MiMeDB: Showing metabocard for Kanamycin B (MMDBc0018784)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 08:57:02 UTC

Update Date

2024-10-15 20:19:23 UTC

Metabolite ID

MMDBc0018784

Metabolite Identification

Common Name

Kanamycin B

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05031423212D          

 48 50  0  0  1  0            999 V2000
   -0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    5.7750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579    4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434    6.1875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    5.7750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434    4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    7.0125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    4.5375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    4.1250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7111    6.5502    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3882    0.1930    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    5.0933    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    0.1433    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6131    6.8195    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    5.6317    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.8875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.1250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    4.1250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  1  0  0  0
  7  3  1  1  0  0  0
 10  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  6  1  0  0  0  0
 12  9  1  0  0  0  0
 12 11  1  0  0  0  0
 13  8  1  0  0  0  0
 15  4  1  0  0  0  0
 15 14  1  0  0  0  0
 16  5  1  0  0  0  0
 16 14  1  0  0  0  0
 17  9  1  0  0  0  0
 18 13  1  0  0  0  0
 19  2  1  0  0  0  0
  4 20  1  1  0  0  0
  5 21  1  1  0  0  0
  8 22  1  1  0  0  0
  9 23  1  6  0  0  0
 24  3  1  0  0  0  0
 10 25  1  6  0  0  0
 11 26  1  6  0  0  0
 12 27  1  1  0  0  0
 13 28  1  6  0  0  0
 14 29  1  1  0  0  0
 30  6  1  0  0  0  0
 30 17  1  0  0  0  0
 31  7  1  0  0  0  0
 31 18  1  0  0  0  0
 15 32  1  6  0  0  0
 17 32  1  6  0  0  0
 16 33  1  6  0  0  0
 18 33  1  6  0  0  0
  4 34  1  6  0  0  0
  5 35  1  6  0  0  0
  6 36  1  6  0  0  0
  7 37  1  6  0  0  0
  8 38  1  6  0  0  0
  9 39  1  1  0  0  0
 10 40  1  1  0  0  0
 11 41  1  1  0  0  0
 12 42  1  6  0  0  0
 13 43  1  1  0  0  0
 14 44  1  6  0  0  0
 15 45  1  1  0  0  0
 16 46  1  1  0  0  0
 17 47  1  1  0  0  0
 18 48  1  1  0  0  0
M  END


  Mrv0541 05031423212D          

 48 50  0  0  1  0            999 V2000
   -0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    5.7750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579    4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434    6.1875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    5.7750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434    4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    7.0125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    4.5375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    4.1250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7111    6.5502    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3882    0.1930    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    5.0933    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    0.1433    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6131    6.8195    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    5.6317    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.8875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.1250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    4.1250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  1  0  0  0
  7  3  1  1  0  0  0
 10  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  6  1  0  0  0  0
 12  9  1  0  0  0  0
 12 11  1  0  0  0  0
 13  8  1  0  0  0  0
 15  4  1  0  0  0  0
 15 14  1  0  0  0  0
 16  5  1  0  0  0  0
 16 14  1  0  0  0  0
 17  9  1  0  0  0  0
 18 13  1  0  0  0  0
 19  2  1  0  0  0  0
  4 20  1  1  0  0  0
  5 21  1  1  0  0  0
  8 22  1  1  0  0  0
  9 23  1  6  0  0  0
 24  3  1  0  0  0  0
 10 25  1  6  0  0  0
 11 26  1  6  0  0  0
 12 27  1  1  0  0  0
 13 28  1  6  0  0  0
 14 29  1  1  0  0  0
 30  6  1  0  0  0  0
 30 17  1  0  0  0  0
 31  7  1  0  0  0  0
 31 18  1  0  0  0  0
 15 32  1  6  0  0  0
 17 32  1  6  0  0  0
 16 33  1  6  0  0  0
 18 33  1  6  0  0  0
  4 34  1  6  0  0  0
  5 35  1  6  0  0  0
  6 36  1  6  0  0  0
  7 37  1  6  0  0  0
  8 38  1  6  0  0  0
  9 39  1  1  0  0  0
 10 40  1  1  0  0  0
 11 41  1  1  0  0  0
 12 42  1  6  0  0  0
 13 43  1  1  0  0  0
 14 44  1  6  0  0  0
 15 45  1  1  0  0  0
 16 46  1  1  0  0  0
 17 47  1  1  0  0  0
 18 48  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0018784

