Hmdb loader

Showing metabocard for Sandosaponin B (HMDB0031883)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (6) Show 6 proteinsXML
enzymes (6) Show 6 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:46:09 UTC
Update Date2022-03-07 02:53:09 UTC
HMDB IDHMDB0031883
Secondary Accession Numbers
  • HMDB31883
Metabolite Identification
Common NameSandosaponin B
DescriptionSandosaponin B belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton. Based on a literature review a small amount of articles have been published on Sandosaponin B.
Structure
Data?1563862185
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031883 (Sandosaponin B)


  Mrv0541 05061306122D          

 67 74  0  0  0  0            999 V2000
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    5.3907   -2.8478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1039   -2.8478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9197   -5.5423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6598   -4.0264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8684   -4.4266    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5328   -2.0228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8184   -2.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8184   -4.9103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3250   -3.6728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3894   -3.2603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9618   -3.6728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9618   -1.1978    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3907   -1.1979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.1409   -5.5423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2473   -2.4354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9618   -2.0229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1829   -9.4479    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 HMDB0031883 (Sandosaponin B)

HMDB0031883
     RDKit          3D
Sandosaponin B
143150  0  0  0  0  0  0  0  0999 V2000
    6.1066   -3.4869    3.7345 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0130   -2.3407    3.3279 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4128   -2.7912    3.7238 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5765   -1.1373    4.1174 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2900    0.1180    3.7367 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5647    0.0837    4.3011 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4274    0.3291    2.2655 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8617    0.5630    1.8379 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6980    1.6432    1.9518 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4765    1.7062    0.4718 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2810    0.8885    0.0474 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6776    0.2825   -1.3162 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3768   -0.3149    0.9740 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3388   -0.9946    1.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0094   -0.5445    0.8310 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9368    0.9369    0.9755 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5550    1.5080    0.8601 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2144    2.3211    2.0997 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6093    0.2967    0.9264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8427    0.6669    0.7748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1304    1.3452   -0.5581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2369    0.4614   -1.5717 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4265    0.3183   -2.2177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1987    0.8671   -3.5194 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9202   -0.0621   -4.4704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0995    0.6028   -5.5506 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.1307   -1.2530   -4.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1682   -0.9437   -3.6426 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.6846   -3.0036   -1.7888 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.2937   -0.3877   -1.7292 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.8049    0.0981   -0.9118 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1376    0.5882    0.3166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0857    1.5939    0.2897 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5053    2.0040    1.5348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9905    1.6594    1.6198 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1792    0.2813    1.4693 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7309    1.4004    2.6680 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0614    2.1241    3.8259 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2586    1.6427    2.4075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4435    1.0870    3.3919 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9245    0.9303    1.1130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1447   -0.2114    1.3353 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1890    2.4875   -0.6813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2649    3.1763   -2.0321 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6542    3.5555    0.2663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5738    3.3794    1.0331 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2453    2.2225   -0.3920 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9245    1.4303   -1.5118 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4007    1.3668   -1.3580 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9619    1.5444    0.0337 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1328    2.9912    0.4105 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7498   -0.7051    1.4119 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8750   -2.1015    1.8721 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2345   -4.2878    2.9869 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0509   -3.1767    3.8856 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5395   -3.9076    4.6853 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1981   -2.1434    3.3291 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5451   -3.7983    3.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4192   -2.9406    4.8035 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4997   -0.9978    4.0005 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7496   -1.3142    5.2138 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7552    0.9578    4.2701 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6545   -0.5607    5.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0887    1.6086    1.6358 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5575    0.2553    2.6713 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1033   -0.1255    0.9894 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7434    1.5073    2.5494 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2968    2.5043    2.3034 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4158    1.2242    0.0301 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5639    2.7026    0.0010 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8089    0.1551   -1.3236 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5147    0.9679   -2.1473 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3200   -0.7497   -1.4338 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4335   -1.8376    2.0228 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0031883 (Sandosaponin B)


  Mrv0541 05061306122D          

 67 74  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0031883

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1(C)CC(O)C2(C)CCC3(C)C(=CCC4C5(C)CCC(OC6OC(C(O)C(O)C6OC6OC(CO)C(O)C(O)C6OC6OC(CO)C(O)C(O)C6O)C(O)=O)C(C)(C=O)C5CCC34C)C2C1

> <INCHI_IDENTIFIER>
InChI=1S/C48H76O19/c1-43(2)16-22-21-8-9-26-45(4)12-11-28(46(5,20-51)25(45)10-13-48(26,7)47(21,6)15-14-44(22,3)27(52)17-43)64-42-38(34(58)33(57)36(65-42)39(60)61)67-41-37(32(56)30(54)24(19-50)63-41)66-40-35(59)31(55)29(53)23(18-49)62-40/h8,20,22-38,40-42,49-50,52-59H,9-19H2,1-7H3,(H,60,61)

