Hmdb loader

Showing metabocard for Glucoiberverin (HMDB0304681)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 11:37:36 UTC
Update Date2021-09-24 11:37:36 UTC
HMDB IDHMDB0304681
Secondary Accession NumbersNone
Metabolite Identification
Common NameGlucoiberverin
DescriptionGlucoiberverin belongs to the class of organic compounds known as alkylglucosinolates. These are organic compounds containing a glucosinolate moiety that carries an alkyl chain. Based on a literature review a significant number of articles have been published on Glucoiberverin.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304681 (Glucoiberverin)


  Mrv1652301212022273D          

 24 24  0  0  0  0            999 V2000
    5.3294    1.2645    2.2586 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3674   -0.9731    0.6239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0261   -0.6400    1.1928 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2981   -1.4663    1.7565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2046    0.5403    1.4798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9123    0.8830    0.0083 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0185   -0.1516    0.2410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2396   -0.2496   -0.9034 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0899   -1.1972   -0.9715 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8875   -0.3889   -1.4082 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6423    0.7982   -0.5354 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2822   -0.0287   -0.9903 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2262    1.7119    2.2446 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4950    0.2693   -2.1757 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8794   -1.8281    0.2504 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1341    0.0393   -2.7113 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5020    2.4642   -2.1107 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.5063    0.8798   -2.7346 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4367    0.7030   -4.0637 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7234    1.4952   -0.1343 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4227   -0.2838   -1.6676 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4554   -0.1560    2.9747 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6359    0.2882    0.8791 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.0197    0.9598   -2.6994 S   0  0  2  0  0  0  0  0  0  0  0  0
  1 22  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  7  1  0  0  0  0
  4 22  1  0  0  0  0
  5  6  1  0  0  0  0
  5 13  1  0  0  0  0
  6  8  1  0  0  0  0
  6 20  1  0  0  0  0
  7 12  2  0  0  0  0
  7 23  1  0  0  0  0
  8  9  1  0  0  0  0
  8 14  1  6  0  0  0
  9 10  1  0  0  0  0
  9 15  1  1  0  0  0
 10 11  1  0  0  0  0
 10 16  1  0  0  0  0
 11 20  1  0  0  0  0
 11 23  1  1  0  0  0
 12 21  1  0  0  0  0
 17 24  1  0  0  0  0
 18 24  2  0  0  0  0
 19 24  2  0  0  0  0
 21 24  1  0  0  0  0
M  CHG  1  17  -1
M  END
Download

3D MOL for HMDB0304681 (Glucoiberverin)

HMDB0304681
     RDKit          3D
Glucoiberverin
 44 44  0  0  0  0  0  0  0  0999 V2000
    5.3843    0.9400   -2.0442 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8570   -0.1911   -0.7225 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.0970    0.1819    0.8549 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6342   -0.1457    0.8779 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7994    0.5503   -0.1252 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3515    0.2507   -0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7889   -0.5550    0.7370 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4865   -1.2504    1.6848 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2389   -2.8624    2.0978 S   0  0  0  0  0  6  0  0  0  0  0  0
    1.0131   -2.9042    3.5985 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5390   -3.5992    1.8186 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0166   -3.5738    1.2721 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.3396    1.0999   -1.2823 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3779    0.6533   -1.1424 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9206    1.1130    0.0786 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2772    1.2951   -0.2177 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9881    2.1686    0.7593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3384    2.3262    0.4296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9426   -0.0319   -0.4838 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7095    0.0056   -1.6470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9527   -1.1658   -0.5690 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7630   -1.7411    0.6972 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6597   -0.8071   -1.2269 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6264   -1.2282   -2.5737 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3691    1.3137   -2.4797 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8696    1.8429   -1.6402 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8362    0.3954   -2.8126 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2870    1.2390    1.1755 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5670   -0.5246    1.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5885   -1.2690    0.7493 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2881    0.1389    1.9086 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9140    1.6462   -0.0067 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1940    0.3022   -1.1530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9296    1.1386   -1.9995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2858    1.8397   -1.2061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8567    1.8881    1.8128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5521    3.2035    0.6271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4470    2.8718   -0.3837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6342   -0.2588    0.3558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6137    0.3436   -1.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4356   -1.9605   -1.1832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1817   -1.1465    1.3603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8652   -1.4245   -0.7298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0684   -2.1084   -2.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  2  0
  9 12  1  0
  6 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 23 14  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
 14 34  1  6
 16 35  1  6
 17 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  1
 20 40  1  0
 21 41  1  6
 22 42  1  0
 23 43  1  1
 24 44  1  0
M  CHG  1  12  -1
M  END
Download

