NP-MRD: Showing NP-Card for Gentamicin A (NP0004840)

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Record Information

Version

2.0

Created at

2020-12-09 02:15:06 UTC

Updated at

2021-07-15 16:50:18 UTC

NP-MRD ID

NP0004840

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gentamicin A

Provided By

NPAtlas

Description

Gentamicin A is found in Apis cerana and Micromonospora. Based on a literature review very few articles have been published on (2R,3S,4R,5R,6S)-5-amino-6-{[(1R,2S,3S,4R,6S)-4,6-diamino-3-{[(2R,3R,4S,5S)-3,5-dihydroxy-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-2-(hydroxymethyl)oxane-3,4-diol.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118093D          

 68 70  0  0  0  0            999 V2000
    7.4366    0.0777    0.2471 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3817    0.9527   -0.1541 N   0  0  1  0  0  0  0  0  0  0  0  0
    5.0616    0.4094    0.1604 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0149    0.2864    1.6835 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2338   -0.7789    2.0937 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3672    1.5833    2.1603 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0217    1.5914    1.8623 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7147    1.2350    0.5826 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2488   -0.0279    0.3876 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0905   -0.1739   -0.3000 C   0  0  2  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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  8  9  1  0  0  0  0
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M  END

     RDKit          3D

 68 70  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652306242118093D          

 68 70  0  0  0  0            999 V2000
    7.4366    0.0777    0.2471 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3817    0.9527   -0.1541 N   0  0  1  0  0  0  0  0  0  0  0  0
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    4.2338   -0.7789    2.0937 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3672    1.5833    2.1603 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0217    1.5914    1.8623 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7147    1.2350    0.5826 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2488   -0.0279    0.3876 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0905   -0.1739   -0.3000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0699   -0.7143    0.5408 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3328    0.0761    1.6388 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2327   -0.8133   -0.4195 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4640   -0.6848    0.1570 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2404    0.3506   -0.3062 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.4284   -0.1640   -0.7548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3465   -0.5827    0.1389 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.7343   -0.0256   -0.2415 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.1365   -0.4342   -1.4900 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1222   -0.4150    1.5832 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.2032   -1.6370    2.2904 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9036    0.3741    1.9940 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0538    1.0339    3.1878 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5770    1.2893    0.8348 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5630    2.2430    1.1189 N   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0479   -2.1010   -1.1933 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9326   -2.1665   -2.3255 N   0  0  1  0  0  0  0  0  0  0  0  0
    0.4011   -2.2539   -1.5359 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1625   -0.9569   -1.5618 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6502   -0.2102   -2.7223 N   0  0  1  0  0  0  0  0  0  0  0  0
    3.9869    1.3904   -0.2596 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6813    1.0998   -1.6021 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1994    0.0300   -0.5733 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8978    0.3348    1.2275 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.9858   -0.5639   -0.3419 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.7146   -1.6415    2.0804 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.9121    2.4614    1.7737 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7470    0.8678   -0.5770 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2271   -1.7361    0.8319 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0740    0.9763    1.5816 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.7542    0.9503   -1.0995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4717   -1.6974   -0.0439 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.7325    1.0875   -0.2256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4069   -0.6503   -2.1051 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.7149   -2.3584    1.8419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0624   -0.3421    2.0905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0051    1.0194    3.5174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5245    1.8488    0.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9297    3.2376    1.0981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1234    2.1469    2.0580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3701   -2.9216   -0.5018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0614   -1.2624   -2.8290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7884   -2.9851   -2.9245 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4401   -2.6577   -2.5907 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8446   -3.0195   -0.9004 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2156   -1.2271   -1.8584 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4085    0.4068   -3.0913 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3788   -0.8632   -3.4899 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3917    2.4248   -0.1933 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1105    1.8043   -1.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
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 11 13  1  0  0  0  0
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 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 13 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
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 29 30  1  0  0  0  0
  8 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31  3  1  0  0  0  0
 29 10  1  0  0  0  0
 24 15  1  0  0  0  0
  1 33  1  0  0  0  0
  1 34  1  0  0  0  0
  1 35  1  0  0  0  0
  2 36  1  0  0  0  0
  3 37  1  6  0  0  0
  4 38  1  1  0  0  0
  5 39  1  0  0  0  0
  6 40  1  0  0  0  0
  6 41  1  0  0  0  0
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 30 66  1  0  0  0  0
 31 67  1  6  0  0  0
 32 68  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0004840

