Neomycin

ID: ALA3754093

PubChem CID: 3000500

Max Phase: Preclinical

Molecular Formula: C23H46N6O13

Molecular Weight: 614.65

Molecule Type: Small molecule

Names and Identifiers

Canonical SMILES:  NCC1OC(OC2C(CO)OC(OC3C(O)C(N)CC(N)C3OC3OC(CN)C(O)C(O)C3N)C2O)C(N)C(O)C1O

Standard InChI:  InChI=1S/C23H46N6O13/c24-2-7-13(32)15(34)10(28)21(37-7)40-18-6(27)1-5(26)12(31)20(18)42-23-17(36)19(9(4-30)39-23)41-22-11(29)16(35)14(33)8(3-25)38-22/h5-23,30-36H,1-4,24-29H2/t5-,6+,7-,8?,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1

Standard InChI Key:  PGBHMTALBVVCIT-UFTIIHCESA-N

Molfile:  

  SciTegic12121614482D

 45 48  0  0  0  0            999 V2000
    2.1208    6.9883    0.0000 C   0  0  2  0  0  0
    3.8852    8.8980    0.0000 C   0  0  2  0  0  0
    2.5770    3.0452    0.0000 C   0  0  2  0  0  0
    6.1068   12.8598    0.0000 C   0  0  2  0  0  0
    5.8068   10.2794    0.0000 C   0  0  2  0  0  0
    1.7936    5.5244    0.0000 C   0  0  2  0  0  0
    2.2232    1.6086    0.0000 C   0  0  1  0  0  0
    5.4884   14.2039    0.0000 C   0  0  1  0  0  0
    4.3069   10.2994    0.0000 C   0  0  1  0  0  0
    6.3846   15.4068    0.0000 C   0  0  2  0  0  0
    3.3303    0.5964    0.0000 C   0  0  2  0  0  0
    3.5539    7.4342    0.0000 O   0  0
    5.0261    7.9814    0.0000 O   0  0
    3.9763    3.5260    0.0000 O   0  0
    7.5717   12.6516    0.0000 O   0  0
    6.7010   11.4816    0.0000 O   0  0
    2.9005    4.5108    0.0000 O   0  0
    1.0167    8.0036    0.0000 C   0  0  2  0  0  0
    4.7604    1.0491    0.0000 C   0  0  1  0  0  0
    7.8744   15.2320    0.0000 C   0  0  1  0  0  0
    6.2513    8.8468    0.0000 C   0  0  2  0  0  0
    8.4679   13.8545    0.0000 C   0  0
    5.0834    2.5139    0.0000 C   0  0  1  0  0  0
    0.3623    5.0758    0.0000 C   0  0  2  0  0  0
   -0.4147    7.5550    0.0000 C   0  0  1  0  0  0
   -0.7419    6.0911    0.0000 C   0  0
    1.0748    1.2604    0.0000 N   0  0
    4.2949   14.3292    0.0000 N   0  0
    3.5974   11.2672    0.0000 O   0  0
    3.0719   -0.5754    0.0000 O   0  0
    5.9097   16.5088    0.0000 O   0  0
    0.1005    3.9047    0.0000 N   0  0
   -1.2980    8.3672    0.0000 N   0  0
    1.2784    9.1747    0.0000 O   0  0
    5.6460    0.2393    0.0000 O   0  0
    8.5913   16.1943    0.0000 O   0  0
    6.5133    2.9697    0.0000 C   0  0
    9.9582   13.6766    0.0001 C   0  0
    7.6689    8.3620    0.0000 C   0  0
   10.3526   12.7577    0.0001 N   0  0
    7.2532    2.2969    0.0000 N   0  0
    7.9010    7.1846    0.0000 O   0  0
    1.6237    2.7433    0.0000 H   0  0
    5.1137   12.9764    0.0000 H   0  0
    3.1511    9.5770    0.0000 H   0  0
  2 12  1  0
  3 17  1  0
  4 16  1  0
  5  9  1  0
  6  1  1  0
  7  3  1  0
  8  4  1  0
  9  2  1  0
 10  8  1  0
 11  7  1  0
  1 12  1  1
 13  2  1  0
 14  3  1  0
 15  4  1  0
  5 16  1  6
  6 17  1  6
 18  1  1  0
 19 11  1  0
 20 10  1  0
 21 13  1  0
 22 15  1  0
 23 14  1  0
 24  6  1  0
 25 18  1  0
 26 24  1  0
  7 27  1  1
  8 28  1  6
  9 29  1  6
 11 30  1  6
 10 31  1  1
 24 32  1  1
 25 33  1  1
 18 34  1  6
 19 35  1  1
 20 36  1  6
 23 37  1  6
 22 38  1  0
 21 39  1  1
 40 38  1  0
 41 37  1  0
 42 39  1  0
  3 43  1  6
  4 44  1  1
  2 45  1  6
 26 25  1  0
 21  5  1  0
 19 23  1  0
 22 20  1  0
M  END

Alternative Forms

1. Parent:

   

   ALA3754093

   (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2R,3R,4R,5S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxycyclohexyl]oxyoxane-3,4-diol

Molecule Features

Natural Product: Yes

Oral: No

Chemical Probe: No

Parenteral: No

Molecule Type: Small molecule

Topical: No

First In Class: No

Black Box: No

Chirality: No

Availability: No

Prodrug: No

Calculated Properties

Molecular Weight: 614.65

Molecular Weight (Monoisotopic): 614.3123

AlogP: -8.90

#Rotatable Bonds: 9

Polar Surface Area: 353.11

Molecular Species: BASE

HBA: 19

HBD: 13

#RO5 Violations: 3

HBA (Lipinski): 19

HBD (Lipinski): 19

#RO5 Violations (Lipinski): 3

CX Acidic pKa: 12.15

CX Basic pKa: 9.71

CX LogP: -8.42

CX LogD: -15.47

Aromatic Rings: ┄

Heavy Atoms: 42

QED Weighted: 0.11

Np Likeness Score: 1.11

References

1. Simon B, Walmsley C, Jackson VJ, Garvey EP, Slater MJ, Berrisford DJ, Gardiner JM..  (2019)  Evaluation of neomycin analogues for HIV-1 RRE RNA recognition identifies enhanced activity simplified neamine analogues.,  29  (2): [PMID:30477891] [10.1016/j.bmcl.2018.11.004]

2. Laev SS, Salakhutdinov NF, Lavrik OI..  (2016)  Tyrosyl-DNA phosphodiesterase inhibitors: Progress and potential.,  24  (21): [PMID:27687971] [10.1016/j.bmc.2016.09.045]

3.  (2016)  7  (8): [10.1039/C6MD00079G]

Source

Source(1):

• Scientific Literature