> <INCHI_KEY>
WIHKYILMSPQBIM-UHFFFAOYSA-N

> <FORMULA>
C48H76O19

> <MOLECULAR_WEIGHT>
957.1056

> <EXACT_MASS>
956.49808025

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
102.23488155881944

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-6-[(4-formyl-9-hydroxy-4,6a,6b,8a,11,11,14b-heptamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,14,14a,14b-icosahydropicen-3-yl)oxy]-3,4-dihydroxyoxane-2-carboxylic acid

> <ALOGPS_LOGP>
1.82

> <JCHEM_LOGP>
0.21317371500000115

> <ALOGPS_LOGS>
-3.47

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.048155670739618

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.265460327132662

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6486744309342773

> <JCHEM_POLAR_SURFACE_AREA>
312.05000000000007

> <JCHEM_REFRACTIVITY>
231.32190000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.24e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-6-[(4-formyl-9-hydroxy-4,6a,6b,8a,11,11,14b-heptamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl)oxy]-3,4-dihydroxyoxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0031883 (Sandosaponin B)

HMDB0031883
     RDKit          3D
Sandosaponin B
143150  0  0  0  0  0  0  0  0999 V2000
    6.1066   -3.4869    3.7345 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0130   -2.3407    3.3279 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4128   -2.7912    3.7238 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5765   -1.1373    4.1174 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2900    0.1180    3.7367 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5647    0.0837    4.3011 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4274    0.3291    2.2655 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8617    0.5630    1.8379 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6980    1.6432    1.9518 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4765    1.7062    0.4718 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2810    0.8885    0.0474 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6776    0.2825   -1.3162 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3768   -0.3149    0.9740 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3388   -0.9946    1.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0094   -0.5445    0.8310 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9368    0.9369    0.9755 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5550    1.5080    0.8601 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2144    2.3211    2.0997 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6093    0.2967    0.9264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8427    0.6669    0.7748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1304    1.3452   -0.5581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2369    0.4614   -1.5717 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4265    0.3183   -2.2177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1987    0.8671   -3.5194 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9202   -0.0621   -4.4704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0995    0.6028   -5.5506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6970   -0.0333   -6.5557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7662    1.9416   -5.4626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1307   -1.2530   -4.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1682   -0.9437   -3.6426 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9194   -1.9276   -2.9170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4614   -3.0927   -3.4548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0113   -1.0012   -2.4331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7495   -1.6521   -1.5136 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0424   -1.9772   -1.8277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3375   -3.2857   -2.0698 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5481   -3.5619   -2.6170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1289   -4.8873   -2.1169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3147   -5.9719   -2.4166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6099   -2.5342   -2.5952 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6846   -3.0036   -1.7888 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2643   -1.1644   -2.1619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2937   -0.3877   -1.7292 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1244   -1.2338   -1.1020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8049    0.0981   -0.9118 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1376    0.5882    0.3166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0857    1.5939    0.2897 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5053    2.0040    1.5348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9905    1.6594    1.6198 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1792    0.2813    1.4693 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7309    1.4004    2.6680 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0614    2.1241    3.8259 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2586    1.6427    2.4075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4435    1.0870    3.3919 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9245    0.9303    1.1130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1447   -0.2114    1.3353 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1890    2.4875   -0.6813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2649    3.1763   -2.0321 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6542    3.5555    0.2663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5738    3.3794    1.0331 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2453    2.2225   -0.3920 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9245    1.4303   -1.5118 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4007    1.3668   -1.3580 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9619    1.5444    0.0337 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1328    2.9912    0.4105 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7498   -0.7051    1.4119 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8750   -2.1015    1.8721 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2345   -4.2878    2.9869 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0509   -3.1767    3.8856 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5395   -3.9076    4.6853 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1981   -2.1434    3.3291 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5451   -3.7983    3.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4192   -2.9406    4.8035 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4997   -0.9978    4.0005 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7496   -1.3142    5.2138 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7552    0.9578    4.2701 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6545   -0.5607    5.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0887    1.6086    1.6358 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5575    0.2553    2.6713 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1033   -0.1255    0.9894 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7434    1.5073    2.5494 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2968    2.5043    2.3034 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4158    1.2242    0.0301 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5639    2.7026    0.0010 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8089    0.1551   -1.3236 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5147    0.9679   -2.1473 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3200   -0.7497   -1.4338 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4335   -1.8376    2.0228 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2734   -1.1308    1.3951 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0133   -0.8876   -0.2295 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3131    1.1692    1.9986 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2724    2.0067    2.5843 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1305    3.3921    1.9338 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0133    2.1265    2.8786 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6571   -0.1045    1.9814 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8231   -0.4471    0.1537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3768   -0.3280    0.6872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2952    1.1541    1.6328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1406    1.7986   -0.4072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2275    1.0107   -1.8383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8073   -0.4549   -5.0366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2989    2.4275   -6.2090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0351   -1.9250   -4.9261 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8236   -1.6444   -3.8914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2353   -2.2406   -2.1008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1954   -3.9003   -2.9499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7070   -0.8938   -3.3365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1117   -1.5389   -2.8950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3311   -3.7857   -3.7128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3283   -4.8188   -1.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1191   -5.0844   -2.5725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3873   -5.6966   -2.1208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1063   -2.4562   -3.6206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2003   -2.2101   -1.4796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7819   -0.6367   -3.0301 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.4285    3.1039    1.6076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4732    2.2346    0.7988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4014    2.0321    2.5759 H   0  0  0  0  0  0  0  0  0  0  0  0
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    7.7980   -2.6109    1.4131 H   0  0  0  0  0  0  0  0  0  0  0  0
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 65138  1  0
 65139  1  0
 65140  1  0
 66141  1  0
 67142  1  0
 67143  1  0
M  END
Download

