693    2.6783   -1.9230 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6203    2.5008    0.3349 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5980    2.3497    1.0418 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5556    3.4121    0.7784 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4176    4.1686    1.9662 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4376    1.2147   -1.2737 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4078    2.2292   -1.6143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0196    1.6686   -1.4749 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1921    0.5007   -2.4473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1854    1.1486   -3.8013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4462   -0.2599   -2.3272 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6766   -0.9936   -3.6658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7162    0.5077   -2.1483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7517    1.5024   -1.2307 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9374   -0.3516   -1.9804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9617    0.5014   -1.5074 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8771    4.6530    3.0062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3667    3.7372    2.9588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6670    3.5543    1.6381 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9367    2.8812    4.1937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5688    0.7880    4.5868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8242   -0.6328    3.6619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9871    0.1015    5.0317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0797    0.2359    0.8839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0681   -2.5367    0.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6861   -1.4706   -1.9887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1643    0.3021    0.0365 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0035342 (TR-Saponin B)


  Mrv0541 05061308232D          

 72 78  0  0  0  0            999 V2000
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 60 38  1  0  0  0  0
 61 41  2  0  0  0  0
 62 41  1  0  0  0  0
 63 42  2  0  0  0  0
 64 43  2  0  0  0  0
 65 46  2  0  0  0  0
 66 11  1  0  0  0  0
 66 46  1  0  0  0  0
 67 21  1  0  0  0  0
 67 44  1  0  0  0  0
 68 30  1  0  0  0  0
 68 45  1  0  0  0  0
 69 35  1  0  0  0  0
 69 44  1  0  0  0  0
 70 36  1  0  0  0  0
 70 45  1  0  0  0  0
 71 39  1  0  0  0  0
 71 42  1  0  0  0  0
 72 40  1  0  0  0  0
 72 43  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035342

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC(C)C(=O)OC1C(OC(=O)C(\C)=C/C)C(C)(C)CC2C3=CCC4C5(C)CCC(OC6OC(C(O)C(OC7OCC(O)C(O)C7O)C6O)C(O)=O)C(C)(C5CCC4(C)C3(C)C(O)C(O)C12CO)C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C52H80O20/c1-12-23(3)42(63)71-39-40(72-43(64)24(4)13-2)52(22-53)26(20-47(39,5)6)25-14-15-28-48(7)18-17-30(50(9,46(65)66-11)29(48)16-19-49(28,8)51(25,10)37(59)38(52)60)68-45-34(58)35(33(57)36(70-45)41(61)62)69-44-32(56)31(55)27(54)21-67-44/h12,14,24,26-40,44-45,53-60H,13,15-22H2,1-11H3,(H,61,62)/b23-12-

> <INCHI_KEY>
LRIKDQQTBDULPI-FMCGGJTJSA-N

> <FORMULA>
C52H80O20

> <MOLECULAR_WEIGHT>
1025.1796

> <EXACT_MASS>
1024.524295

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
110.05947625834335

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-{[7,8-dihydroxy-8a-(hydroxymethyl)-4-(methoxycarbonyl)-4,6a,6b,11,11,14b-hexamethyl-10-{[(2Z)-2-methylbut-2-enoyl]oxy}-9-[(2-methylbutanoyl)oxy]-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,14,14a,14b-icosahydropicen-3-yl]oxy}-3,5-dihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxane-2-carboxylic acid

> <ALOGPS_LOGP>
2.67

> <JCHEM_LOGP>
2.9114335286666604

> <ALOGPS_LOGS>
-4.05

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.956489440628975

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2825076744618737

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4275873951363875

> <JCHEM_POLAR_SURFACE_AREA>
314.9600000000001

> <JCHEM_REFRACTIVITY>
251.1295000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.21e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-{[7,8-dihydroxy-8a-(hydroxymethyl)-4-(methoxycarbonyl)-4,6a,6b,11,11,14b-hexamethyl-10-{[(2Z)-2-methylbut-2-enoyl]oxy}-9-[(2-methylbutanoyl)oxy]-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy}-3,5-dihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0035342 (TR-Saponin B)

