MiMeDB: Showing metabocard for Glysperin B (MMDBc0021034)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 11:09:42 UTC

Update Date

2022-08-31 06:47:14 UTC

Metabolite ID

MMDBc0021034

Metabolite Identification

Common Name

Glysperin B

Description

Glysperin B belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. Glysperin B is a very strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152113092D          

 83 87  0  0  1  0            999 V2000
  -19.9989   13.5763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.9266   12.6726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.9869   10.0028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2739    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9884    7.7943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8462    7.7943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4186    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7041    6.9693    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1331    7.7943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4186    6.5568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5594    7.7943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7028    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1318    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5607    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.5977   11.1652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7908    8.7150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -19.5139   12.9088    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  -15.7471   12.5864    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  -13.3225    9.2492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7041    7.7943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1331    6.9693    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.9333   10.4116    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  -11.4552    7.9613    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  -16.2320   13.2538    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  -17.3881   12.4139    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  -14.1430    9.1629    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  -17.0525   13.1676    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  -17.0893    9.5717    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  -16.6044    8.9042    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  -11.3157    6.6337    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  -13.9936    7.7418    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  -16.7538   10.3253    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  -11.8677    7.2468    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  -14.4785    8.4092    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  -18.6935   12.9951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9897    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.9031   11.7464    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  -15.7839    8.9904    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  -13.1731    7.8280    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  -10.5620    6.9693    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1551    8.2068    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -19.8495   12.1552    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8965   14.0075    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4173    7.7943    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2752    7.7943    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -18.2085   12.3276    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -14.7773   11.2515    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3059    9.3824    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -14.6279    9.8304    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -17.5374   13.8350    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -17.9098    9.4854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -16.9400    8.1505    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4872    5.8268    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3292    6.9881    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -18.3579   13.7488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9897    9.0318    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -16.0827   11.8327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.8376    8.5817    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8475    6.5568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -15.4484    9.7441    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6482    7.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -17.2387   10.9928    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.6882    7.1606    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2990    8.3230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -19.1784   13.6625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.4115   13.3400    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.4182   11.0790    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2791    8.0045    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.7169   13.9212    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.8730   13.0813    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.9635    9.0767    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5676   12.5001    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.5743   10.2391    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.4249    8.8180    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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  5  4  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  2  0  0  0  0
 11  4  1  0  0  0  0
 12  5  1  0  0  0  0
 13  6  1  0  0  0  0
 14  6  1  0  0  0  0
 17  1  1  0  0  0  0
 18  2  1  1  0  0  0
 19  3  2  0  0  0  0
 20  7  2  0  0  0  0
 20  8  1  0  0  0  0
 21  9  2  0  0  0  0
 21 10  1  0  0  0  0
 22 15  1  6  0  0  0
 23 16  1  6  0  0  0
 24 18  1  0  0  0  0
 26 19  1  0  0  0  0
 27 24  1  0  0  0  0
 27 25  1  0  0  0  0
 29 28  1  0  0  0  0
 32 22  1  0  0  0  0
 32 28  1  0  0  0  0
 33 23  1  0  0  0  0
 33 30  1  0  0  0  0
 34 26  1  0  0  0  0
 34 31  1  0  0  0  0
 35 17  1  0  0  0  0
 36 20  1  0  0  0  0
 37 25  1  0  0  0  0
 38 29  1  0  0  0  0
 39 31  1  0  0  0  0
 40 30  1  0  0  0  0
 41 11  1  0  0  0  0
 17 42  1  1  0  0  0
 24 43  1  1  0  0  0
 44 12  1  0  0  0  0
 44 13  1  0  0  0  0
 45 14  1  0  0  0  0
 45 36  1  0  0  0  0
 25 46  1  6  0  0  0
 46 35  2  0  0  0  0
 47 15  1  0  0  0  0
 48 16  1  0  0  0  0
 26 49  1  1  0  0  0
 27 50  1  6  0  0  0
 28 51  1  1  0  0  0
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 30 53  1  1  0  0  0
 31 54  1  6  0  0  0
 35 55  1  4  0  0  0
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 57 18  1  0  0  0  0
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 58 19  1  0  0  0  0
 58 39  1  0  0  0  0
 59 21  1  0  0  0  0
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 34 64  1  1  0  0  0
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 37 80  1  1  0  0  0
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 40 83  1  6  0  0  0
M  END