PDB for HMDB0031883 (Sandosaponin 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       9.719  -0.286   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.739  -0.286   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.063  -5.316   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.061  -5.316   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.717 -10.346   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.832  -7.516   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.354  -8.263   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.728  -3.776   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.394  -4.546   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.394  -9.166   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.607  -6.856   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.727  -6.086   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.728  -8.396   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.729  -6.086   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.395  -6.856   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.395  -2.236   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.063  -2.236   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -7.275 -18.406   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -9.942 -10.706   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.263 -10.346   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.062  -4.546   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.395  -3.776   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -5.941 -17.636   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -8.609 -11.476   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.061  -8.396   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.394  -6.086   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.063  -3.776   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.607  -8.396   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -4.608 -18.406   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -8.609 -13.016   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.274 -17.636   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -7.275 -13.786   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.941  -6.856   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -5.941  -8.396   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -3.274 -16.096   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -4.608  -6.086   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -5.941 -13.016   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -4.608  -9.166   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -4.608  -4.546   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -4.608 -15.326   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -5.941 -11.476   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -3.274  -8.396   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       8.729  -1.466   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       8.729  -4.546   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       2.061  -6.856   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       0.727  -9.166   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       6.062  -6.086   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       4.728  -6.856   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0      -7.275 -19.946   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0     -11.276 -11.476   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0       0.264 -11.793   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      11.396  -4.546   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      -4.608 -19.946   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      -9.942 -13.786   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      -1.940 -18.406   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      -7.275 -15.326   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      -7.275  -6.086   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      -7.275  -9.166   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      -1.940 -15.326   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      -3.274  -3.776   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      -5.941  -3.776   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      -5.941 -16.096   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      -7.275 -10.706   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      -1.940  -9.166   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      -3.274  -6.856   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      -4.608 -13.786   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0      -4.608 -10.706   0.000  0.00  0.00           O+0
CONECT    1   43                                                            
CONECT    2   43                                                            
CONECT    3   44                                                            
CONECT    4   45                                                            
CONECT    5   46                                                            
CONECT    6   47                                                            
CONECT    7   48                                                            
CONECT    8    9   21                                                       
CONECT    9    8   26                                                       
CONECT   10   13   25                                                       
CONECT   11   12   28                                                       
CONECT   12   11   45                                                       
CONECT   13   10   48                                                       
CONECT   14   15   44                                                       
CONECT   15   14   47                                                       
CONECT   16   22   43                                                       
CONECT   17   27   43                                                       
CONECT   18   23   49                                                       
CONECT   19   24   50                                                       
CONECT   20   46   51                                                       
CONECT   21    8   22   47                                                  
CONECT   22   16   21   44                                                  
CONECT   23   18   29   62                                                  
CONECT   24   19   30   63                                                  
CONECT   25   10   45   46                                                  
CONECT   26    9   45   48                                                  
CONECT   27   17   44   52                                                  
CONECT   28   11   46   64                                                  
CONECT   29   23   31   53                                                  
CONECT   30   24   32   54                                                  
CONECT   31   29   35   55                                                  
CONECT   32   30   37   56                                                  
CONECT   33   34   36   57                                                  
CONECT   34   33   38   58                                                  
CONECT   35   31   40   59                                                  
CONECT   36   33   39   65                                                  
CONECT   37   32   41   66                                                  
CONECT   38   34   42   67                                                  
CONECT   39   36   60   61                                                  
CONECT   40   35   62   66                                                  
CONECT   41   37   63   67                                                  
CONECT   42   38   64   65                                                  
CONECT   43    1    2   16   17                                             
CONECT   44    3   14   22   27                                             
CONECT   45    4   12   25   26                                             
CONECT   46    5   20   25   28                                             
CONECT   47    6   15   21   48                                             
CONECT   48    7   13   26   47                                             
CONECT   49   18                                                            
CONECT   50   19                                                            
CONECT   51   20                                                            
CONECT   52   27                                                            
CONECT   53   29                                                            
CONECT   54   30                                                            
CONECT   55   31                                                            
CONECT   56   32                                                            
CONECT   57   33                                                            
CONECT   58   34                                                            
CONECT   59   35                                                            
CONECT   60   39                                                            
CONECT   61   39                                                            
CONECT   62   23   40                                                       
CONECT   63   24   41                                                       
CONECT   64   28   42                                                       
CONECT   65   36   42                                                       
CONECT   66   37   40                                                       
CONECT   67   38   41                                                       
MASTER        0    0    0    0    0    0    0    0   67    0  148    0
END
Download

