MiMeDB: Showing metabocard for kanamycin 3'-phosphate (MMDBc0056048)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:14:15 UTC

Update Date

2022-08-12 20:09:33 UTC

Metabolite ID

MMDBc0056048

Metabolite Identification

Common Name

kanamycin 3'-phosphate

Description

kanamycin A 3'-phosphate(2+), also known as kanamycin 3'-phosphoric acid, belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines. Based on a literature review very few articles have been published on kanamycin A 3'-phosphate(2+).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222142D          

 52 54  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
   -3.5724    1.2375    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
   -0.7145    3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 C   0  0  1  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
   -1.4289    5.7750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    5.7750    0.0000 C   0  0  1  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    0.0000    0.0000 C   0  0  2  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
   -1.4289    2.4750    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    3.3000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
   -2.1434    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
   -3.5724    2.0625    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 N   0  3  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
   -3.5724    6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    7.0125    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   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    4.5375    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
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164   -0.9355    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
   -1.4289    4.9500    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
   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 P   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
   -3.5724    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    6.6000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    6.6000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    5.3625    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
   -3.5724    5.3625    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   -0.8250    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
   -1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    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
  9  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 14  4  1  0  0  0  0
 14 12  1  0  0  0  0
 15  5  1  0  0  0  0
 15 12  1  0  0  0  0
 16 10  1  0  0  0  0
 16 13  1  0  0  0  0
 17 11  1  0  0  0  0
 18 13  1  0  0  0  0
 19  2  1  0  0  0  0
  4 20  1  6  0  0  0
  5 21  1  6  0  0  0
  8 22  1  1  0  0  0
 23  3  1  0  0  0  0
  9 24  1  1  0  0  0
 10 25  1  6  0  0  0
 11 26  1  6  0  0  0
 12 27  1  6  0  0  0
 13 28  1  6  0  0  0
 32  6  1  0  0  0  0
 32 18  1  0  0  0  0
 33  7  1  0  0  0  0
 33 17  1  0  0  0  0
 14 34  1  6  0  0  0
 17 34  1  6  0  0  0
 15 35  1  1  0  0  0
 18 35  1  6  0  0  0
 16 36  1  6  0  0  0
 37 29  1  0  0  0  0
 37 30  1  0  0  0  0
 37 31  2  0  0  0  0
 37 36  1  0  0  0  0
  4 38  1  1  0  0  0
  5 39  1  1  0  0  0
  6 40  1  6  0  0  0
  7 41  1  6  0  0  0
  8 42  1  6  0  0  0
  9 43  1  1  0  0  0
 10 44  1  1  0  0  0
 11 45  1  1  0  0  0
 12 46  1  1  0  0  0
 13 47  1  1  0  0  0
 14 48  1  6  0  0  0
 15 49  1  6  0  0  0
 16 50  1  6  0  0  0
 17 51  1  1  0  0  0
 18 52  1  1  0  0  0
M  CHG  2  19   1  20   1
M  END


  Mrv1652306172222142D          

 52 54  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
   -3.5724    1.2375    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
   -0.7145    3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 C   0  0  1  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
   -1.4289    5.7750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    5.7750    0.0000 C   0  0  1  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    0.0000    0.0000 C   0  0  2  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
   -1.4289    2.4750    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    3.3000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
   -2.1434    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
   -3.5724    2.0625    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 N   0  3  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
   -3.5724    6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    7.0125    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   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    4.5375    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
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164   -0.9355    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
   -1.4289    4.9500    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
   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 P   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
   -3.5724    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    6.6000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    6.6000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    5.3625    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
   -3.5724    5.3625    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   -0.8250    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
   -1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    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
  9  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 14  4  1  0  0  0  0
 14 12  1  0  0  0  0
 15  5  1  0  0  0  0
 15 12  1  0  0  0  0
 16 10  1  0  0  0  0
 16 13  1  0  0  0  0
 17 11  1  0  0  0  0
 18 13  1  0  0  0  0
 19  2  1  0  0  0  0
  4 20  1  6  0  0  0
  5 21  1  6  0  0  0
  8 22  1  1  0  0  0
 23  3  1  0  0  0  0
  9 24  1  1  0  0  0
 10 25  1  6  0  0  0
 11 26  1  6  0  0  0
 12 27  1  6  0  0  0
 13 28  1  6  0  0  0
 32  6  1  0  0  0  0
 32 18  1  0  0  0  0
 33  7  1  0  0  0  0
 33 17  1  0  0  0  0
 14 34  1  6  0  0  0
 17 34  1  6  0  0  0
 15 35  1  1  0  0  0
 18 35  1  6  0  0  0
 16 36  1  6  0  0  0
 37 29  1  0  0  0  0
 37 30  1  0  0  0  0
 37 31  2  0  0  0  0
 37 36  1  0  0  0  0
  4 38  1  1  0  0  0
  5 39  1  1  0  0  0
  6 40  1  6  0  0  0
  7 41  1  6  0  0  0
  8 42  1  6  0  0  0
  9 43  1  1  0  0  0
 10 44  1  1  0  0  0
 11 45  1  1  0  0  0
 12 46  1  1  0  0  0
 13 47  1  1  0  0  0
 14 48  1  6  0  0  0
 15 49  1  6  0  0  0
 16 50  1  6  0  0  0
 17 51  1  1  0  0  0
 18 52  1  1  0  0  0
M  CHG  2  19   1  20   1
M  END
> <DATABASE_ID>
MMDBc0056048