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(N)C[C@@]([H])(N)[C@]([H])(O[C@@]2([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(N)[C@@]2([H])O)[C@@]([H])(O)[C@]1([H])O[C@@]1([H])O[C@]([H])(CN)[C@@]([H])(O)[C@]([H])(O)[C@@]1([H])N

> <INCHI_IDENTIFIER>
InChI=1S/C18H37N5O10/c19-2-6-11(26)12(27)9(23)17(30-6)32-15-4(20)1-5(21)16(14(15)29)33-18-13(28)8(22)10(25)7(3-24)31-18/h4-18,24-29H,1-3,19-23H2/t4-,5+,6+,7+,8-,9+,10+,11+,12+,13+,14-,15+,16-,17+,18+/m0/s1

> <INCHI_KEY>
SKKLOUVUUNMCJE-FQSMHNGLSA-N

> <FORMULA>
C18H37N5O10

> <MOLECULAR_WEIGHT>
483.5139

> <EXACT_MASS>
483.254042429

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
47.71634365313935

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-4-amino-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,4R,5S,6R)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,5-diol

> <ALOGPS_LOGP>
-3.01

> <JCHEM_LOGP>
-7.167795245666667

> <ALOGPS_LOGS>
-0.80

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA>
13.004888165599127

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.488072502607203

> <JCHEM_PKA_STRONGEST_BASIC>
9.760920681985683

> <JCHEM_POLAR_SURFACE_AREA>
288.4

> <JCHEM_REFRACTIVITY>
107.79199999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.59e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-4-amino-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,4R,5S,6R)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   24  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   34  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   43  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   44  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   45  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   46  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   47  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   48  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    4    5                                                       
CONECT    2    6   19                                                       
CONECT    3    7   24                                                       
CONECT    4    1   15   20   34                                             
CONECT    5    1   16   21   35                                             
CONECT    6    2   11   30   36                                             
CONECT    7    3   10   31   37                                             
CONECT    8   10   13   22   38                                             
CONECT    9   12   17   23   39                                             
CONECT   10    7    8   25   40                                             
CONECT   11    6   12   26   41                                             
CONECT   12    9   11   27   42                                             
CONECT   13    8   18   28   43                                             
CONECT   14   15   16   29   44                                             
CONECT   15    4   14   32   45                                             
CONECT   16    5   14   33   46                                             
CONECT   17    9   30   32   47                                             
CONECT   18   13   31   33   48                                             
CONECT   19    2                                                            
CONECT   20    4                                                            
CONECT   21    5                                                            
CONECT   22    8                                                            
CONECT   23    9                                                            
CONECT   24    3                                                            
CONECT   25   10                                                            
CONECT   26   11                                                            
CONECT   27   12                                                            
CONECT   28   13                                                            
CONECT   29   14                                                            
CONECT   30    6   17                                                       
CONECT   31    7   18                                                       
CONECT   32   15   17                                                       
CONECT   33   16   18                                                       
CONECT   34    4                                                            
CONECT   35    5                                                            
CONECT   36    6                                                            
CONECT   37    7                                                            
CONECT   38    8                                                            
CONECT   39    9                                                            
CONECT   40   10                                                            
CONECT   41   11                                                            
CONECT   42   12                                                            
CONECT   43   13                                                            
CONECT   44   14                                                            
CONECT   45   15                                                            
CONECT   46   16                                                            
CONECT   47   17                                                            
CONECT   48   18                                                            
MASTER        0    0    0    0    0    0    0    0   48    0  100    0
END

Synonyms

Value	Source
2'-Amino-2'-deoxykanamycin	ChEBI
Nebramycin factor 5	ChEBI
Nebramycin V	ChEBI
O-3-Amino-3-deoxy-alpha-D-glucopyranosyl-(1->4)-O-(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl-(1->6))-2-deoxy-D-streptamine	ChEBI
Kanamycin b	Kegg
O-3-Amino-3-deoxy-a-D-glucopyranosyl-(1->4)-O-(2,6-diamino-2,6-dideoxy-a-D-glucopyranosyl-(1->6))-2-deoxy-D-streptamine	Generator
O-3-Amino-3-deoxy-α-D-glucopyranosyl-(1->4)-O-(2,6-diamino-2,6-dideoxy-α-D-glucopyranosyl-(1->6))-2-deoxy-D-streptamine	Generator
Bekanamycin	ChEBI
Kanendomycin	MeSH
Bekanamycin sulfate (1:1)	MeSH
Aminodeoxykanamycin	MeSH
Bekanamycin sulfate	MeSH