3D PDB for HMDB0031883 (Sandosaponin B)

COMPND    HMDB0031883
HETATM    1  C1  UNL     1       6.107  -3.487   3.735  1.00  0.00           C  
HETATM    2  C2  UNL     1       7.013  -2.341   3.328  1.00  0.00           C  
HETATM    3  C3  UNL     1       8.413  -2.791   3.724  1.00  0.00           C  
HETATM    4  C4  UNL     1       6.576  -1.137   4.117  1.00  0.00           C  
HETATM    5  C5  UNL     1       7.290   0.118   3.737  1.00  0.00           C  
HETATM    6  O1  UNL     1       8.565   0.084   4.301  1.00  0.00           O  
HETATM    7  C6  UNL     1       7.427   0.329   2.266  1.00  0.00           C  
HETATM    8  C7  UNL     1       8.862   0.563   1.838  1.00  0.00           C  
HETATM    9  C8  UNL     1       6.698   1.643   1.952  1.00  0.00           C  
HETATM   10  C9  UNL     1       6.477   1.706   0.472  1.00  0.00           C  
HETATM   11  C10 UNL     1       5.281   0.889   0.047  1.00  0.00           C  
HETATM   12  C11 UNL     1       5.678   0.283  -1.316  1.00  0.00           C  
HETATM   13  C12 UNL     1       5.377  -0.315   0.974  1.00  0.00           C  
HETATM   14  C13 UNL     1       4.339  -0.995   1.354  1.00  0.00           C  
HETATM   15  C14 UNL     1       3.009  -0.544   0.831  1.00  0.00           C  
HETATM   16  C15 UNL     1       2.937   0.937   0.975  1.00  0.00           C  
HETATM   17  C16 UNL     1       1.555   1.508   0.860  1.00  0.00           C  
HETATM   18  C17 UNL     1       1.214   2.321   2.100  1.00  0.00           C  
HETATM   19  C18 UNL     1       0.609   0.297   0.926  1.00  0.00           C  
HETATM   20  C19 UNL     1      -0.843   0.667   0.775  1.00  0.00           C  
HETATM   21  C20 UNL     1      -1.130   1.345  -0.558  1.00  0.00           C  
HETATM   22  O2  UNL     1      -1.237   0.461  -1.572  1.00  0.00           O  
HETATM   23  C21 UNL     1      -2.427   0.318  -2.218  1.00  0.00           C  
HETATM   24  O3  UNL     1      -2.199   0.867  -3.519  1.00  0.00           O  
HETATM   25  C22 UNL     1      -1.920  -0.062  -4.470  1.00  0.00           C  
HETATM   26  C23 UNL     1      -1.100   0.603  -5.551  1.00  0.00           C  
HETATM   27  O4  UNL     1      -0.697  -0.033  -6.556  1.00  0.00           O  
HETATM   28  O5  UNL     1      -0.766   1.942  -5.463  1.00  0.00           O  
HETATM   29  C24 UNL     1      -1.131  -1.253  -4.029  1.00  0.00           C  
HETATM   30  O6  UNL     1       0.168  -0.944  -3.643  1.00  0.00           O  
HETATM   31  C25 UNL     1      -1.919  -1.928  -2.917  1.00  0.00           C  
HETATM   32  O7  UNL     1      -2.461  -3.093  -3.455  1.00  0.00           O  
HETATM   33  C26 UNL     1      -3.011  -1.001  -2.433  1.00  0.00           C  
HETATM   34  O8  UNL     1      -3.750  -1.652  -1.514  1.00  0.00           O  
HETATM   35  C27 UNL     1      -5.042  -1.977  -1.828  1.00  0.00           C  
HETATM   36  O9  UNL     1      -5.338  -3.286  -2.070  1.00  0.00           O  
HETATM   37  C28 UNL     1      -6.548  -3.562  -2.617  1.00  0.00           C  
HETATM   38  C29 UNL     1      -7.129  -4.887  -2.117  1.00  0.00           C  
HETATM   39  O10 UNL     1      -6.315  -5.972  -2.417  1.00  0.00           O  
HETATM   40  C30 UNL     1      -7.610  -2.534  -2.595  1.00  0.00           C  
HETATM   41  O11 UNL     1      -8.685  -3.004  -1.789  1.00  0.00           O  
HETATM   42  C31 UNL     1      -7.264  -1.164  -2.162  1.00  0.00           C  
HETATM   43  O12 UNL     1      -8.294  -0.388  -1.729  1.00  0.00           O  
HETATM   44  C32 UNL     1      -6.124  -1.234  -1.102  1.00  0.00           C  
HETATM   45  O13 UNL     1      -5.805   0.098  -0.912  1.00  0.00           O  
HETATM   46  C33 UNL     1      -6.138   0.588   0.317  1.00  0.00           C  
HETATM   47  O14 UNL     1      -7.086   1.594   0.290  1.00  0.00           O  
HETATM   48  C34 UNL     1      -7.505   2.004   1.535  1.00  0.00           C  
HETATM   49  C35 UNL     1      -8.991   1.659   1.620  1.00  0.00           C  
HETATM   50  O15 UNL     1      -9.179   0.281   1.469  1.00  0.00           O  
HETATM   51  C36 UNL     1      -6.731   1.400   2.668  1.00  0.00           C  
HETATM   52  O16 UNL     1      -7.061   2.124   3.826  1.00  0.00           O  
HETATM   53  C37 UNL     1      -5.259   1.643   2.407  1.00  0.00           C  
HETATM   54  O17 UNL     1      -4.444   1.087   3.392  1.00  0.00           O  