3D SDF for HMDB0304681 (Glucoiberverin)


  Mrv1652301212022273D          

 24 24  0  0  0  0            999 V2000
    5.3294    1.2645    2.2586 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3674   -0.9731    0.6239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0261   -0.6400    1.1928 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2981   -1.4663    1.7565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2046    0.5403    1.4798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9123    0.8830    0.0083 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0185   -0.1516    0.2410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2396   -0.2496   -0.9034 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0899   -1.1972   -0.9715 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8875   -0.3889   -1.4082 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6423    0.7982   -0.5354 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2822   -0.0287   -0.9903 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2262    1.7119    2.2446 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4950    0.2693   -2.1757 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8794   -1.8281    0.2504 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1341    0.0393   -2.7113 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5020    2.4642   -2.1107 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.5063    0.8798   -2.7346 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4367    0.7030   -4.0637 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7234    1.4952   -0.1343 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4227   -0.2838   -1.6676 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4554   -0.1560    2.9747 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6359    0.2882    0.8791 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.0197    0.9598   -2.6994 S   0  0  2  0  0  0  0  0  0  0  0  0
  1 22  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  7  1  0  0  0  0
  4 22  1  0  0  0  0
  5  6  1  0  0  0  0
  5 13  1  0  0  0  0
  6  8  1  0  0  0  0
  6 20  1  0  0  0  0
  7 12  2  0  0  0  0
  7 23  1  0  0  0  0
  8  9  1  0  0  0  0
  8 14  1  6  0  0  0
  9 10  1  0  0  0  0
  9 15  1  1  0  0  0
 10 11  1  0  0  0  0
 10 16  1  0  0  0  0
 11 20  1  0  0  0  0
 11 23  1  1  0  0  0
 12 21  1  0  0  0  0
 17 24  1  0  0  0  0
 18 24  2  0  0  0  0
 19 24  2  0  0  0  0
 21 24  1  0  0  0  0
M  CHG  1  17  -1
M  END
> <DATABASE_ID>
HMDB0304681

> <DATABASE_NAME>
hmdb

> <SMILES>
CSCCC\C(S[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)=N/OS([O-])(=O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H21NO9S3/c1-22-4-2-3-7(12-21-24(17,18)19)23-11-10(16)9(15)8(14)6(5-13)20-11/h6,8-11,13-16H,2-5H2,1H3,(H,17,18,19)/p-1/b12-7+/t6-,8-,9+,10-,11+/m1/s1

> <INCHI_KEY>
ZCZCVJVUJGULMO-BZVDQRPCSA-M

> <FORMULA>
C11H20NO9S3

> <MOLECULAR_WEIGHT>
406.46

> <EXACT_MASS>
406.03056833

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
38.506932840907176

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(E)-[4-(methylsulfanyl)-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}butylidene]amino sulfate

> <ALOGPS_LOGP>
-0.67

> <JCHEM_LOGP>
-2.6372762498584708

> <ALOGPS_LOGS>
-1.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.447672738839596

> <JCHEM_PKA_STRONGEST_ACIDIC>
-3.5006623024768366

> <JCHEM_PKA_STRONGEST_BASIC>
-0.2786908706054433

> <JCHEM_POLAR_SURFACE_AREA>
168.94

> <JCHEM_REFRACTIVITY>
86.13959999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.83e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(E)-[4-(methylsulfanyl)-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}butylidene]amino sulfate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304681 (Glucoiberverin)