  Mrv1652305152113092D          

 83 87  0  0  1  0            999 V2000
  -19.9989   13.5763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.9266   12.6726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.2739    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9884    7.7943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8462    7.7943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4186    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7041    6.9693    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1331    7.7943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4186    6.5568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5594    7.7943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7028    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1318    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5607    8.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -12.1126    6.4202    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.8141    7.6556    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.2689    9.6579    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0472    7.3331    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6580    8.4955    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.7236   11.6602    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.1195    8.2368    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.5087    7.0744    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6052    6.1454    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  2  0  0  0  0
 11  4  1  0  0  0  0
 12  5  1  0  0  0  0
 13  6  1  0  0  0  0
 14  6  1  0  0  0  0
 17  1  1  0  0  0  0
 18  2  1  1  0  0  0
 19  3  2  0  0  0  0
 20  7  2  0  0  0  0
 20  8  1  0  0  0  0
 21  9  2  0  0  0  0
 21 10  1  0  0  0  0
 22 15  1  6  0  0  0
 23 16  1  6  0  0  0
 24 18  1  0  0  0  0
 26 19  1  0  0  0  0
 27 24  1  0  0  0  0
 27 25  1  0  0  0  0
 29 28  1  0  0  0  0
 32 22  1  0  0  0  0
 32 28  1  0  0  0  0
 33 23  1  0  0  0  0
 33 30  1  0  0  0  0
 34 26  1  0  0  0  0
 34 31  1  0  0  0  0
 35 17  1  0  0  0  0
 36 20  1  0  0  0  0
 37 25  1  0  0  0  0
 38 29  1  0  0  0  0
 39 31  1  0  0  0  0
 40 30  1  0  0  0  0
 41 11  1  0  0  0  0
 17 42  1  1  0  0  0
 24 43  1  1  0  0  0
 44 12  1  0  0  0  0
 44 13  1  0  0  0  0
 45 14  1  0  0  0  0
 45 36  1  0  0  0  0
 25 46  1  6  0  0  0
 46 35  2  0  0  0  0
 47 15  1  0  0  0  0
 48 16  1  0  0  0  0
 26 49  1  1  0  0  0
 27 50  1  6  0  0  0
 28 51  1  1  0  0  0
 29 52  1  6  0  0  0
 30 53  1  1  0  0  0
 31 54  1  6  0  0  0
 35 55  1  4  0  0  0
 56 36  2  0  0  0  0
 57 18  1  0  0  0  0
 57 37  1  0  0  0  0
 58 19  1  0  0  0  0
 58 39  1  0  0  0  0
 59 21  1  0  0  0  0
 40 59  1  1  0  0  0
 60 22  1  0  0  0  0
 60 38  1  0  0  0  0
 61 23  1  0  0  0  0
 61 40  1  0  0  0  0
 32 62  1  6  0  0  0
 37 62  1  6  0  0  0
 33 63  1  6  0  0  0
 39 63  1  1  0  0  0
 34 64  1  1  0  0  0
 38 64  1  1  0  0  0
 17 65  1  1  0  0  0
 18 66  1  6  0  0  0
 22 67  1  1  0  0  0
 23 68  1  1  0  0  0
 24 69  1  6  0  0  0
 25 70  1  1  0  0  0
 26 71  1  6  0  0  0
 27 72  1  6  0  0  0
 28 73  1  6  0  0  0
 29 74  1  1  0  0  0
 30 75  1  6  0  0  0
 31 76  1  1  0  0  0
 32 77  1  6  0  0  0
 33 78  1  6  0  0  0
 34 79  1  1  0  0  0
 37 80  1  1  0  0  0
 38 81  1  6  0  0  0
 39 82  1  6  0  0  0
 40 83  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0021034

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](C)(N)C(O)=N[C@@]1([H])[C@@]([H])(O[C@@]2([H])[C@]([H])(CO)O[C@@]([H])(O[C@]3([H])[C@@]([H])(O)C(=C)O[C@@]([H])(O[C@@]4([H])[C@]([H])(CO)O[C@@]([H])(OC5=CC=C(C=C5)C(=O)NCCCNCCCCN)[C@@]4([H])O)[C@]3([H])O)[C@]([H])(O)[C@@]2([H])O)O[C@]([H])(C)[C@]([H])(N)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C40H66N6O18/c1-17(42)35(55)46-25-27(50)24(43)18(2)57-37(25)62-32-22(15-47)60-38(29(52)28(32)51)64-34-26(49)19(3)58-39(31(34)54)63-33-23(16-48)61-40(30(33)53)59-21-9-7-20(8-10-21)36(56)45-14-6-13-44-12-5-4-11-41/h7-10,17-18,22-34,37-40,44,47-54H,3-6,11-16,41-43H2,1-2H3,(H,45,56)(H,46,55)/t17-,18-,22+,23+,24+,25-,26+,27+,28-,29-,30+,31-,32+,33+,34-,37-,38+,39+,40-/m1/s1