HETATM   55  C38 UNL     1      -4.924   0.930   1.113  1.00  0.00           C  
HETATM   56  O18 UNL     1      -4.145  -0.211   1.335  1.00  0.00           O  
HETATM   57  C39 UNL     1      -0.189   2.487  -0.681  1.00  0.00           C  
HETATM   58  C40 UNL     1      -0.265   3.176  -2.032  1.00  0.00           C  
HETATM   59  C41 UNL     1      -0.654   3.556   0.266  1.00  0.00           C  
HETATM   60  O19 UNL     1      -1.574   3.379   1.033  1.00  0.00           O  
HETATM   61  C42 UNL     1       1.245   2.223  -0.392  1.00  0.00           C  
HETATM   62  C43 UNL     1       1.925   1.430  -1.512  1.00  0.00           C  
HETATM   63  C44 UNL     1       3.401   1.367  -1.358  1.00  0.00           C  
HETATM   64  C45 UNL     1       3.962   1.544   0.034  1.00  0.00           C  
HETATM   65  C46 UNL     1       4.133   2.991   0.410  1.00  0.00           C  
HETATM   66  C47 UNL     1       6.750  -0.705   1.412  1.00  0.00           C  
HETATM   67  C48 UNL     1       6.875  -2.102   1.872  1.00  0.00           C  
HETATM   68  H1  UNL     1       6.235  -4.288   2.987  1.00  0.00           H  
HETATM   69  H2  UNL     1       5.051  -3.177   3.886  1.00  0.00           H  
HETATM   70  H3  UNL     1       6.539  -3.908   4.685  1.00  0.00           H  
HETATM   71  H4  UNL     1       9.198  -2.143   3.329  1.00  0.00           H  
HETATM   72  H5  UNL     1       8.545  -3.798   3.247  1.00  0.00           H  
HETATM   73  H6  UNL     1       8.419  -2.941   4.804  1.00  0.00           H  
HETATM   74  H7  UNL     1       5.500  -0.998   4.001  1.00  0.00           H  
HETATM   75  H8  UNL     1       6.750  -1.314   5.214  1.00  0.00           H  
HETATM   76  H9  UNL     1       6.755   0.958   4.270  1.00  0.00           H  
HETATM   77  H10 UNL     1       8.655  -0.561   5.048  1.00  0.00           H  
HETATM   78  H11 UNL     1       9.089   1.609   1.636  1.00  0.00           H  
HETATM   79  H12 UNL     1       9.558   0.255   2.671  1.00  0.00           H  
HETATM   80  H13 UNL     1       9.103  -0.125   0.989  1.00  0.00           H  
HETATM   81  H14 UNL     1       5.743   1.507   2.549  1.00  0.00           H  
HETATM   82  H15 UNL     1       7.297   2.504   2.303  1.00  0.00           H  
HETATM   83  H16 UNL     1       7.416   1.224   0.030  1.00  0.00           H  
HETATM   84  H17 UNL     1       6.564   2.703   0.001  1.00  0.00           H  
HETATM   85  H18 UNL     1       6.809   0.155  -1.324  1.00  0.00           H  
HETATM   86  H19 UNL     1       5.515   0.968  -2.147  1.00  0.00           H  
HETATM   87  H20 UNL     1       5.320  -0.750  -1.434  1.00  0.00           H  
HETATM   88  H21 UNL     1       4.433  -1.838   2.023  1.00  0.00           H  
HETATM   89  H22 UNL     1       2.273  -1.131   1.395  1.00  0.00           H  
HETATM   90  H23 UNL     1       3.013  -0.888  -0.230  1.00  0.00           H  
HETATM   91  H24 UNL     1       3.313   1.169   1.999  1.00  0.00           H  
HETATM   92  H25 UNL     1       0.272   2.007   2.584  1.00  0.00           H  
HETATM   93  H26 UNL     1       1.131   3.392   1.934  1.00  0.00           H  
HETATM   94  H27 UNL     1       2.013   2.126   2.879  1.00  0.00           H  
HETATM   95  H28 UNL     1       0.657  -0.105   1.981  1.00  0.00           H  
HETATM   96  H29 UNL     1       0.823  -0.447   0.154  1.00  0.00           H  
HETATM   97  H30 UNL     1      -1.377  -0.328   0.687  1.00  0.00           H  
HETATM   98  H31 UNL     1      -1.295   1.154   1.633  1.00  0.00           H  
HETATM   99  H32 UNL     1      -2.141   1.799  -0.407  1.00  0.00           H  
HETATM  100  H33 UNL     1      -3.227   1.011  -1.838  1.00  0.00           H  
HETATM  101  H34 UNL     1      -2.807  -0.455  -5.037  1.00  0.00           H  
HETATM  102  H35 UNL     1      -0.299   2.427  -6.209  1.00  0.00           H  
HETATM  103  H36 UNL     1      -1.035  -1.925  -4.926  1.00  0.00           H  
HETATM  104  H37 UNL     1       0.824  -1.644  -3.891  1.00  0.00           H  
HETATM  105  H38 UNL     1      -1.235  -2.241  -2.101  1.00  0.00           H  
HETATM  106  H39 UNL     1      -2.195  -3.900  -2.950  1.00  0.00           H  
HETATM  107  H40 UNL     1      -3.707  -0.894  -3.336  1.00  0.00           H  
HETATM  108  H41 UNL     1      -5.112  -1.539  -2.895  1.00  0.00           H  
HETATM  109  H42 UNL     1      -6.331  -3.786  -3.713  1.00  0.00           H  