HMDB0035342
     RDKit          3D
TR-Saponin B
152158  0  0  0  0  0  0  0  0999 V2000
   -7.4445    3.6679    2.7219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1501    2.6005    3.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8875    1.3092    3.3437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6633    0.3347    4.1547 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8567    0.9015    2.4286 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2150    1.7592    1.7717 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4674   -0.4108    2.1738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4448   -0.7381    1.2606 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9530   -1.4704    0.0444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1688   -1.0549   -0.4441 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2713   -1.8959   -0.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0865   -3.0479    0.0803 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6092   -1.5614   -0.9042 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0679   -0.3076   -0.1596 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5703   -2.6582   -0.4321 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5838   -2.7435    1.0755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8175   -1.4766   -1.0053 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0079   -2.7830   -1.7156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9102   -3.9004   -0.8852 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5174   -1.3729   -0.3395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4091   -2.1827    0.8879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3363   -1.4827    1.9117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4740   -0.4829    2.6525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7767   -2.5258    2.9034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3955   -1.3230   -1.2801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3768   -2.1566   -1.2944 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3289   -1.8801   -2.3499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0548   -0.4104   -2.1315 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3288    0.0926   -2.2947 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7710    0.4844   -3.6512 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2734   -0.9982   -1.8188 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6741   -0.5312   -1.5895 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7770    0.6471   -0.6600 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0470    1.1538   -0.6977 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8325    0.9559    0.4015 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2853    2.1222    1.0279 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5961    1.8124    2.3491 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5676    2.7555    2.9147 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9902    2.6505    4.0958 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0242    3.7919    2.1040 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0757    0.3920    2.5172 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0241    0.4133    3.5681 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8116   -0.1185    1.3108 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1464    0.2824    1.2993 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0117   -0.8070    1.3062 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7269   -0.8946    2.5124 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8193   -1.7540    2.3353 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9340   -0.9745    1.6637 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8967   -1.8164    1.1394 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2954   -0.1247    0.5887 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1036    0.0246   -0.5260 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9669   -0.7107    0.1403 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4124    0.1508   -0.7973 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0948    0.2211    0.0026 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8105   -0.9184   -0.7277 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7705    1.7062   -0.9168 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3693    2.6783   -1.9230 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6203    2.5008    0.3349 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5980    2.3497    1.0418 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5556    3.4121    0.7784 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4176    4.1686    1.9662 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4376    1.2147   -1.2737 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4078    2.2292   -1.6143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0196    1.6686   -1.4749 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1921    0.5007   -2.4473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1854    1.1486   -3.8013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4462   -0.2599   -2.3272 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6766   -0.9936   -3.6658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7162    0.5077   -2.1483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7517    1.5024   -1.2307 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9374   -0.3516   -1.9804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9617    0.5014   -1.5074 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8771    4.6530    3.0062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3667    3.7372    2.9588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6670    3.5543    1.6381 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9367    2.8812    4.1937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5688    0.7880    4.5868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8242   -0.6328    3.6619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9871    0.1015    5.0317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0797    0.2359    0.8839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0681   -2.5367    0.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6861   -1.4706   -1.9887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1643    0.3021    0.0365 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7292    0.3025   -0.8187 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6139   -0.5449    0.7669 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5834   -2.5392   -0.8338 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1931   -3.6569   -0.7885 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5616   -3.8044    1.4427 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5491   -2.3375    1.4946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7693   -2.2121    1.5756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4944   -2.9486   -2.6398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1209   -2.7861   -2.0128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9922   -4.6857   -1.4826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4032   -0.2835    0.1206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3420   -2.0705    1.2560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5718   -3.2492    0.8354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5366    0.4866    2.1002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8737   -0.3934    3.6813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4472   -0.8614    2.6683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2482   -3.3989    2.4315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8234   -2.9144    3.3733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3490   -2.0809    3.7224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3518   -2.9524   -0.5865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4847   -2.2416   -3.3196 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5655   -2.4152   -1.9275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1286   -0.4125   -0.9581 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5169    1.5138   -3.9583 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9033    0.5045   -3.6538 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5374   -0.3095   -4.3660 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9283   -1.4376   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3287   -1.7353   -2.6504 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2544   -0.4280   -2.5195 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1713   -1.3972   -1.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6166    0.2092    0.3708 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3527    0.3602    1.1996 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6498    1.9085    2.9243 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4056    4.6026    2.5646 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2779   -0.2896    2.8755 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9647   -0.4220    4.0948 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8054   -1.2258    1.3535 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4020   -1.7322    1.2779 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.1095   -2.2404    3.2638 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4903   -2.5395    1.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4178   -0.3528    2.4439 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.2207   -1.4635    0.2731 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.0411    0.8478    1.0863 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.5895    0.8777   -0.4221 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0759   -1.7204   -0.2886 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6395    1.1143   -0.5927 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7815    0.8780   -0.5780 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7121   -0.7725   -1.6806 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6121    3.1299   -2.5692 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1767    2.1576   -2.4860 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8965    3.5167   -1.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5559    3.8528    2.5878 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3168    4.1294    2.6030 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2472    5.2501    1.7391 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0367    0.7212   -0.3238 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5746    2.7649   -2.5480 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4455    3.0347   -0.8193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6665    2.5270   -1.7268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0735    1.3430   -0.4256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2241    1.2244   -4.2154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8995    2.2428   -3.7821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5969    0.6871   -4.5764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6559   -0.6940   -4.1354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7052   -2.0660   -3.5882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9257   -0.7526   -4.4240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8935    1.0291   -3.1471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6247    1.7648   -0.9029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2946   -0.7043   -2.9665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4085    0.9849   -2.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  9 17  1  0
 17 18  1  0
 18 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 22 24  1  0
 20 25  1  0
 25 26  2  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 29 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
 34 35  1  0
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 38 40  1  0
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 41 42  1  0
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 43 44  1  0
 44 45  1  0
 45 46  1  0
 46 47  1  0
 47 48  1  0
 48 49  1  0
 48 50  1  0
 50 51  1  0
 50 52  1  0
 52 53  1  0
 43 54  1  0
 54 55  1  0
 33 56  1  0
 56 57  1  0
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 58 59  2  0
 58 60  1  0
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 56 62  1  0
 62 63  1  0
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 69 71  1  0
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 22  8  1  0
 67 25  1  0
 71 17  1  0
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 54 35  1  0
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  1 73  1  0
  1 74  1  0
  1 75  1  0
  2 76  1  0
  4 77  1  0
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  8 80  1  0
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 13 82  1  0
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 68147  1  0
 68148  1  0
 69149  1  0
 70150  1  0
 71151  1  0
 72152  1  0
M  END
Download