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(N)C[C@@]([H])([NH3+])[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])(C[NH3+])[C@@]([H])(O)[C@]([H])(OP(O)(O)=O)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C18H37N4O14P/c19-2-6-10(25)16(36-37(29,30)31)13(28)18(32-6)35-15-5(21)1-4(20)14(12(15)27)34-17-11(26)8(22)9(24)7(3-23)33-17/h4-18,23-28H,1-3,19-22H2,(H2,29,30,31)/p+2/t4-,5+,6-,7-,8+,9-,10-,11-,12-,13-,14+,15-,16+,17-,18-/m1/s1

> <INCHI_KEY>
BYGWYFIZOSNIDM-CAFUKSGOSA-P

> <FORMULA>
C18H39N4O14P

> <MOLECULAR_WEIGHT>
566.497

> <EXACT_MASS>
566.21894179

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
52.288356657325494

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,3S,4R,5S)-5-amino-2-{[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2R,3R,4S,5R,6R)-6-(azaniumylmethyl)-3,5-dihydroxy-4-(phosphonooxy)oxan-2-yl]oxy}-3-hydroxycyclohexan-1-aminium

> <JCHEM_LOGP>
-9.56607142762064

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
6.111832837028749

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0960978102851096

> <JCHEM_PKA_STRONGEST_BASIC>
9.610713139492594

> <JCHEM_POLAR_SURFACE_AREA>
332.38000000000005

> <JCHEM_REFRACTIVITY>
139.59299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,3S,4R,5S)-5-amino-2-{[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2R,3R,4S,5R,6R)-6-(ammoniomethyl)-3,5-dihydroxy-4-(phosphonooxy)oxan-2-yl]oxy}-3-hydroxycyclohexan-1-aminium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  11.550   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.000   4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667  10.780   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.335  10.780   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.001  11.550   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.335   9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.001   8.470   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      -6.668   3.850   0.000  0.00  0.00           N+1
HETATM   20  N   UNK     0      -1.334   8.470   0.000  0.00  0.00           N+1
HETATM   21  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0      -6.668  11.550   0.000  0.00  0.00           N+0
HETATM   23  O   UNK     0      -1.334  13.090   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -4.001  13.090   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -6.668   8.470   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -4.001   3.850   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -1.334  -3.850   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -3.437  -4.414   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -1.897  -1.746   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -2.667   9.240   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -4.001   6.930   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   37  P   UNK     0      -2.667  -3.080   0.000  0.00  0.00           P+0
HETATM   38  H   UNK     0      -2.667   7.700   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0      -0.000   3.080   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0      -6.668   0.770   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0      -2.667  12.320   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0      -5.335  12.320   0.000  0.00  0.00           H+0
HETATM   43  H   UNK     0      -4.001  10.010   0.000  0.00  0.00           H+0
HETATM   44  H   UNK     0      -5.335  -1.540   0.000  0.00  0.00           H+0
HETATM   45  H   UNK     0      -6.668  10.010   0.000  0.00  0.00           H+0
HETATM   46  H   UNK     0      -4.001   5.390   0.000  0.00  0.00           H+0
HETATM   47  H   UNK     0      -2.667  -1.540   0.000  0.00  0.00           H+0
HETATM   48  H   UNK     0      -1.334   5.390   0.000  0.00  0.00           H+0
HETATM   49  H   UNK     0      -2.667   3.080   0.000  0.00  0.00           H+0
HETATM   50  H   UNK     0      -4.001   0.770   0.000  0.00  0.00           H+0
HETATM   51  H   UNK     0      -5.335   7.700   0.000  0.00  0.00           H+0
HETATM   52  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
CONECT    1    4    5                                                       
CONECT    2    6   19                                                       
CONECT    3    7   23                                                       
CONECT    4    1   14   20   38                                             
CONECT    5    1   15   21   39                                             
CONECT    6    2   10   32   40                                             
CONECT    7    3    9   33   41                                             
CONECT    8    9   11   22   42                                             
CONECT    9    7    8   24   43                                             
CONECT   10    6   16   25   44                                             
CONECT   11    8   17   26   45                                             
CONECT   12   14   15   27   46                                             
CONECT   13   16   18   28   47                                             
CONECT   14    4   12   34   48                                             
CONECT   15    5   12   35   49                                             
CONECT   16   10   13   36   50                                             
CONECT   17   11   33   34   51                                             
CONECT   18   13   32   35   52                                             
CONECT   19    2                                                            
CONECT   20    4                                                            
CONECT   21    5                                                            
CONECT   22    8                                                            
CONECT   23    3                                                            
CONECT   24    9                                                            
CONECT   25   10                                                            
CONECT   26   11                                                            
CONECT   27   12                                                            
CONECT   28   13                                                            
CONECT   29   37                                                            
CONECT   30   37                                                            
CONECT   31   37                                                            
CONECT   32    6   18                                                       
CONECT   33    7   17                                                       
CONECT   34   14   17                                                       
CONECT   35   15   18                                                       
CONECT   36   16   37                                                       
CONECT   37   29   30   31   36                                             
CONECT   38    4                                                            
CONECT   39    5                                                            
CONECT   40    6                                                            
CONECT   41    7                                                            
CONECT   42    8                                                            
CONECT   43    9                                                            
CONECT   44   10                                                            
CONECT   45   11                                                            
CONECT   46   12                                                            
CONECT   47   13                                                            
CONECT   48   14                                                            
CONECT   49   15                                                            
CONECT   50   16                                                            
CONECT   51   17                                                            
CONECT   52   18                                                            
MASTER        0    0    0    0    0    0    0    0   52    0  108    0
END