HETATM  110  H43 UNL     1      -7.328  -4.819  -1.006  1.00  0.00           H  
HETATM  111  H44 UNL     1      -8.119  -5.084  -2.573  1.00  0.00           H  
HETATM  112  H45 UNL     1      -5.387  -5.697  -2.121  1.00  0.00           H  
HETATM  113  H46 UNL     1      -8.106  -2.456  -3.621  1.00  0.00           H  
HETATM  114  H47 UNL     1      -9.200  -2.210  -1.480  1.00  0.00           H  
HETATM  115  H48 UNL     1      -6.782  -0.637  -3.030  1.00  0.00           H  
HETATM  116  H49 UNL     1      -8.722   0.149  -2.468  1.00  0.00           H  
HETATM  117  H50 UNL     1      -6.519  -1.696  -0.195  1.00  0.00           H  
HETATM  118  H51 UNL     1      -6.620  -0.268   0.877  1.00  0.00           H  
HETATM  119  H52 UNL     1      -7.428   3.104   1.608  1.00  0.00           H  
HETATM  120  H53 UNL     1      -9.473   2.235   0.799  1.00  0.00           H  
HETATM  121  H54 UNL     1      -9.401   2.032   2.576  1.00  0.00           H  
HETATM  122  H55 UNL     1      -9.699   0.156   0.639  1.00  0.00           H  
HETATM  123  H56 UNL     1      -6.949   0.321   2.817  1.00  0.00           H  
HETATM  124  H57 UNL     1      -7.615   1.581   4.435  1.00  0.00           H  
HETATM  125  H58 UNL     1      -5.107   2.709   2.267  1.00  0.00           H  
HETATM  126  H59 UNL     1      -5.035   0.846   4.143  1.00  0.00           H  
HETATM  127  H60 UNL     1      -4.308   1.624   0.505  1.00  0.00           H  
HETATM  128  H61 UNL     1      -4.367  -0.694   2.161  1.00  0.00           H  
HETATM  129  H62 UNL     1      -0.137   2.530  -2.888  1.00  0.00           H  
HETATM  130  H63 UNL     1       0.563   3.946  -2.009  1.00  0.00           H  
HETATM  131  H64 UNL     1      -1.200   3.809  -2.095  1.00  0.00           H  
HETATM  132  H65 UNL     1      -0.164   4.521   0.280  1.00  0.00           H  
HETATM  133  H66 UNL     1       1.703   3.227  -0.536  1.00  0.00           H  
HETATM  134  H67 UNL     1       1.408   0.464  -1.585  1.00  0.00           H  
HETATM  135  H68 UNL     1       1.733   1.932  -2.496  1.00  0.00           H  
HETATM  136  H69 UNL     1       3.657   0.344  -1.708  1.00  0.00           H  
HETATM  137  H70 UNL     1       3.900   2.171  -1.979  1.00  0.00           H  
HETATM  138  H71 UNL     1       5.015   3.148   1.053  1.00  0.00           H  
HETATM  139  H72 UNL     1       3.347   3.367   1.105  1.00  0.00           H  
HETATM  140  H73 UNL     1       4.104   3.670  -0.468  1.00  0.00           H  
HETATM  141  H74 UNL     1       7.336  -0.685   0.432  1.00  0.00           H  
HETATM  142  H75 UNL     1       6.055  -2.716   1.460  1.00  0.00           H  
HETATM  143  H76 UNL     1       7.798  -2.611   1.413  1.00  0.00           H  
CONECT    1    2   68   69   70
CONECT    2    3    4   67
CONECT    3   71   72   73
CONECT    4    5   74   75
CONECT    5    6    7   76
CONECT    6   77
CONECT    7    8    9   66
CONECT    8   78   79   80
CONECT    9   10   81   82
CONECT   10   11   83   84
CONECT   11   12   13   64
CONECT   12   85   86   87
CONECT   13   14   14   66
CONECT   14   15   88
CONECT   15   16   89   90
CONECT   16   17   64   91
CONECT   17   18   19   61
CONECT   18   92   93   94
CONECT   19   20   95   96
CONECT   20   21   97   98
CONECT   21   22   57   99
CONECT   22   23
CONECT   23   24   33  100
CONECT   24   25
CONECT   25   26   29  101
CONECT   26   27   27   28
CONECT   28  102
CONECT   29   30   31  103
CONECT   30  104
CONECT   31   32   33  105
CONECT   32  106
CONECT   33   34  107
CONECT   34   35
CONECT   35   36   44  108
CONECT   36   37
CONECT   37   38   40  109
CONECT   38   39  110  111
CONECT   39  112
CONECT   40   41   42  113
CONECT   41  114
CONECT   42   43   44  115
CONECT   43  116
CONECT   44   45  117
CONECT   45   46
CONECT   46   47   55  118
CONECT   47   48
CONECT   48   49   51  119
CONECT   49   50  120  121
CONECT   50  122
CONECT   51   52   53  123
CONECT   52  124
CONECT   53   54   55  125
CONECT   54  126
CONECT   55   56  127
CONECT   56  128
CONECT   57   58   59   61
CONECT   58  129  130  131
CONECT   59   60   60  132
CONECT   61   62  133
CONECT   62   63  134  135
CONECT   63   64  136  137
CONECT   64   65
CONECT   65  138  139  140
CONECT   66   67  141
CONECT   67  142  143
END
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SMILES for HMDB0031883 (Sandosaponin B)