> <INCHI_KEY>
PGEKDAOSVRPCSY-AMGOUKICSA-N

> <FORMULA>
C40H66N6O18

> <MOLECULAR_WEIGHT>
918.992

> <EXACT_MASS>
918.443359309

> <JCHEM_ACCEPTOR_COUNT>
23

> <JCHEM_ATOM_COUNT>
130

> <JCHEM_AVERAGE_POLARIZABILITY>
97.02617183146016

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
14

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-N-[(2R,3R,4S,5R,6R)-5-amino-2-{[(2S,3R,4R,5R,6S)-6-{[(2R,3R,4R,5R)-2-{[(2S,3R,4S,5S)-5-[4-({3-[(4-aminobutyl)amino]propyl}carbamoyl)phenoxy]-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}-3,5-dihydroxy-6-methylideneoxan-4-yl]oxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy}-4-hydroxy-6-methyloxan-3-yl]propanimidic acid

> <ALOGPS_LOGP>
-0.82

> <JCHEM_LOGP>
-7.627035396044565

> <ALOGPS_LOGS>
-2.53

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_PKA>
11.891496196380244

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.296162765353256

> <JCHEM_PKA_STRONGEST_BASIC>
10.691862405552113

> <JCHEM_POLAR_SURFACE_AREA>
387.46000000000015

> <JCHEM_REFRACTIVITY>
218.87600000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
21