PDB for HMDB0035342 (TR-Saponin 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       0.503   8.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.806   1.867   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.165   4.920   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.714   4.079   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.180   4.560   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.160   4.560   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.838  -0.470   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.198  -0.644   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.182  -5.500   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.885  -2.941   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.668  -6.412   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.831   7.230   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.717   2.956   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.171   1.070   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.505   0.300   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.505  -4.320   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.506  -2.010   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.172  -1.240   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.171  -3.550   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.504   2.610   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      21.841  -1.240   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.836  -0.470   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.831   5.690   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.230   2.558   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.837   0.300   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.504   1.070   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      23.175  -2.010   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.505  -1.240   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.838  -3.550   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      12.506  -3.550   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      23.175  -3.550   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      21.841  -4.320   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      17.840  -2.010   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      16.507  -4.320   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      17.840  -3.550   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      16.507  -1.240   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       4.504  -2.010   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       3.170  -1.240   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       1.836   2.610   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       1.836   1.070   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      16.507   0.300   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       0.503   4.920   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -0.831   1.070   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      20.508  -3.550   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      15.173  -3.550   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      12.162  -5.500   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       3.170   3.380   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       9.838  -2.010   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       7.171  -2.010   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      11.172  -4.320   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0       5.837  -1.240   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       3.170   0.300   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0       1.836  -2.010   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      24.509  -1.240   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      24.509  -4.320   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      21.841  -5.860   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      19.174  -1.240   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      16.507  -5.860   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0       4.504  -3.550   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       2.544  -2.647   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      15.173   1.070   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      17.840   1.070   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0       1.836   5.690   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      -1.920  -0.019   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      11.635  -6.947   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      13.679  -5.232   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0      20.508  -2.010   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      13.839  -4.320   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0      19.174  -4.320   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0      15.173  -2.010   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0       0.503   3.380   0.000  0.00  0.00           O+0
HETATM   72  O   UNK     0       0.503   0.300   0.000  0.00  0.00           O+0
CONECT    1   12                                                            
CONECT    2   13                                                            
CONECT    3   23                                                            
CONECT    4   24                                                            
CONECT    5   47                                                            
CONECT    6   47                                                            
CONECT    7   48                                                            
CONECT    8   49                                                            
CONECT    9   50                                                            
CONECT   10   51                                                            
CONECT   11   66                                                            
CONECT   12    1   23                                                       
CONECT   13    2   24                                                       
CONECT   14   15   25                                                       
CONECT   15   14   28                                                       
CONECT   16   19   29                                                       
CONECT   17   18   30                                                       
CONECT   18   17   48                                                       
CONECT   19   16   49                                                       
CONECT   20   26   47                                                       
CONECT   21   27   67                                                       
CONECT   22   52   53                                                       
CONECT   23    3   12   42                                                  
CONECT   24    4   13   43                                                  
CONECT   25   14   26   51                                                  
CONECT   26   20   25   52                                                  
CONECT   27   21   31   54                                                  
CONECT   28   15   48   49                                                  
CONECT   29   16   48   50                                                  
CONECT   30   17   50   68                                                  
CONECT   31   27   32   55                                                  
CONECT   32   31   44   56                                                  
CONECT   33   35   36   57                                                  
CONECT   34   35   45   58                                                  
CONECT   35   33   34   69                                                  
CONECT   36   33   41   70                                                  
CONECT   37   38   51   59                                                  
CONECT   38   37   52   60                                                  
CONECT   39   40   47   71                                                  
CONECT   40   39   52   72                                                  
CONECT   41   36   61   62                                                  
CONECT   42   23   63   71                                                  
CONECT   43   24   64   72                                                  
CONECT   44   32   67   69                                                  
CONECT   45   34   68   70                                                  
CONECT   46   50   65   66                                                  
CONECT   47    5    6   20   39                                             
CONECT   48    7   18   28   29                                             
CONECT   49    8   19   28   51                                             
CONECT   50    9   29   30   46                                             
CONECT   51   10   25   37   49                                             
CONECT   52   22   26   38   40                                             
CONECT   53   22                                                            
CONECT   54   27                                                            
CONECT   55   31                                                            
CONECT   56   32                                                            
CONECT   57   33                                                            
CONECT   58   34                                                            
CONECT   59   37                                                            
CONECT   60   38                                                            
CONECT   61   41                                                            
CONECT   62   41                                                            
CONECT   63   42                                                            
CONECT   64   43                                                            
CONECT   65   46                                                            
CONECT   66   11   46                                                       
CONECT   67   21   44                                                       
CONECT   68   30   45                                                       
CONECT   69   35   44                                                       
CONECT   70   36   45                                                       
CONECT   71   39   42                                                       
CONECT   72   40   43                                                       
MASTER        0    0    0    0    0    0    0    0   72    0  156    0
END
Download