CC1(C)CC(O)C2(C)CCC3(C)C(=CCC4C5(C)CCC(OC6OC(C(O)C(O)C6OC6OC(CO)C(O)C(O)C6OC6OC(CO)C(O)C(O)C6O)C(O)=O)C(C)(C=O)C5CCC34C)C2C1
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INCHI for HMDB0031883 (Sandosaponin B)

InChI=1S/C48H76O19/c1-43(2)16-22-21-8-9-26-45(4)12-11-28(46(5,20-51)25(45)10-13-48(26,7)47(21,6)15-14-44(22,3)27(52)17-43)64-42-38(34(58)33(57)36(65-42)39(60)61)67-41-37(32(56)30(54)24(19-50)63-41)66-40-35(59)31(55)29(53)23(18-49)62-40/h8,20,22-38,40-42,49-50,52-59H,9-19H2,1-7H3,(H,60,61)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-6-[(4-formyl-9-hydroxy-4,6a,6b,8a,11,11,14b-heptamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,14,14a,14b-icosahydropicen-3-yl)oxy]-3,4-dihydroxyoxane-2-carboxylateHMDB
Sandosapogenol (3,22-dihydroxyolean-12-en-24-al)-3-O-beta-glucopyranosyl(1-2)-beta-D-galactopyranosyl(1-2)-beta-D-glucupyranosiduronic acidHMDB
Chemical FormulaC48H76O19
Average Molecular Weight957.1056
Monoisotopic Molecular Weight956.49808025
IUPAC Name5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-6-[(4-formyl-9-hydroxy-4,6a,6b,8a,11,11,14b-heptamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,14,14a,14b-icosahydropicen-3-yl)oxy]-3,4-dihydroxyoxane-2-carboxylic acid
Traditional Name5-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-6-[(4-formyl-9-hydroxy-4,6a,6b,8a,11,11,14b-heptamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl)oxy]-3,4-dihydroxyoxane-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
CC1(C)CC(O)C2(C)CCC3(C)C(=CCC4C5(C)CCC(OC6OC(C(O)C(O)C6OC6OC(CO)C(O)C(O)C6OC6OC(CO)C(O)C(O)C6O)C(O)=O)C(C)(C=O)C5CCC34C)C2C1
InChI Identifier
InChI=1S/C48H76O19/c1-43(2)16-22-21-8-9-26-45(4)12-11-28(46(5,20-51)25(45)10-13-48(26,7)47(21,6)15-14-44(22,3)27(52)17-43)64-42-38(34(58)33(57)36(65-42)39(60)61)67-41-37(32(56)30(54)24(19-50)63-41)66-40-35(59)31(55)29(53)23(18-49)62-40/h8,20,22-38,40-42,49-50,52-59H,9-19H2,1-7H3,(H,60,61)
InChI KeyWIHKYILMSPQBIM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene glycosides
Direct ParentTriterpene saponins
Alternative Parents
Substituents
  • Triterpene saponin
  • Triterpenoid
  • Oligosaccharide
  • Steroid
  • Fatty acyl glycoside
  • 1-o-glucuronide
  • O-glucuronide
  • Glucuronic acid or derivatives
  • Glycosyl compound
  • O-glycosyl compound
  • Beta-hydroxy acid
  • Pyran
  • Oxane
  • Fatty acyl
  • Hydroxy acid
  • Cyclic alcohol
  • Secondary alcohol
  • Organoheterocyclic compound
  • Polyol
  • Oxacycle
  • Carboxylic acid derivative
  • Monocarboxylic acid or derivatives
  • Acetal
  • Carboxylic acid
  • Primary alcohol
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Carbonyl group
  • Alcohol
  • Aldehyde
  • Organooxygen compound
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point212 - 213 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.32 g/LALOGPS
logP1.82ALOGPS
logP0.21ChemAxon
logS-3.5ALOGPS
pKa (Strongest Acidic)3.27ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area312.05 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity231.32 m³·mol⁻¹ChemAxon
Polarizability102.23 ųChemAxon
Number of Rings8ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-327.05730932474
DeepCCS[M+Na]+301.45930932474
AllCCS[M+H]+302.232859911
AllCCS[M+H-H2O]+302.532859911
AllCCS[M+NH4]+301.932859911
AllCCS[M+Na]+301.932859911
AllCCS[M-H]-258.132859911
AllCCS[M+Na-2H]-264.332859911
AllCCS[M+HCOO]-271.132859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 10V, Positive-QTOFsplash10-052r-0200916506-7317476d61dfcb593d282016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 20V, Positive-QTOFsplash10-0a4r-0100904200-b9f669e6c930ed3392dd2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 40V, Positive-QTOFsplash10-0a4i-0502903100-8d848a8246cd345c48d82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 10V, Negative-QTOFsplash10-0550-2422805329-44dcfd5ce1924953c0372016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 20V, Negative-QTOFsplash10-06tr-1902813302-fe462a825097fd98389a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 40V, Negative-QTOFsplash10-056r-3901711000-1b16c941e28c8b92569d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 10V, Negative-QTOFsplash10-0a4i-0000000029-ea9a5ea32089915fda5d2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 20V, Negative-QTOFsplash10-0a4i-4100001179-fb0a6e1d72188d64603b2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 40V, Negative-QTOFsplash10-0a4u-9200001170-334fa018d45360ec21312021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 10V, Positive-QTOFsplash10-0c09-0000200009-c79503f349418c8e29e82021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 20V, Positive-QTOFsplash10-0ap0-0260403109-e3f3a6da07ebeaca29432021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Sandosaponin B 40V, Positive-QTOFsplash10-0ldr-6410003391-0b879f329b016d188fae2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008568
KNApSAcK IDC00057202
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound73981728
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.