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.74e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-amino-N-[(2R,3R,4S,5R,6R)-5-amino-2-{[(2S,3R,4R,5R,6S)-6-{[(2R,3R,4R,5R)-2-{[(2S,3R,4S,5S)-5-[4-({3-[(4-aminobutyl)amino]propyl}carbamoyl)phenoxy]-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}-3,5-dihydroxy-6-methylideneoxan-4-yl]oxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy}-4-hydroxy-6-methyloxan-3-yl]propanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0     -37.331  25.342   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -27.863  23.655   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -24.242  18.672   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.378  15.319   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.712  14.549   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -9.046  14.549   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -15.715  15.319   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -14.381  13.009   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -17.048  14.549   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -15.715  12.239   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.044  14.549   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -5.045  15.319   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -7.713  15.319   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -10.380  15.319   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -29.116  20.842   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -22.009  16.268   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -36.426  24.097   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -29.395  23.495   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0     -24.869  17.265   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0     -14.381  14.549   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -17.048  13.009   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0     -29.742  19.435   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0     -21.383  14.861   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -30.300  24.740   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -32.458  23.173   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -26.400  17.104   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -31.831  24.579   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -31.900  17.867   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -30.995  16.621   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -21.123  12.383   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -26.121  14.451   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -31.274  19.274   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -22.153  13.527   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -27.027  15.697   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -34.894  24.257   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -13.047  15.319   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -31.553  21.927   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -29.463  16.782   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -24.590  14.612   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -19.716  13.009   0.000  0.00  0.00           C+0
HETATM   41  N   UNK     0       0.289  15.319   0.000  0.00  0.00           N+0
HETATM   42  N   UNK     0     -37.052  22.690   0.000  0.00  0.00           N+0
HETATM   43  N   UNK     0     -29.673  26.147   0.000  0.00  0.00           N+0
HETATM   44  N   UNK     0      -6.379  14.549   0.000  0.00  0.00           N+0
HETATM   45  N   UNK     0     -11.714  14.549   0.000  0.00  0.00           N+0
HETATM   46  N   UNK     0     -33.989  23.012   0.000  0.00  0.00           N+0
HETATM   47  O   UNK     0     -27.584  21.003   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0     -21.104  17.514   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0     -27.305  18.350   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0     -32.737  25.825   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0     -33.432  17.706   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0     -31.621  15.214   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0     -21.443  10.877   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0     -26.748  13.045   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0     -34.268  25.664   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0     -13.047  16.859   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0     -30.021  22.088   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0     -23.963  16.019   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0     -18.382  12.239   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0     -28.837  18.189   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0     -19.877  14.541   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0     -32.179  20.520   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0     -23.685  13.366   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0     -28.558  15.536   0.000  0.00  0.00           O+0
HETATM   65  H   UNK     0     -35.800  25.503   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0     -28.768  24.901   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0     -30.647  20.681   0.000  0.00  0.00           H+0
HETATM   68  H   UNK     0     -22.921  14.942   0.000  0.00  0.00           H+0
HETATM   69  H   UNK     0     -31.205  25.986   0.000  0.00  0.00           H+0
HETATM   70  H   UNK     0     -33.363  24.418   0.000  0.00  0.00           H+0
HETATM   71  H   UNK     0     -27.932  16.943   0.000  0.00  0.00           H+0
HETATM   72  H   UNK     0     -30.926  23.334   0.000  0.00  0.00           H+0
HETATM   73  H   UNK     0     -32.805  19.113   0.000  0.00  0.00           H+0
HETATM   74  H   UNK     0     -32.526  16.460   0.000  0.00  0.00           H+0
HETATM   75  H   UNK     0     -22.610  11.984   0.000  0.00  0.00           H+0
HETATM   76  H   UNK     0     -27.653  14.290   0.000  0.00  0.00           H+0
HETATM   77  H   UNK     0     -30.369  18.028   0.000  0.00  0.00           H+0
HETATM   78  H   UNK     0     -20.622  13.688   0.000  0.00  0.00           H+0
HETATM   79  H   UNK     0     -25.495  15.858   0.000  0.00  0.00           H+0
HETATM   80  H   UNK     0     -33.084  21.766   0.000  0.00  0.00           H+0
HETATM   81  H   UNK     0     -30.090  15.375   0.000  0.00  0.00           H+0
HETATM   82  H   UNK     0     -25.216  13.205   0.000  0.00  0.00           H+0
HETATM   83  H   UNK     0     -19.796  11.471   0.000  0.00  0.00           H+0
CONECT    1   17                                                            
CONECT    2   18                                                            
CONECT    3   19                                                            
CONECT    4    5   11                                                       
CONECT    5    4   12                                                       
CONECT    6   13   14                                                       
CONECT    7    9   20                                                       
CONECT    8   10   20                                                       
CONECT    9    7   21                                                       
CONECT   10    8   21                                                       
CONECT   11    4   41                                                       
CONECT   12    5   44                                                       
CONECT   13    6   44                                                       
CONECT   14    6   45                                                       
CONECT   15   22   47                                                       
CONECT   16   23   48                                                       
CONECT   17    1   35   42   65                                             
CONECT   18    2   24   57   66                                             
CONECT   19    3   26   58                                                  
CONECT   20    7    8   36                                                  
CONECT   21    9   10   59                                                  
CONECT   22   15   32   60   67                                             
CONECT   23   16   33   61   68                                             
CONECT   24   18   27   43   69                                             
CONECT   25   27   37   46   70                                             
CONECT   26   19   34   49   71                                             
CONECT   27   24   25   50   72                                             
CONECT   28   29   32   51   73                                             
CONECT   29   28   38   52   74                                             
CONECT   30   33   40   53   75                                             
CONECT   31   34   39   54   76                                             
CONECT   32   22   28   62   77                                             
CONECT   33   23   30   63   78                                             
CONECT   34   26   31   64   79                                             
CONECT   35   17   46   55                                                  
CONECT   36   20   45   56                                                  
CONECT   37   25   57   62   80                                             
CONECT   38   29   60   64   81                                             
CONECT   39   31   58   63   82                                             
CONECT   40   30   59   61   83                                             
CONECT   41   11                                                            
CONECT   42   17                                                            
CONECT   43   24                                                            
CONECT   44   12   13                                                       
CONECT   45   14   36                                                       
CONECT   46   25   35                                                       
CONECT   47   15                                                            
CONECT   48   16                                                            
CONECT   49   26                                                            
CONECT   50   27                                                            
CONECT   51   28                                                            
CONECT   52   29                                                            
CONECT   53   30                                                            
CONECT   54   31                                                            
CONECT   55   35                                                            
CONECT   56   36                                                            
CONECT   57   18   37                                                       
CONECT   58   19   39                                                       
CONECT   59   21   40                                                       
CONECT   60   22   38                                                       
CONECT   61   23   40                                                       
CONECT   62   32   37                                                       
CONECT   63   33   39                                                       
CONECT   64   34   38                                                       
CONECT   65   17                                                            
CONECT   66   18                                                            
CONECT   67   22                                                            
CONECT   68   23                                                            
CONECT   69   24                                                            
CONECT   70   25                                                            
CONECT   71   26                                                            
CONECT   72   27                                                            
CONECT   73   28                                                            
CONECT   74   29                                                            
CONECT   75   30                                                            
CONECT   76   31                                                            
CONECT   77   32                                                            
CONECT   78   33                                                            
CONECT   79   34                                                            
CONECT   80   37                                                            
CONECT   81   38                                                            
CONECT   82   39                                                            
CONECT   83   40                                                            
MASTER        0    0    0    0    0    0    0    0   83    0  174    0
END