3D PDB for HMDB0035342 (TR-Saponin B)

COMPND    HMDB0035342
HETATM    1  C1  UNL     1      -7.444   3.668   2.722  1.00  0.00           C  
HETATM    2  C2  UNL     1      -8.150   2.600   3.477  1.00  0.00           C  
HETATM    3  C3  UNL     1      -7.888   1.309   3.344  1.00  0.00           C  
HETATM    4  C4  UNL     1      -8.663   0.335   4.155  1.00  0.00           C  
HETATM    5  C5  UNL     1      -6.857   0.901   2.429  1.00  0.00           C  
HETATM    6  O1  UNL     1      -6.215   1.759   1.772  1.00  0.00           O  
HETATM    7  O2  UNL     1      -6.467  -0.411   2.174  1.00  0.00           O  
HETATM    8  C6  UNL     1      -5.445  -0.738   1.261  1.00  0.00           C  
HETATM    9  C7  UNL     1      -5.953  -1.470   0.044  1.00  0.00           C  
HETATM   10  O3  UNL     1      -7.169  -1.055  -0.444  1.00  0.00           O  
HETATM   11  C8  UNL     1      -8.271  -1.896  -0.415  1.00  0.00           C  
HETATM   12  O4  UNL     1      -8.086  -3.048   0.080  1.00  0.00           O  
HETATM   13  C9  UNL     1      -9.609  -1.561  -0.904  1.00  0.00           C  
HETATM   14  C10 UNL     1     -10.068  -0.308  -0.160  1.00  0.00           C  
HETATM   15  C11 UNL     1     -10.570  -2.658  -0.432  1.00  0.00           C  
HETATM   16  C12 UNL     1     -10.584  -2.743   1.075  1.00  0.00           C  
HETATM   17  C13 UNL     1      -4.817  -1.477  -1.005  1.00  0.00           C  
HETATM   18  C14 UNL     1      -5.008  -2.783  -1.716  1.00  0.00           C  
HETATM   19  O5  UNL     1      -4.910  -3.900  -0.885  1.00  0.00           O  
HETATM   20  C15 UNL     1      -3.517  -1.373  -0.340  1.00  0.00           C  
HETATM   21  C16 UNL     1      -3.409  -2.183   0.888  1.00  0.00           C  
HETATM   22  C17 UNL     1      -4.336  -1.483   1.912  1.00  0.00           C  
HETATM   23  C18 UNL     1      -3.474  -0.483   2.653  1.00  0.00           C  
HETATM   24  C19 UNL     1      -4.777  -2.526   2.903  1.00  0.00           C  
HETATM   25  C20 UNL     1      -2.396  -1.323  -1.280  1.00  0.00           C  
HETATM   26  C21 UNL     1      -1.377  -2.157  -1.294  1.00  0.00           C  
HETATM   27  C22 UNL     1      -0.329  -1.880  -2.350  1.00  0.00           C  
HETATM   28  C23 UNL     1      -0.055  -0.410  -2.131  1.00  0.00           C  
HETATM   29  C24 UNL     1       1.329   0.093  -2.295  1.00  0.00           C  
HETATM   30  C25 UNL     1       1.771   0.484  -3.651  1.00  0.00           C  
HETATM   31  C26 UNL     1       2.273  -0.998  -1.819  1.00  0.00           C  
HETATM   32  C27 UNL     1       3.674  -0.531  -1.590  1.00  0.00           C  
HETATM   33  C28 UNL     1       3.777   0.647  -0.660  1.00  0.00           C  
HETATM   34  O6  UNL     1       5.047   1.154  -0.698  1.00  0.00           O  
HETATM   35  C29 UNL     1       5.832   0.956   0.402  1.00  0.00           C  
HETATM   36  O7  UNL     1       6.285   2.122   1.028  1.00  0.00           O  
HETATM   37  C30 UNL     1       6.596   1.812   2.349  1.00  0.00           C  
HETATM   38  C31 UNL     1       7.568   2.756   2.915  1.00  0.00           C  
HETATM   39  O8  UNL     1       7.990   2.651   4.096  1.00  0.00           O  
HETATM   40  O9  UNL     1       8.024   3.792   2.104  1.00  0.00           O  
HETATM   41  C32 UNL     1       7.076   0.392   2.517  1.00  0.00           C  
HETATM   42  O10 UNL     1       8.024   0.413   3.568  1.00  0.00           O  
HETATM   43  C33 UNL     1       7.812  -0.118   1.311  1.00  0.00           C  