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])O[C@]([H])(O[C@@]2([H])[C@]([H])(O[H])[C@@]([H])(O[C@@]3([H])OC([H])([H])[C@@]([H])(O[H])[C@]([H])(N([H])C([H])([H])[H])[C@@]3([H])O[H])[C@]([H])(N([H])[H])C([H])([H])[C@]2([H])N([H])[H])[C@]([H])(N([H])[H])[C@@]([H])(O[H])[C@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C18H36N4O10/c1-22-10-7(24)4-29-18(13(10)27)32-16-6(20)2-5(19)15(14(16)28)31-17-9(21)12(26)11(25)8(3-23)30-17/h5-18,22-28H,2-4,19-21H2,1H3/t5-,6+,7+,8+,9+,10-,11+,12+,13+,14-,15+,16-,17+,18+/m0/s1

> <INCHI_KEY>
LKKVGKXCMYHKSL-QVNYEEQUSA-N

> <FORMULA>
C18H36N4O10

> <MOLECULAR_WEIGHT>
468.504

> <EXACT_MASS>
468.243143375

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
46.15566262968318

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.67

> <JCHEM_LOGP>
-5.997998113333334

> <ALOGPS_LOGS>
-0.67

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_PKA>
12.920493247812498

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.426138476213985

> <JCHEM_PKA_STRONGEST_BASIC>
9.538845804738667

> <JCHEM_POLAR_SURFACE_AREA>
248.39000000000001

> <JCHEM_REFRACTIVITY>
104.9466

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.00e+02 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 68 70  0  0  0  0  0  0  0  0999 V2000
    7.4366    0.0777    0.2471 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3817    0.9527   -0.1541 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0616    0.4094    0.1604 C   0  0  1  0  0  0  0  0  0  0  0  0
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    4.2338   -0.7789    2.0937 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.0217    1.5914    1.8623 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.2488   -0.0279    0.3876 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0905   -0.1739   -0.3000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0699   -0.7143    0.5408 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3328    0.0761    1.6388 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.4640   -0.6848    0.1570 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2404    0.3506   -0.3062 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.4284   -0.1640   -0.7548 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.7343   -0.0256   -0.2415 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.4011   -2.2539   -1.5359 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1625   -0.9569   -1.5618 C   0  0  1  0  0  0  0  0  0  0  0  0
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    3.9869    1.3904   -0.2596 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6813    1.0998   -1.6021 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4085    0.4068   -3.0913 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3788   -0.8632   -3.4899 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3917    2.4248   -0.1933 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1105    1.8043   -1.9964 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
  4  6  1  0
  6  7  1  0
  7  8  1  0
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  9 10  1  0
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 13 26  1  0
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 26 28  1  0
 28 29  1  0
 29 30  1  0
  8 31  1  0
 31 32  1  0
 31  3  1  0
 29 10  1  0
 24 15  1  0
  1 33  1  0
  1 34  1  0
  1 35  1  0
  2 36  1  0
  3 37  1  6
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  6 40  1  0
  6 41  1  0
  8 42  1  6
 10 43  1  6
 11 44  1  1
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 13 46  1  6
 15 47  1  6
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 22 54  1  1
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 24 56  1  6
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 27 60  1  0
 27 61  1  0
 28 62  1  0
 28 63  1  0
 29 64  1  6
 30 65  1  0
 30 66  1  0
 31 67  1  6
 32 68  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       7.437   0.078   0.247  0.00  0.00           C+0
HETATM    2  N   UNK     0       6.382   0.953  -0.154  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.062   0.409   0.160  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.015   0.286   1.684  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.234  -0.779   2.094  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.367   1.583   2.160  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.022   1.591   1.862  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.715   1.235   0.583  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.249  -0.028   0.388  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.091  -0.174  -0.300  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.070  -0.714   0.541  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.333   0.076   1.639  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.233  -0.813  -0.420  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.464  -0.685   0.157  0.00  0.00           O+0