HMDB0304681
     RDKit          3D
Glucoiberverin
 44 44  0  0  0  0  0  0  0  0999 V2000
    5.3843    0.9400   -2.0442 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8570   -0.1911   -0.7225 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.0970    0.1819    0.8549 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6342   -0.1457    0.8779 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7994    0.5503   -0.1252 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3515    0.2507   -0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7889   -0.5550    0.7370 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4865   -1.2504    1.6848 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2389   -2.8624    2.0978 S   0  0  0  0  0  6  0  0  0  0  0  0
    1.0131   -2.9042    3.5985 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5390   -3.5992    1.8186 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0166   -3.5738    1.2721 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.3396    1.0999   -1.2823 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3779    0.6533   -1.1424 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9206    1.1130    0.0786 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2772    1.2951   -0.2177 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9881    2.1686    0.7593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3384    2.3262    0.4296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9426   -0.0319   -0.4838 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7095    0.0056   -1.6470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9527   -1.1658   -0.5690 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7630   -1.7411    0.6972 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6597   -0.8071   -1.2269 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6264   -1.2282   -2.5737 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3691    1.3137   -2.4797 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8696    1.8429   -1.6402 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8362    0.3954   -2.8126 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2870    1.2390    1.1755 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5670   -0.5246    1.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5885   -1.2690    0.7493 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2881    0.1389    1.9086 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9140    1.6462   -0.0067 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1940    0.3022   -1.1530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9296    1.1386   -1.9995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2858    1.8397   -1.2061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8567    1.8881    1.8128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5521    3.2035    0.6271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4470    2.8718   -0.3837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6342   -0.2588    0.3558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6137    0.3436   -1.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4356   -1.9605   -1.1832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1817   -1.1465    1.3603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8652   -1.4245   -0.7298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0684   -2.1084   -2.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  2  0
  9 12  1  0
  6 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 23 14  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
 14 34  1  6
 16 35  1  6
 17 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  1
 20 40  1  0
 21 41  1  6
 22 42  1  0
 23 43  1  1
 24 44  1  0
M  CHG  1  12  -1
M  END
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PDB for HMDB0304681 (Glucoiberverin)

HEADER    PROTEIN                                 21-JAN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JAN-20         0                                  
HETATM    1  C   UNK     0       5.329   1.264   2.259  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.367  -0.973   0.624  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.026  -0.640   1.193  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.298  -1.466   1.757  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.205   0.540   1.480  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.912   0.883   0.008  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.018  -0.152   0.241  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.240  -0.250  -0.903  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.090  -1.197  -0.972  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.888  -0.389  -1.408  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.642   0.798  -0.535  0.00  0.00           C+0
HETATM   12  N   UNK     0       1.282  -0.029  -0.990  0.00  0.00           N+0
HETATM   13  O   UNK     0      -4.226   1.712   2.245  0.00  0.00           O+0
HETATM   14  O   UNK     0      -4.495   0.269  -2.176  0.00  0.00           O+0
HETATM   15  O   UNK     0      -2.879  -1.828   0.250  0.00  0.00           O+0
HETATM   16  O   UNK     0      -2.134   0.039  -2.711  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.502   2.464  -2.111  0.00  0.00           O-1
HETATM   18  O   UNK     0       4.506   0.880  -2.735  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.437   0.703  -4.064  0.00  0.00           O+0
HETATM   20  O   UNK     0      -2.723   1.495  -0.134  0.00  0.00           O+0
HETATM   21  O   UNK     0       2.423  -0.284  -1.668  0.00  0.00           O+0
HETATM   22  S   UNK     0       4.455  -0.156   2.975  0.00  0.00           S+0
HETATM   23  S   UNK     0      -0.636   0.288   0.879  0.00  0.00           S+0
HETATM   24  S   UNK     0       3.020   0.960  -2.699  0.00  0.00           S+0
CONECT    1   22                                                            
CONECT    2    3    4                                                       
CONECT    3    2    7                                                       
CONECT    4    2   22                                                       
CONECT    5    6   13                                                       
CONECT    6    5    8   20                                                  
CONECT    7    3   12   23                                                  
CONECT    8    6    9   14                                                  
CONECT    9    8   10   15                                                  
CONECT   10    9   11   16                                                  
CONECT   11   10   20   23                                                  
CONECT   12    7   21                                                       
CONECT   13    5                                                            
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16   10                                                            
CONECT   17   24                                                            
CONECT   18   24                                                            
CONECT   19   24                                                            
CONECT   20    6   11                                                       
CONECT   21   12   24                                                       
CONECT   22    1    4                                                       
CONECT   23    7   11                                                       
CONECT   24   17   18   19   21                                             
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END
Download