Synonyms

Not Available

Molecular Formula

C₄₀H₆₆N₆O₁₈

Average Mass

918.992

Monoisotopic Mass

918.443359309

IUPAC Name

(2R)-2-amino-N-[(2R,3R,4S,5R,6R)-5-amino-2-{[(2S,3R,4R,5R,6S)-6-{[(2R,3R,4R,5R)-2-{[(2S,3R,4S,5S)-5-[4-({3-[(4-aminobutyl)amino]propyl}carbamoyl)phenoxy]-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}-3,5-dihydroxy-6-methylideneoxan-4-yl]oxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy}-4-hydroxy-6-methyloxan-3-yl]propanimidic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@](C)(N)C(O)=N[C@@]1([H])[C@@]([H])(O[C@@]2([H])[C@]([H])(CO)O[C@@]([H])(O[C@]3([H])[C@@]([H])(O)C(=C)O[C@@]([H])(O[C@@]4([H])[C@]([H])(CO)O[C@@]([H])(OC5=CC=C(C=C5)C(=O)NCCCNCCCCN)[C@@]4([H])O)[C@]3([H])O)[C@]([H])(O)[C@@]2([H])O)O[C@]([H])(C)[C@]([H])(N)[C@]1([H])O

InChI Identifier

InChI=1S/C40H66N6O18/c1-17(42)35(55)46-25-27(50)24(43)18(2)57-37(25)62-32-22(15-47)60-38(29(52)28(32)51)64-34-26(49)19(3)58-39(31(34)54)63-33-23(16-48)61-40(30(33)53)59-21-9-7-20(8-10-21)36(56)45-14-6-13-44-12-5-4-11-41/h7-10,17-18,22-34,37-40,44,47-54H,3-6,11-16,41-43H2,1-2H3,(H,45,56)(H,46,55)/t17-,18-,22+,23+,24+,25-,26+,27+,28-,29-,30+,31-,32+,33+,34-,37-,38+,39+,40-/m1/s1

InChI Key

PGEKDAOSVRPCSY-AMGOUKICSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminoglycosides

Alternative Parents

Substituents

Aminoglycoside core
Phenolic glycoside
O-glycosyl compound
Glycosyl compound
Disaccharide
Benzoic acid or derivatives
Benzamide
Phenoxy compound
Phenol ether
Benzoyl
Benzenoid
Oxane
Monocyclic benzene moiety
Tetrahydrofuran
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Amino acid or derivatives
1,2-aminoalcohol
Oxacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Secondary amine
Secondary aliphatic amine
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Acetal
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organonitrogen compound
Primary aliphatic amine
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.74 g/L	ALOGPS
logP	-0.82	ALOGPS
logP	-7.6	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	3.3	ChemAxon
pKa (Strongest Basic)	10.69	ChemAxon
Physiological Charge	4	ChemAxon
Hydrogen Acceptor Count	23	ChemAxon
Hydrogen Donor Count	14	ChemAxon
Polar Surface Area	387.46 Å²	ChemAxon
Rotatable Bond Count	21	ChemAxon
Refractivity	218.88 m³·mol⁻¹	ChemAxon
Polarizability	97.03 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	1	Human	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78443098

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139589104

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Glysperin B (MMDBc0021034)

MOL for #<Metabolite:0x00007f46e16a3608>

3D MOL for #<Metabolite:0x00007f46e16a3608>

3D SDF for #<Metabolite:0x00007f46e16a3608>

3D-SDF for #<Metabolite:0x00007f46e16a3608>

PDB for #<Metabolite:0x00007f46e16a3608>

3D PDB for #<Metabolite:0x00007f46e16a3608>

SMILES for #<Metabolite:0x00007f46e16a3608>

INCHI for #<Metabolite:0x00007f46e16a3608>

Structure for #<Metabolite:0x00007f46e16a3608>

3D Structure for #<Metabolite:0x00007f46e16a3608>