HETATM   44  O11 UNL     1       9.146   0.282   1.299  1.00  0.00           O  
HETATM   45  C34 UNL     1      10.012  -0.807   1.306  1.00  0.00           C  
HETATM   46  O12 UNL     1      10.727  -0.895   2.512  1.00  0.00           O  
HETATM   47  C35 UNL     1      11.819  -1.754   2.335  1.00  0.00           C  
HETATM   48  C36 UNL     1      12.934  -0.975   1.664  1.00  0.00           C  
HETATM   49  O13 UNL     1      13.897  -1.816   1.139  1.00  0.00           O  
HETATM   50  C37 UNL     1      12.295  -0.125   0.589  1.00  0.00           C  
HETATM   51  O14 UNL     1      13.104   0.025  -0.526  1.00  0.00           O  
HETATM   52  C38 UNL     1      10.967  -0.711   0.140  1.00  0.00           C  
HETATM   53  O15 UNL     1      10.412   0.151  -0.797  1.00  0.00           O  
HETATM   54  C39 UNL     1       7.095   0.221   0.003  1.00  0.00           C  
HETATM   55  O16 UNL     1       6.810  -0.918  -0.728  1.00  0.00           O  
HETATM   56  C40 UNL     1       2.770   1.706  -0.917  1.00  0.00           C  
HETATM   57  C41 UNL     1       3.369   2.678  -1.923  1.00  0.00           C  
HETATM   58  C42 UNL     1       2.620   2.501   0.335  1.00  0.00           C  
HETATM   59  O17 UNL     1       1.598   2.350   1.042  1.00  0.00           O  
HETATM   60  O18 UNL     1       3.556   3.412   0.778  1.00  0.00           O  
HETATM   61  C43 UNL     1       3.418   4.169   1.966  1.00  0.00           C  
HETATM   62  C44 UNL     1       1.438   1.215  -1.274  1.00  0.00           C  
HETATM   63  C45 UNL     1       0.408   2.229  -1.614  1.00  0.00           C  
HETATM   64  C46 UNL     1      -1.020   1.669  -1.475  1.00  0.00           C  
HETATM   65  C47 UNL     1      -1.192   0.501  -2.447  1.00  0.00           C  
HETATM   66  C48 UNL     1      -1.185   1.149  -3.801  1.00  0.00           C  
HETATM   67  C49 UNL     1      -2.446  -0.260  -2.327  1.00  0.00           C  
HETATM   68  C50 UNL     1      -2.677  -0.994  -3.666  1.00  0.00           C  
HETATM   69  C51 UNL     1      -3.716   0.508  -2.148  1.00  0.00           C  
HETATM   70  O19 UNL     1      -3.752   1.502  -1.231  1.00  0.00           O  
HETATM   71  C52 UNL     1      -4.937  -0.352  -1.980  1.00  0.00           C  
HETATM   72  O20 UNL     1      -5.962   0.501  -1.507  1.00  0.00           O  
HETATM   73  H1  UNL     1      -7.877   4.653   3.006  1.00  0.00           H  
HETATM   74  H2  UNL     1      -6.367   3.737   2.959  1.00  0.00           H  
HETATM   75  H3  UNL     1      -7.667   3.554   1.638  1.00  0.00           H  
HETATM   76  H4  UNL     1      -8.937   2.881   4.194  1.00  0.00           H  
HETATM   77  H5  UNL     1      -9.569   0.788   4.587  1.00  0.00           H  
HETATM   78  H6  UNL     1      -8.824  -0.633   3.662  1.00  0.00           H  
HETATM   79  H7  UNL     1      -7.987   0.102   5.032  1.00  0.00           H  
HETATM   80  H8  UNL     1      -5.080   0.236   0.884  1.00  0.00           H  
HETATM   81  H9  UNL     1      -6.068  -2.537   0.412  1.00  0.00           H  
HETATM   82  H10 UNL     1      -9.686  -1.471  -1.989  1.00  0.00           H  
HETATM   83  H11 UNL     1      -9.164   0.302   0.037  1.00  0.00           H  
HETATM   84  H12 UNL     1     -10.729   0.303  -0.819  1.00  0.00           H  
HETATM   85  H13 UNL     1     -10.614  -0.545   0.767  1.00  0.00           H  
HETATM   86  H14 UNL     1     -11.583  -2.539  -0.834  1.00  0.00           H  