3D PDB for HMDB0304681 (Glucoiberverin)

COMPND    HMDB0304681
HETATM    1  C1  UNL     1       5.384   0.940  -2.044  1.00  0.00           C  
HETATM    2  S1  UNL     1       5.857  -0.191  -0.723  1.00  0.00           S  
HETATM    3  C2  UNL     1       5.097   0.182   0.855  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.634  -0.146   0.878  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.799   0.550  -0.125  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.351   0.251  -0.078  1.00  0.00           C  
HETATM    7  N1  UNL     1       0.789  -0.555   0.737  1.00  0.00           N  
HETATM    8  O1  UNL     1       1.486  -1.250   1.685  1.00  0.00           O  
HETATM    9  S2  UNL     1       1.239  -2.862   2.098  1.00  0.00           S  
HETATM   10  O2  UNL     1       1.013  -2.904   3.598  1.00  0.00           O  
HETATM   11  O3  UNL     1       2.539  -3.599   1.819  1.00  0.00           O  
HETATM   12  O4  UNL     1      -0.017  -3.574   1.272  1.00  0.00           O1-
HETATM   13  S3  UNL     1       0.340   1.100  -1.282  1.00  0.00           S  
HETATM   14  C6  UNL     1      -1.378   0.653  -1.142  1.00  0.00           C  
HETATM   15  O5  UNL     1      -1.921   1.113   0.079  1.00  0.00           O  
HETATM   16  C7  UNL     1      -3.277   1.295  -0.218  1.00  0.00           C  
HETATM   17  C8  UNL     1      -3.988   2.169   0.759  1.00  0.00           C  
HETATM   18  O6  UNL     1      -5.338   2.326   0.430  1.00  0.00           O  
HETATM   19  C9  UNL     1      -3.943  -0.032  -0.484  1.00  0.00           C  
HETATM   20  O7  UNL     1      -4.710   0.006  -1.647  1.00  0.00           O  
HETATM   21  C10 UNL     1      -2.953  -1.166  -0.569  1.00  0.00           C  
HETATM   22  O8  UNL     1      -2.763  -1.741   0.697  1.00  0.00           O  
HETATM   23  C11 UNL     1      -1.660  -0.807  -1.227  1.00  0.00           C  
HETATM   24  O9  UNL     1      -1.626  -1.228  -2.574  1.00  0.00           O  
HETATM   25  H1  UNL     1       6.369   1.314  -2.480  1.00  0.00           H  
HETATM   26  H2  UNL     1       4.870   1.843  -1.640  1.00  0.00           H  
HETATM   27  H3  UNL     1       4.836   0.395  -2.813  1.00  0.00           H  
HETATM   28  H4  UNL     1       5.287   1.239   1.175  1.00  0.00           H  
HETATM   29  H5  UNL     1       5.567  -0.525   1.610  1.00  0.00           H  
HETATM   30  H6  UNL     1       3.588  -1.269   0.749  1.00  0.00           H  
HETATM   31  H7  UNL     1       3.288   0.139   1.909  1.00  0.00           H  
HETATM   32  H8  UNL     1       2.914   1.646  -0.007  1.00  0.00           H  
HETATM   33  H9  UNL     1       3.194   0.302  -1.153  1.00  0.00           H  
HETATM   34  H10 UNL     1      -1.930   1.139  -1.999  1.00  0.00           H  
HETATM   35  H11 UNL     1      -3.286   1.840  -1.206  1.00  0.00           H  
HETATM   36  H12 UNL     1      -3.857   1.888   1.813  1.00  0.00           H  
HETATM   37  H13 UNL     1      -3.552   3.204   0.627  1.00  0.00           H  
HETATM   38  H14 UNL     1      -5.447   2.872  -0.384  1.00  0.00           H  
HETATM   39  H15 UNL     1      -4.634  -0.259   0.356  1.00  0.00           H  
HETATM   40  H16 UNL     1      -5.614   0.344  -1.483  1.00  0.00           H  
HETATM   41  H17 UNL     1      -3.436  -1.961  -1.183  1.00  0.00           H  
HETATM   42  H18 UNL     1      -3.182  -1.146   1.360  1.00  0.00           H  
HETATM   43  H19 UNL     1      -0.865  -1.425  -0.730  1.00  0.00           H  
HETATM   44  H20 UNL     1      -2.068  -2.108  -2.676  1.00  0.00           H  
CONECT    1    2   25   26   27
CONECT    2    3
CONECT    3    4   28   29
CONECT    4    5   30   31
CONECT    5    6   32   33
CONECT    6    7    7   13
CONECT    7    8
CONECT    8    9
CONECT    9   10   10   11   11
CONECT    9   12
CONECT   13   14
CONECT   14   15   23   34
CONECT   15   16
CONECT   16   17   19   35
CONECT   17   18   36   37
CONECT   18   38
CONECT   19   20   21   39
CONECT   20   40
CONECT   21   22   23   41
CONECT   22   42
CONECT   23   24   43
CONECT   24   44
END
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SMILES for HMDB0304681 (Glucoiberverin)