HETATM   15  C   UNK     0      -3.240   0.351  -0.306  0.00  0.00           C+0
HETATM   16  O   UNK     0      -4.428  -0.164  -0.755  0.00  0.00           O+0
HETATM   17  C   UNK     0      -5.346  -0.583   0.139  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.734  -0.026  -0.242  0.00  0.00           C+0
HETATM   19  O   UNK     0      -7.136  -0.434  -1.490  0.00  0.00           O+0
HETATM   20  C   UNK     0      -5.122  -0.415   1.583  0.00  0.00           C+0
HETATM   21  O   UNK     0      -5.203  -1.637   2.290  0.00  0.00           O+0
HETATM   22  C   UNK     0      -3.904   0.374   1.994  0.00  0.00           C+0
HETATM   23  O   UNK     0      -4.054   1.034   3.188  0.00  0.00           O+0
HETATM   24  C   UNK     0      -3.577   1.289   0.835  0.00  0.00           C+0
HETATM   25  N   UNK     0      -2.563   2.243   1.119  0.00  0.00           N+0
HETATM   26  C   UNK     0      -1.048  -2.101  -1.193  0.00  0.00           C+0
HETATM   27  N   UNK     0      -1.933  -2.167  -2.325  0.00  0.00           N+0
HETATM   28  C   UNK     0       0.401  -2.254  -1.536  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.163  -0.957  -1.562  0.00  0.00           C+0
HETATM   30  N   UNK     0       0.650  -0.210  -2.722  0.00  0.00           N+0
HETATM   31  C   UNK     0       3.987   1.390  -0.260  0.00  0.00           C+0
HETATM   32  O   UNK     0       3.681   1.100  -1.602  0.00  0.00           O+0
HETATM   33  H   UNK     0       8.199   0.030  -0.573  0.00  0.00           H+0
HETATM   34  H   UNK     0       7.898   0.335   1.228  0.00  0.00           H+0
HETATM   35  H   UNK     0       6.991  -0.948   0.379  0.00  0.00           H+0
HETATM   36  H   UNK     0       6.497   1.936   0.149  0.00  0.00           H+0
HETATM   37  H   UNK     0       4.986  -0.564  -0.342  0.00  0.00           H+0
HETATM   38  H   UNK     0       6.016   0.169   2.127  0.00  0.00           H+0
HETATM   39  H   UNK     0       4.715  -1.642   2.080  0.00  0.00           H+0
HETATM   40  H   UNK     0       4.471   1.596   3.264  0.00  0.00           H+0
HETATM   41  H   UNK     0       4.912   2.461   1.774  0.00  0.00           H+0
HETATM   42  H   UNK     0       1.989   1.952   0.102  0.00  0.00           H+0
HETATM   43  H   UNK     0       0.747   0.868  -0.577  0.00  0.00           H+0
HETATM   44  H   UNK     0       0.227  -1.736   0.832  0.00  0.00           H+0
HETATM   45  H   UNK     0       0.074   0.976   1.582  0.00  0.00           H+0
HETATM   46  H   UNK     0      -1.151   0.008  -1.182  0.00  0.00           H+0
HETATM   47  H   UNK     0      -2.754   0.950  -1.099  0.00  0.00           H+0
HETATM   48  H   UNK     0      -5.472  -1.697  -0.044  0.00  0.00           H+0
HETATM   49  H   UNK     0      -7.497  -0.420   0.494  0.00  0.00           H+0
HETATM   50  H   UNK     0      -6.732   1.087  -0.226  0.00  0.00           H+0
HETATM   51  H   UNK     0      -6.407  -0.650  -2.105  0.00  0.00           H+0
HETATM   52  H   UNK     0      -5.984   0.186   2.008  0.00  0.00           H+0
HETATM   53  H   UNK     0      -4.715  -2.358   1.842  0.00  0.00           H+0
HETATM   54  H   UNK     0      -3.062  -0.342   2.091  0.00  0.00           H+0
HETATM   55  H   UNK     0      -5.005   1.019   3.517  0.00  0.00           H+0
HETATM   56  H   UNK     0      -4.524   1.849   0.610  0.00  0.00           H+0
HETATM   57  H   UNK     0      -2.930   3.238   1.098  0.00  0.00           H+0
HETATM   58  H   UNK     0      -2.123   2.147   2.058  0.00  0.00           H+0
HETATM   59  H   UNK     0      -1.370  -2.922  -0.502  0.00  0.00           H+0
HETATM   60  H   UNK     0      -2.061  -1.262  -2.829  0.00  0.00           H+0
HETATM   61  H   UNK     0      -1.788  -2.985  -2.925  0.00  0.00           H+0
HETATM   62  H   UNK     0       0.440  -2.658  -2.591  0.00  0.00           H+0
HETATM   63  H   UNK     0       0.845  -3.019  -0.900  0.00  0.00           H+0
HETATM   64  H   UNK     0       2.216  -1.227  -1.858  0.00  0.00           H+0
HETATM   65  H   UNK     0       1.409   0.407  -3.091  0.00  0.00           H+0
HETATM   66  H   UNK     0       0.379  -0.863  -3.490  0.00  0.00           H+0
HETATM   67  H   UNK     0       4.392   2.425  -0.193  0.00  0.00           H+0
HETATM   68  H   UNK     0       3.111   1.804  -1.996  0.00  0.00           H+0
CONECT    1    2   33   34   35                                             
CONECT    2    1    3   36                                                  
CONECT    3    2    4   31   37                                             
CONECT    4    3    5    6   38                                             
CONECT    5    4   39                                                       