HETATM   87  H15 UNL     1     -10.193  -3.657  -0.788  1.00  0.00           H  
HETATM   88  H16 UNL     1     -10.562  -3.804   1.443  1.00  0.00           H  
HETATM   89  H17 UNL     1     -11.549  -2.337   1.495  1.00  0.00           H  
HETATM   90  H18 UNL     1      -9.769  -2.212   1.576  1.00  0.00           H  
HETATM   91  H19 UNL     1      -4.494  -2.949  -2.640  1.00  0.00           H  
HETATM   92  H20 UNL     1      -6.121  -2.786  -2.013  1.00  0.00           H  
HETATM   93  H21 UNL     1      -4.992  -4.686  -1.483  1.00  0.00           H  
HETATM   94  H22 UNL     1      -3.403  -0.283   0.121  1.00  0.00           H  
HETATM   95  H23 UNL     1      -2.342  -2.070   1.256  1.00  0.00           H  
HETATM   96  H24 UNL     1      -3.572  -3.249   0.835  1.00  0.00           H  
HETATM   97  H25 UNL     1      -3.537   0.487   2.100  1.00  0.00           H  
HETATM   98  H26 UNL     1      -3.874  -0.393   3.681  1.00  0.00           H  
HETATM   99  H27 UNL     1      -2.447  -0.861   2.668  1.00  0.00           H  
HETATM  100  H28 UNL     1      -5.248  -3.399   2.432  1.00  0.00           H  
HETATM  101  H29 UNL     1      -3.823  -2.914   3.373  1.00  0.00           H  
HETATM  102  H30 UNL     1      -5.349  -2.081   3.722  1.00  0.00           H  
HETATM  103  H31 UNL     1      -1.352  -2.952  -0.586  1.00  0.00           H  
HETATM  104  H32 UNL     1      -0.485  -2.242  -3.320  1.00  0.00           H  
HETATM  105  H33 UNL     1       0.566  -2.415  -1.927  1.00  0.00           H  
HETATM  106  H34 UNL     1      -0.129  -0.412  -0.958  1.00  0.00           H  
HETATM  107  H35 UNL     1       1.517   1.514  -3.958  1.00  0.00           H  
HETATM  108  H36 UNL     1       2.903   0.505  -3.654  1.00  0.00           H  
HETATM  109  H37 UNL     1       1.537  -0.310  -4.366  1.00  0.00           H  
HETATM  110  H38 UNL     1       1.928  -1.438  -0.856  1.00  0.00           H  
HETATM  111  H39 UNL     1       2.329  -1.735  -2.650  1.00  0.00           H  
HETATM  112  H40 UNL     1       4.254  -0.428  -2.519  1.00  0.00           H  
HETATM  113  H41 UNL     1       4.171  -1.397  -1.053  1.00  0.00           H  
HETATM  114  H42 UNL     1       3.617   0.209   0.371  1.00  0.00           H  
HETATM  115  H43 UNL     1       5.353   0.360   1.200  1.00  0.00           H  
HETATM  116  H44 UNL     1       5.650   1.909   2.924  1.00  0.00           H  
HETATM  117  H45 UNL     1       8.406   4.603   2.565  1.00  0.00           H  
HETATM  118  H46 UNL     1       6.278  -0.290   2.876  1.00  0.00           H  
HETATM  119  H47 UNL     1       7.965  -0.422   4.095  1.00  0.00           H  
HETATM  120  H48 UNL     1       7.805  -1.226   1.354  1.00  0.00           H  
HETATM  121  H49 UNL     1       9.402  -1.732   1.278  1.00  0.00           H  
HETATM  122  H50 UNL     1      12.110  -2.240   3.264  1.00  0.00           H  
HETATM  123  H51 UNL     1      11.490  -2.540   1.600  1.00  0.00           H  
HETATM  124  H52 UNL     1      13.418  -0.353   2.444  1.00  0.00           H  
HETATM  125  H53 UNL     1      14.221  -1.463   0.273  1.00  0.00           H  
HETATM  126  H54 UNL     1      12.041   0.848   1.086  1.00  0.00           H  
HETATM  127  H55 UNL     1      13.590   0.878  -0.422  1.00  0.00           H  
HETATM  128  H56 UNL     1      11.076  -1.720  -0.289  1.00  0.00           H  
HETATM  129  H57 UNL     1      10.639   1.114  -0.593  1.00  0.00           H  
HETATM  130  H58 UNL     1       7.781   0.878  -0.578  1.00  0.00           H  