CSCCC\C(S[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)=N/OS([O-])(=O)=O
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INCHI for HMDB0304681 (Glucoiberverin)

InChI=1S/C11H21NO9S3/c1-22-4-2-3-7(12-21-24(17,18)19)23-11-10(16)9(15)8(14)6(5-13)20-11/h6,8-11,13-16H,2-5H2,1H3,(H,17,18,19)/p-1/b12-7+/t6-,8-,9+,10-,11+/m1/s1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC11H20NO9S3
Average Molecular Weight406.46
Monoisotopic Molecular Weight406.03056833
IUPAC Name(E)-[4-(methylsulfanyl)-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}butylidene]amino sulfate
Traditional Name(E)-[4-(methylsulfanyl)-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl}butylidene]amino sulfate
CAS Registry NumberNot Available
SMILES
CSCCC\C(S[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)=N/OS([O-])(=O)=O
InChI Identifier
InChI=1S/C11H21NO9S3/c1-22-4-2-3-7(12-21-24(17,18)19)23-11-10(16)9(15)8(14)6(5-13)20-11/h6,8-11,13-16H,2-5H2,1H3,(H,17,18,19)/p-1/b12-7+/t6-,8-,9+,10-,11+/m1/s1
InChI KeyZCZCVJVUJGULMO-BZVDQRPCSA-M
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkylglucosinolates. These are organic compounds containing a glucosinolate moiety that carries an alkyl chain.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentAlkylglucosinolates
Alternative Parents
Substituents
  • Alkylglucosinolate
  • Glycosyl compound
  • S-glycosyl compound
  • Oxane
  • Monothioacetal
  • Organic sulfuric acid or derivatives
  • Secondary alcohol
  • Polyol
  • Oxacycle
  • Thioether
  • Organoheterocyclic compound
  • Sulfenyl compound
  • Dialkylthioether
  • Primary alcohol
  • Alcohol
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Organonitrogen compound
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
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
logP-0.67ALOGPS
logP-2.6ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)-3.5ChemAxon
pKa (Strongest Basic)-0.28ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area168.94 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity86.14 m³·mol⁻¹ChemAxon
Polarizability38.51 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+185.49932859911
AllCCS[M+H-H2O]+183.21732859911
AllCCS[M+Na]+188.19232859911
AllCCS[M+NH4]+187.59432859911
AllCCS[M-H]-177.78132859911
AllCCS[M+Na-2H]-178.20732859911
AllCCS[M+HCOO]-178.80432859911
DeepCCS[M+H]+186.41230932474
DeepCCS[M-H]-184.01430932474
DeepCCS[M-2H]-216.90230932474
DeepCCS[M+Na]+192.22430932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202212.5247 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20227.19 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1792.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid245.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid92.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid170.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid100.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid433.4 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid509.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)127.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid837.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid385.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1287.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid281.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid306.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate365.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA257.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water167.9 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
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 IDNot Available
KNApSAcK IDNot Available
Chemspider ID7827560
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9548637
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 ReferencesNot Available