3-[5-(2-amino-1-benzyl-1H-benzo[d]imidazol-3-ium-3-yl)pentyl]-1-benzyl-1H-benzo[d]imidazol-3-ium-2-amine

ID: ALA3559469

PubChem CID: 118753791

Max Phase: Preclinical

Molecular Formula: C35H36N6O4

Molecular Weight: 516.69

Molecule Type: Small molecule

Names and Identifiers

Canonical SMILES:  Nc1n(Cc2ccccc2)c2ccccc2[n+]1CCCCC[n+]1c(N)n(Cc2ccccc2)c2ccccc21.O=C([O-])C(=O)[O-]

Standard InChI:  InChI=1S/C33H34N6.C2H2O4/c34-32-36(28-18-8-10-20-30(28)38(32)24-26-14-4-1-5-15-26)22-12-3-13-23-37-29-19-9-11-21-31(29)39(33(37)35)25-27-16-6-2-7-17-27;3-1(4)2(5)6/h1-2,4-11,14-21,34-35H,3,12-13,22-25H2;(H,3,4)(H,5,6)

Standard InChI Key:  VLBIDOMUJPAYNY-UHFFFAOYSA-N

Molfile:  

     RDKit          2D

 45 49  0  0  0  0  0  0  0  0999 V2000
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    4.3698   -3.3191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9438   -3.3191    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0828   -2.9063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6568   -2.0765    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3698   -4.1447    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2 15  1  0
  3  1  2  0
  4  2  2  0
  5  4  1  0
  6  3  1  0
  7  1  1  0
  8  2  1  0
  9  7  2  0
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 12  5  1  0
 13  3  1  0
 14  4  1  0
 15 27  1  0
 16  1  1  0
 17 11  1  0
 18 12  1  0
 19  7  1  0
 20  8  1  0
 21 10  1  0
 22  9  1  0
 23 17  2  0
 24 17  1  0
 25 18  2  0
 26 18  1  0
 27 29  1  0
 28 16  1  0
 29 28  1  0
 30 20  2  0
 31 30  1  0
 32 33  1  0
 33 19  2  0
 34 23  1  0
 35 25  1  0
 36 26  2  0
 37 24  2  0
 38 37  1  0
 39 36  1  0
  6  9  1  0
 22 32  2  0
 38 34  2  0
  5 10  1  0
 31 21  2  0
 39 35  2  0
 41 40  1  0
 42 40  1  0
 43 41  1  0
 44 40  2  0
 45 41  2  0
M  CHG  4   1   1   2   1  42  -1  43  -1
M  END

Molecule Features

Natural Product: No

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: 516.69

Molecular Weight (Monoisotopic): 516.2990

AlogP: 5.30

#Rotatable Bonds: 10

Polar Surface Area: 69.66

Molecular Species: NEUTRAL

HBA: 4

HBD: 2

#RO5 Violations: 2

HBA (Lipinski): 6

HBD (Lipinski): 4

#RO5 Violations (Lipinski): 2

CX Acidic pKa: ┄

CX Basic pKa: ┄

CX LogP: -1.80

CX LogD: -1.80

Aromatic Rings: 6

Heavy Atoms: 39

QED Weighted: 0.19

Np Likeness Score: -0.36

References

1. Ramström H, Bourotte M, Philippe C, Schmitt M, Haiech J, Bourguignon JJ..  (2004)  Heterocyclic bis-cations as starting hits for design of inhibitors of the bifunctional enzyme histidine-containing protein kinase/phosphatase from Bacillus subtilis.,  47  (9): [PMID:15084125] [10.1021/jm021043o]

Source

Source(1):

• Scientific Literature