CONECT    6    4    7   40   41                                             
CONECT    7    6    8                                                       
CONECT    8    7    9   31   42                                             
CONECT    9    8   10                                                       
CONECT   10    9   11   29   43                                             
CONECT   11   10   12   13   44                                             
CONECT   12   11   45                                                       
CONECT   13   11   14   26   46                                             
CONECT   14   13   15                                                       
CONECT   15   14   16   24   47                                             
CONECT   16   15   17                                                       
CONECT   17   16   18   20   48                                             
CONECT   18   17   19   49   50                                             
CONECT   19   18   51                                                       
CONECT   20   17   21   22   52                                             
CONECT   21   20   53                                                       
CONECT   22   20   23   24   54                                             
CONECT   23   22   55                                                       
CONECT   24   22   25   15   56                                             
CONECT   25   24   57   58                                                  
CONECT   26   13   27   28   59                                             
CONECT   27   26   60   61                                                  
CONECT   28   26   29   62   63                                             
CONECT   29   28   30   10   64                                             
CONECT   30   29   65   66                                                  
CONECT   31    8   32    3   67                                             
CONECT   32   31   68                                                       
CONECT   33    1                                                            
CONECT   34    1                                                            
CONECT   35    1                                                            
CONECT   36    2                                                            
CONECT   37    3                                                            
CONECT   38    4                                                            
CONECT   39    5                                                            
CONECT   40    6                                                            
CONECT   41    6                                                            
CONECT   42    8                                                            
CONECT   43   10                                                            
CONECT   44   11                                                            
CONECT   45   12                                                            
CONECT   46   13                                                            
CONECT   47   15                                                            
CONECT   48   17                                                            
CONECT   49   18                                                            
CONECT   50   18                                                            
CONECT   51   19                                                            
CONECT   52   20                                                            
CONECT   53   21                                                            
CONECT   54   22                                                            
CONECT   55   23                                                            
CONECT   56   24                                                            
CONECT   57   25                                                            
CONECT   58   25                                                            
CONECT   59   26                                                            
CONECT   60   27                                                            
CONECT   61   27                                                            
CONECT   62   28                                                            
CONECT   63   28                                                            
CONECT   64   29                                                            
CONECT   65   30                                                            
CONECT   66   30                                                            
CONECT   67   31                                                            
CONECT   68   32                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  140    0
END