Synonyms

Value	Source
Kanamycin 3'-phosphate	ChEBI
Kanamycin a 3'-phosphate dication	ChEBI
Kanamycin 3'-phosphoric acid	Generator
Kanamycin a 3'-phosphoric acid dication	Generator
Kanamycin a 3'-phosphoric acid(2+)	Generator

Molecular Formula

C₁₈H₃₉N₄O₁₄P

Average Mass

566.497

Monoisotopic Mass

566.21894179

IUPAC Name

(1R,2S,3S,4R,5S)-5-amino-2-{[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2R,3R,4S,5R,6R)-6-(azaniumylmethyl)-3,5-dihydroxy-4-(phosphonooxy)oxan-2-yl]oxy}-3-hydroxycyclohexan-1-aminium

Traditional Name

(1R,2S,3S,4R,5S)-5-amino-2-{[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2R,3R,4S,5R,6R)-6-(ammoniomethyl)-3,5-dihydroxy-4-(phosphonooxy)oxan-2-yl]oxy}-3-hydroxycyclohexan-1-aminium

CAS Registry Number

Not Available

SMILES

[H][C@]1(N)C[C@@]([H])([NH3+])[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])(C[NH3+])[C@@]([H])(O)[C@]([H])(OP(O)(O)=O)[C@@]1([H])O

InChI Identifier

InChI=1S/C18H37N4O14P/c19-2-6-10(25)16(36-37(29,30)31)13(28)18(32-6)35-15-5(21)1-4(20)14(12(15)27)34-17-11(26)8(22)9(24)7(3-23)33-17/h4-18,23-28H,1-3,19-22H2,(H2,29,30,31)/p+2/t4-,5+,6-,7-,8+,9-,10-,11-,12-,13-,14+,15-,16+,17-,18-/m1/s1

InChI Key

BYGWYFIZOSNIDM-CAFUKSGOSA-P

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminocyclitol glycosides

Alternative Parents

Substituents

Amino cyclitol glycoside
Glycosyl compound
O-glycosyl compound
Aminocyclitol or derivatives
Cyclohexanol
Cyclohexylamine
Cyclitol or derivatives
Monosaccharide
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Alkyl phosphate
Cyclic alcohol
Secondary alcohol
1,2-aminoalcohol
Organoheterocyclic compound
Acetal
Oxacycle
Organic nitrogen compound
Primary amine
Primary aliphatic amine
Hydrocarbon derivative
Organic oxide
Alcohol
Organonitrogen compound
Organopnictogen compound
Amine
Primary alcohol
Organic cation
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

ammonium ion (CHEBI:57909 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-9.6	ChemAxon
pKa (Strongest Acidic)	1.1	ChemAxon
pKa (Strongest Basic)	9.61	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	12	ChemAxon
Polar Surface Area	332.38 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	139.59 m³·mol⁻¹	ChemAxon
Polarizability	52.29 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

Not Available

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
Bacteria	Proteobacteria	5	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Human sputum; Human subgingival plaque
Bacteria	Firmicutes	4	Human ; Human feces; Human subgingival plaque; Human saliva
Bacteria	Actinobacteria	2

Exposure Sources

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

26330962

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

49791946

PDB ID

Not Available

ChEBI ID

57909

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 3'-phosphate (MMDBc0056048)

MOL for #<Metabolite:0x00007fdb4d4412b0>

3D MOL for #<Metabolite:0x00007fdb4d4412b0>

3D SDF for #<Metabolite:0x00007fdb4d4412b0>

3D-SDF for #<Metabolite:0x00007fdb4d4412b0>

PDB for #<Metabolite:0x00007fdb4d4412b0>

3D PDB for #<Metabolite:0x00007fdb4d4412b0>

SMILES for #<Metabolite:0x00007fdb4d4412b0>

INCHI for #<Metabolite:0x00007fdb4d4412b0>

Structure for #<Metabolite:0x00007fdb4d4412b0>

3D Structure for #<Metabolite:0x00007fdb4d4412b0>