Enzymes

Enzyme Details
1. UDP-glucuronosyltransferase 2B4
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGTs are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isozyme is active on polyhydroxylated estrogens (such as estriol, 4-hydroxyestrone and 2-hydroxyestriol) and xenobiotics (such as 4-methylumbelliferone, 1-naphthol, 4-nitrophenol, 2-aminophenol, 4-hydroxybiphenyl and menthol). It is capable of 6 alpha-hydroxyglucuronidation of hyodeoxycholic acid.
Gene Name:
UGT2B4
Uniprot ID:
P06133
Molecular weight:
60512.035
Enzyme Details
2. UDP-glucuronosyltransferase 1-4
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate.
Gene Name:
UGT1A4
Uniprot ID:
P22310
Molecular weight:
60024.535
Enzyme Details
3. UDP-glucuronosyltransferase 2B7
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. Its unique specificity for 3,4-catechol estrogens and estriol suggests it may play an important role in regulating the level and activity of these potent and active estrogen metabolites. Is also active with androsterone, hyodeoxycholic acid and tetrachlorocatechol (in vitro).
Gene Name:
UGT2B7
Uniprot ID:
P16662
Molecular weight:
60720.15
Enzyme Details
4. UDP-glucuronosyltransferase 1-1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
UGT1A1
Uniprot ID:
P22309
Molecular weight:
59590.91
Enzyme Details
5. UDP-glucuronosyltransferase 1-9
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform has specificity for phenols.
Gene Name:
UGT1A9
Uniprot ID:
O60656
Molecular weight:
59940.495
Enzyme Details
6. UDP-glucuronosyltransferase 1-6
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform has specificity for phenols.
Gene Name:
UGT1A6
Uniprot ID:
P19224
Molecular weight:
60750.215