(E)-3-[1-(2-Ethylaminoethyl)-2-hexyl-1H-benzimidazol-5-yl]-N-hydroxyacrylamide dihydrochloride salt

ID: ALA3216532

PubChem CID: 53364268

Max Phase: Preclinical

Molecular Formula: C20H32Cl2N4O2

Molecular Weight: 358.49

Molecule Type: Small molecule

Names and Identifiers

Canonical SMILES:  CCCCCCc1nc2cc(/C=C/C(=O)NO)ccc2n1CCNCC.Cl.Cl

Standard InChI:  InChI=1S/C20H30N4O2.2ClH/c1-3-5-6-7-8-19-22-17-15-16(10-12-20(25)23-26)9-11-18(17)24(19)14-13-21-4-2;;/h9-12,15,21,26H,3-8,13-14H2,1-2H3,(H,23,25);2*1H/b12-10+;;

Standard InChI Key:  PGKBWDGSAZKENE-PFNYCKIMSA-N

Molfile:  

     RDKit          2D

 28 27  0  0  0  0  0  0  0  0999 V2000
   11.7896   -1.0380    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -6.2216    1.4644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9153    0.7255    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6217    1.4865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2318    2.6643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5151    0.7033    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5596    1.2941    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5889    0.0182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7138    1.2033    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2917    0.7475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2917   -0.7475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7138   -1.2033    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0028    1.5132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3155    0.7475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3155   -0.7475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0028   -1.5132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0872    0.0382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8208    1.3475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3215    1.3677    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0552    2.6770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5559    2.6972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1425    3.7441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1855   -2.6254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6552   -2.9294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1277   -4.3539    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5974   -4.6579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9752   -5.7969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2896   -1.0380    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0
  3  4  2  0
  2  5  2  0
  2  6  1  0
  6  7  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
  8 12  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 11 16  2  0
 10 13  2  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
  8 17  1  0
 23 24  1  0
 26 27  1  0
 25 26  1  0
 24 25  1  0
 12 23  1  0
  4 14  1  0
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: 358.49

Molecular Weight (Monoisotopic): 358.2369

AlogP: 3.29

#Rotatable Bonds: 11

Polar Surface Area: 79.18

Molecular Species: BASE

HBA: 5

HBD: 3

#RO5 Violations: ┄

HBA (Lipinski): 6

HBD (Lipinski): 3

#RO5 Violations (Lipinski): ┄

CX Acidic pKa: 9.44

CX Basic pKa: 10.20

CX LogP: 2.59

CX LogD: 0.90

Aromatic Rings: 2

Heavy Atoms: 26

QED Weighted: 0.25

Np Likeness Score: -0.82

References

1. Wang H, Yu N, Chen D, Lee KC, Lye PL, Chang JW, Deng W, Ng MC, Lu T, Khoo ML, Poulsen A, Sangthongpitag K, Wu X, Hu C, Goh KC, Wang X, Fang L, Goh KL, Khng HH, Goh SK, Yeo P, Liu X, Bonday Z, Wood JM, Dymock BW, Kantharaj E, Sun ET..  (2011)  Discovery of (2E)-3-{2-butyl-1-[2-(diethylamino)ethyl]-1H-benzimidazol-5-yl}-N-hydroxyacrylamide (SB939), an orally active histone deacetylase inhibitor with a superior preclinical profile.,  54  (13): [PMID:21634430] [10.1021/jm2003552]

Source

Source(1):

• Scientific Literature