HETATM  131  H59 UNL     1       6.712  -0.773  -1.681  1.00  0.00           H  
HETATM  132  H60 UNL     1       2.612   3.130  -2.569  1.00  0.00           H  
HETATM  133  H61 UNL     1       4.177   2.158  -2.486  1.00  0.00           H  
HETATM  134  H62 UNL     1       3.896   3.517  -1.408  1.00  0.00           H  
HETATM  135  H63 UNL     1       2.556   3.853   2.588  1.00  0.00           H  
HETATM  136  H64 UNL     1       4.317   4.129   2.603  1.00  0.00           H  
HETATM  137  H65 UNL     1       3.247   5.250   1.739  1.00  0.00           H  
HETATM  138  H66 UNL     1       1.037   0.721  -0.324  1.00  0.00           H  
HETATM  139  H67 UNL     1       0.575   2.765  -2.548  1.00  0.00           H  
HETATM  140  H68 UNL     1       0.445   3.035  -0.819  1.00  0.00           H  
HETATM  141  H69 UNL     1      -1.666   2.527  -1.727  1.00  0.00           H  
HETATM  142  H70 UNL     1      -1.074   1.343  -0.426  1.00  0.00           H  
HETATM  143  H71 UNL     1      -2.224   1.224  -4.215  1.00  0.00           H  
HETATM  144  H72 UNL     1      -0.900   2.243  -3.782  1.00  0.00           H  
HETATM  145  H73 UNL     1      -0.597   0.687  -4.576  1.00  0.00           H  
HETATM  146  H74 UNL     1      -3.656  -0.694  -4.135  1.00  0.00           H  
HETATM  147  H75 UNL     1      -2.705  -2.066  -3.588  1.00  0.00           H  
HETATM  148  H76 UNL     1      -1.926  -0.753  -4.424  1.00  0.00           H  
HETATM  149  H77 UNL     1      -3.893   1.029  -3.147  1.00  0.00           H  
HETATM  150  H78 UNL     1      -4.625   1.765  -0.903  1.00  0.00           H  
HETATM  151  H79 UNL     1      -5.295  -0.704  -2.967  1.00  0.00           H  
HETATM  152  H80 UNL     1      -6.408   0.985  -2.249  1.00  0.00           H  
CONECT    1    2   73   74   75
CONECT    2    3    3   76
CONECT    3    4    5
CONECT    4   77   78   79
CONECT    5    6    6    7
CONECT    7    8
CONECT    8    9   22   80
CONECT    9   10   17   81
CONECT   10   11
CONECT   11   12   12   13
CONECT   13   14   15   82
CONECT   14   83   84   85
CONECT   15   16   86   87
CONECT   16   88   89   90
CONECT   17   18   20   71
CONECT   18   19   91   92
CONECT   19   93
CONECT   20   21   25   94
CONECT   21   22   95   96
CONECT   22   23   24
CONECT   23   97   98   99
CONECT   24  100  101  102
CONECT   25   26   26   67
CONECT   26   27  103
CONECT   27   28  104  105
CONECT   28   29   65  106
CONECT   29   30   31   62
CONECT   30  107  108  109
CONECT   31   32  110  111
CONECT   32   33  112  113
CONECT   33   34   56  114
CONECT   34   35
CONECT   35   36   54  115
CONECT   36   37
CONECT   37   38   41  116
CONECT   38   39   39   40
CONECT   40  117
CONECT   41   42   43  118
CONECT   42  119
CONECT   43   44   54  120
CONECT   44   45
CONECT   45   46   52  121
CONECT   46   47
CONECT   47   48  122  123
CONECT   48   49   50  124
CONECT   49  125
CONECT   50   51   52  126
CONECT   51  127
CONECT   52   53  128
CONECT   53  129
CONECT   54   55  130
CONECT   55  131
CONECT   56   57   58   62
CONECT   57  132  133  134
CONECT   58   59   59   60
CONECT   60   61
CONECT   61  135  136  137
CONECT   62   63  138
CONECT   63   64  139  140
CONECT   64   65  141  142
CONECT   65   66   67
CONECT   66  143  144  145
CONECT   67   68   69
CONECT   68  146  147  148
CONECT   69   70   71  149
CONECT   70  150
CONECT   71   72  151
CONECT   72  152
END
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SMILES for HMDB0035342 (TR-Saponin B)