Molecular Formula

C₁₈H₃₇N₅O₁₀

Average Mass

483.5139

Monoisotopic Mass

483.254042429

IUPAC Name

(2S,3R,4S,5S,6R)-4-amino-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,4R,5S,6R)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,5-diol

Traditional Name

(2S,3R,4S,5S,6R)-4-amino-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,4R,5S,6R)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,5-diol

CAS Registry Number

Not Available

SMILES

[H][C@]1(N)C[C@@]([H])(N)[C@]([H])(O[C@@]2([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(N)[C@@]2([H])O)[C@@]([H])(O)[C@]1([H])O[C@@]1([H])O[C@]([H])(CN)[C@@]([H])(O)[C@]([H])(O)[C@@]1([H])N

InChI Identifier

InChI=1S/C18H37N5O10/c19-2-6-11(26)12(27)9(23)17(30-6)32-15-4(20)1-5(21)16(14(15)29)33-18-13(28)8(22)10(25)7(3-24)31-18/h4-18,24-29H,1-3,19-23H2/t4-,5+,6+,7+,8-,9+,10+,11+,12+,13+,14-,15+,16-,17+,18+/m0/s1

InChI Key

SKKLOUVUUNMCJE-FQSMHNGLSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are glycosidically linked to a pyranose of furanose unit at the C4- and C6-positions.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

4,6-disubstituted 2-deoxystreptamines

Alternative Parents

Substituents

4,6-disubstituted 2-deoxystreptamine
Glycosyl compound
O-glycosyl compound
Aminocyclitol or derivatives
Cyclohexanol
Cyclohexylamine
Cyclitol or derivatives
Monosaccharide
Oxane
Cyclic alcohol
1,2-aminoalcohol
Secondary alcohol
Organoheterocyclic compound
Acetal
Oxacycle
Alcohol
Organonitrogen compound
Primary aliphatic amine
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Amine
Primary alcohol
Primary amine
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

kanamycins (CHEBI:28098 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	75.9 g/L	ALOGPS
logP	-3	ALOGPS
logP	-7.2	ChemAxon
logS	-0.8	ALOGPS
pKa (Strongest Acidic)	12.49	ChemAxon
pKa (Strongest Basic)	9.76	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	288.4 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	107.79 m³·mol⁻¹	ChemAxon
Polarizability	47.72 Å³	ChemAxon
Number of Rings	3	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 GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_5_244) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0aw9-0219800000-8bffd56b3f946b4cdee9	2016-08-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-08fr-0917100000-f152e80b7cd2e86983e6	2016-08-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08fv-5914000000-9311fd0d8e2f4f2007c8	2016-08-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001r-9366600000-242a7eebeb0e0273b309	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-006x-9536300000-520e4218f16dc8c4b90d	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0udi-5793000000-2ae8be694bf4f51aa2b2	2016-08-03	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	Proteobacteria	11	Human ; Human subgingival plaque; Human feces; Human sputum
Bacteria	Actinobacteria	1

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

DB13673

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00018692

Chemspider ID

Not Available

KEGG Compound ID

C00825

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Bekanamycin

METLIN ID

Not Available

PubChem Compound

439318

PDB ID

Not Available

ChEBI ID

28098

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for Kanamycin B (MMDBc0018784)

MOL for #<Metabolite:0x00007fab2ce515a8>

3D MOL for #<Metabolite:0x00007fab2ce515a8>

3D SDF for #<Metabolite:0x00007fab2ce515a8>

3D-SDF for #<Metabolite:0x00007fab2ce515a8>

PDB for #<Metabolite:0x00007fab2ce515a8>

3D PDB for #<Metabolite:0x00007fab2ce515a8>

SMILES for #<Metabolite:0x00007fab2ce515a8>

INCHI for #<Metabolite:0x00007fab2ce515a8>

Structure for #<Metabolite:0x00007fab2ce515a8>

3D Structure for #<Metabolite:0x00007fab2ce515a8>