RDKit          3D

68 70  0  0  0  0  0  0  0  0999 V2000
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    5.0149    0.2864    1.6835 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2338   -0.7789    2.0937 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3672    1.5833    2.1603 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0217    1.5914    1.8623 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7147    1.2350    0.5826 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2488   -0.0279    0.3876 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0905   -0.1739   -0.3000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0699   -0.7143    0.5408 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3328    0.0761    1.6388 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2327   -0.8133   -0.4195 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4640   -0.6848    0.1570 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2404    0.3506   -0.3062 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.4284   -0.1640   -0.7548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3465   -0.5827    0.1389 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.7343   -0.0256   -0.2415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1365   -0.4342   -1.4900 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.2032   -1.6370    2.2904 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.0479   -2.1010   -1.1933 C   0  0  1  0  0  0  0  0  0  0  0  0
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    1.1625   -0.9569   -1.5618 C   0  0  1  0  0  0  0  0  0  0  0  0
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    3.9869    1.3904   -0.2596 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6813    1.0998   -1.6021 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.9858   -0.5639   -0.3419 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7470    0.8678   -0.5770 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0614   -1.2624   -2.8290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7884   -2.9851   -2.9245 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4401   -2.6577   -2.5907 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8446   -3.0195   -0.9004 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2156   -1.2271   -1.8584 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.3788   -0.8632   -3.4899 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3917    2.4248   -0.1933 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1105    1.8043   -1.9964 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
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
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 22 23  1  0
 22 24  1  0
 24 25  1  0
 13 26  1  0
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 28 29  1  0
 29 30  1  0
  8 31  1  0
 31 32  1  0
 31  3  1  0
 29 10  1  0
 24 15  1  0
  1 33  1  0
  1 34  1  0
  1 35  1  0
  2 36  1  0
  3 37  1  6
  4 38  1  1
  5 39  1  0
  6 40  1  0
  6 41  1  0
  8 42  1  6
 10 43  1  6
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 24 56  1  6
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 25 58  1  0
 26 59  1  1
 27 60  1  0
 27 61  1  0
 28 62  1  0
 28 63  1  0
 29 64  1  6
 30 65  1  0
 30 66  1  0
 31 67  1  6
 32 68  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Gentamicin a3 OF gentamicin a	MeSH
Gentamicin a1 OF gentamicin a	MeSH
Gentamicin a2 OF gentamicin a	MeSH
Gentamicin a4 OF gentamicin a	MeSH

Chemical Formula

C₁₈H₃₆N₄O₁₀

Average Mass

468.5040 Da

Monoisotopic Mass

468.24314 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

CN[C@H]1[C@H](O)CO[C@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N)[C@@H]2O)[C@@H]1O

InChI Identifier

InChI=1S/C18H36N4O10/c1-22-10-7(24)4-29-18(13(10)27)32-16-6(20)2-5(19)15(14(16)28)31-17-9(21)12(26)11(25)8(3-23)30-17/h5-18,22-28H,2-4,19-21H2,1H3/t5-,6+,7+,8+,9+,10-,11+,12+,13+,14-,15+,16-,17+,18+/m0/s1

InChI Key

LKKVGKXCMYHKSL-QVNYEEQUSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Apis cerana	LOTUS Database	35616633
Micromonospora	NPAtlas	14274893

Chemical Taxonomy

Description

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

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2.7	ALOGPS
logP	-6	ChemAxon
logS	-0.67	ALOGPS
pKa (Strongest Acidic)	12.43	ChemAxon
pKa (Strongest Basic)	9.54	ChemAxon
Physiological Charge	4	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	248.39 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	104.95 m³·mol⁻¹	ChemAxon
Polarizability	46.16 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

External Links

NPAtlas ID

NPA001612

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

30791434

KEGG Compound ID

C01917

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12810388

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Gentamicin A (NP0004840)

MOL for NP0004840 (Gentamicin A)

3D MOL for NP0004840 (Gentamicin A)

3D SDF for NP0004840 (Gentamicin A)

3D-SDF for NP0004840 (Gentamicin A)

PDB for NP0004840 (Gentamicin A)

3D PDB for NP0004840 (Gentamicin A)

SMILES for NP0004840 (Gentamicin A)

INCHI for NP0004840 (Gentamicin A)

Structure for NP0004840 (Gentamicin A)

3D Structure for NP0004840 (Gentamicin A)