CCC(C)C(=O)OC1C(OC(=O)C(\C)=C/C)C(C)(C)CC2C3=CCC4C5(C)CCC(OC6OC(C(O)C(OC7OCC(O)C(O)C7O)C6O)C(O)=O)C(C)(C5CCC4(C)C3(C)C(O)C(O)C12CO)C(=O)OC
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INCHI for HMDB0035342 (TR-Saponin B)

InChI=1S/C52H80O20/c1-12-23(3)42(63)71-39-40(72-43(64)24(4)13-2)52(22-53)26(20-47(39,5)6)25-14-15-28-48(7)18-17-30(50(9,46(65)66-11)29(48)16-19-49(28,8)51(25,10)37(59)38(52)60)68-45-34(58)35(33(57)36(70-45)41(61)62)69-44-32(56)31(55)27(54)21-67-44/h12,14,24,26-40,44-45,53-60H,13,15-22H2,1-11H3,(H,61,62)/b23-12-
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View in JSmolView Stereo Labels
Synonyms
ValueSource
6-{[7,8-dihydroxy-8a-(hydroxymethyl)-4-(methoxycarbonyl)-4,6a,6b,11,11,14b-hexamethyl-10-{[(2Z)-2-methylbut-2-enoyl]oxy}-9-[(2-methylbutanoyl)oxy]-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,14,14a,14b-icosahydropicen-3-yl]oxy}-3,5-dihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxane-2-carboxylateHMDB
Chemical FormulaC52H80O20
Average Molecular Weight1025.1796
Monoisotopic Molecular Weight1024.524295
IUPAC Name6-{[7,8-dihydroxy-8a-(hydroxymethyl)-4-(methoxycarbonyl)-4,6a,6b,11,11,14b-hexamethyl-10-{[(2Z)-2-methylbut-2-enoyl]oxy}-9-[(2-methylbutanoyl)oxy]-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,14,14a,14b-icosahydropicen-3-yl]oxy}-3,5-dihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxane-2-carboxylic acid
Traditional Name6-{[7,8-dihydroxy-8a-(hydroxymethyl)-4-(methoxycarbonyl)-4,6a,6b,11,11,14b-hexamethyl-10-{[(2Z)-2-methylbut-2-enoyl]oxy}-9-[(2-methylbutanoyl)oxy]-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy}-3,5-dihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxane-2-carboxylic acid
CAS Registry Number288153-02-6
SMILES
CCC(C)C(=O)OC1C(OC(=O)C(\C)=C/C)C(C)(C)CC2C3=CCC4C5(C)CCC(OC6OC(C(O)C(OC7OCC(O)C(O)C7O)C6O)C(O)=O)C(C)(C5CCC4(C)C3(C)C(O)C(O)C12CO)C(=O)OC
InChI Identifier
InChI=1S/C52H80O20/c1-12-23(3)42(63)71-39-40(72-43(64)24(4)13-2)52(22-53)26(20-47(39,5)6)25-14-15-28-48(7)18-17-30(50(9,46(65)66-11)29(48)16-19-49(28,8)51(25,10)37(59)38(52)60)68-45-34(58)35(33(57)36(70-45)41(61)62)69-44-32(56)31(55)27(54)21-67-44/h12,14,24,26-40,44-45,53-60H,13,15-22H2,1-11H3,(H,61,62)/b23-12-
InChI KeyLRIKDQQTBDULPI-FMCGGJTJSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cucurbitacin glycosides. These are polycyclic compounds containing a carbohydrate derivative glycosidically linked to a curcubitane nucleus.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSteroids and steroid derivatives
Sub ClassSteroidal glycosides
Direct ParentCucurbitacin glycosides
Alternative Parents
Substituents
  • Cucurbitacin glycoside skeleton
  • Cucurbitacin skeleton
  • Triterpenoid
  • 22-hydroxysteroid
  • 20-hydroxysteroid
  • Steroid ester
  • 16-hydroxysteroid
  • Hydroxysteroid
  • Oxosteroid
  • 11-oxosteroid
  • Delta-5-steroid
  • Hexose monosaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • Monosaccharide
  • Oxane
  • Cyclic alcohol
  • Tertiary alcohol
  • Carboxylic acid ester
  • Ketone
  • Secondary alcohol
  • Polyol
  • Carboxylic acid derivative
  • Monocarboxylic acid or derivatives
  • Acetal
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxide
  • Organic oxygen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organooxygen compound
  • Alcohol
  • Primary alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
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 Solubility0.092 g/LALOGPS
logP2.67ALOGPS
logP2.91ChemAxon
logS-4ALOGPS
pKa (Strongest Acidic)3.28ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area314.96 ŲChemAxon
Rotatable Bond Count15ChemAxon
Refractivity251.13 m³·mol⁻¹ChemAxon
Polarizability110.06 ųChemAxon
Number of Rings7ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-344.47130932474
DeepCCS[M+Na]+318.50830932474
AllCCS[M+H]+318.432859911
AllCCS[M+H-H2O]+318.632859911
AllCCS[M+NH4]+318.132859911
AllCCS[M+Na]+318.032859911
AllCCS[M-H]-253.932859911
AllCCS[M+Na-2H]-260.432859911
AllCCS[M+HCOO]-267.432859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 10V, Positive-QTOFsplash10-0ar1-9000006465-1528a0c4c5b0793eef222016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 20V, Positive-QTOFsplash10-00mk-6100009561-9037a7cf76afad3ff2ea2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 40V, Positive-QTOFsplash10-016r-9100006630-370f3ffb3c37da312f8b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 10V, Negative-QTOFsplash10-0601-9210002226-597bed4beff0f6f359012016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 20V, Negative-QTOFsplash10-014j-8700007797-4b88f4517b950dbb9b602016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 40V, Negative-QTOFsplash10-00ke-9400003520-5b4b15cba2ef90e7733c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 10V, Positive-QTOFsplash10-004i-9000001023-20b4b410b559c45495982021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 20V, Positive-QTOFsplash10-054p-9200062572-b00aab0cedff042ad7862021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 40V, Positive-QTOFsplash10-0ar0-7611096102-5bb1936572c7faa0f4ae2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 10V, Negative-QTOFsplash10-00dj-9100000002-1ae8a2c9498bcf3be2652021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 20V, Negative-QTOFsplash10-0zmj-9300000013-f69869370e5509b823fe2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - TR-Saponin B 40V, Negative-QTOFsplash10-0a4i-9200000021-f48ed4eeb466f9d755212021-09-23Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • 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 IDFDB014014
KNApSAcK IDC00037962
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131751713
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.