(R)-4-((8-chloro-2,5-dioxo-3-(pyridin-2-ylmethyl)-2,3-dihydro-1H-benzo[e][1,4]diazepin-4(5H)-yl)methyl)-2-methyl-N-(5-methylpyrimidin-2-yl)benzamide

ID: ALA4451752

PubChem CID: 132214241

Max Phase: Preclinical

Molecular Formula: C29H25ClN6O3

Molecular Weight: 541.01

Molecule Type: Unknown

Names and Identifiers

Canonical SMILES:  Cc1cnc(NC(=O)c2ccc(CN3C(=O)c4ccc(Cl)cc4NC(=O)[C@H]3Cc3ccccn3)cc2C)nc1

Standard InChI:  InChI=1S/C29H25ClN6O3/c1-17-14-32-29(33-15-17)35-26(37)22-8-6-19(11-18(22)2)16-36-25(13-21-5-3-4-10-31-21)27(38)34-24-12-20(30)7-9-23(24)28(36)39/h3-12,14-15,25H,13,16H2,1-2H3,(H,34,38)(H,32,33,35,37)/t25-/m1/s1

Standard InChI Key:  FFGKAPZKYVEJJX-RUZDIDTESA-N

Molfile:  

 
     RDKit          2D

 39 43  0  0  0  0  0  0  0  0999 V2000
   14.7245  -11.2095    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7234  -12.0291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.4314  -12.4380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.4296  -10.8007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1393  -12.0245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1383  -11.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7803  -10.6890    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7856  -12.5359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5822  -10.8650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5877  -12.3488    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.9394  -11.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6071  -13.3334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.0886  -10.2236    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7566  -11.6008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1621  -10.8914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1012  -12.9846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9151  -12.9843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9766  -10.8900    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.3821  -10.1813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9704   -9.4744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1490   -9.4806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7472  -10.1898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3205  -13.6913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.1336  -13.6913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.5412  -12.9857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.1295  -12.2787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3177  -12.2821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3583  -12.9843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.7657  -12.2759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.7682  -13.6913    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.0167  -10.8011    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   22.5853  -13.6899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.9903  -14.3963    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.8067  -14.3953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2149  -13.6863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.8007  -12.9770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.9856  -12.9815    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.5422  -14.3991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.0321  -13.6838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  5  2  0
  6  4  2  0
  4  1  1  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  7  9  1  0
  8 10  1  0
  9 11  1  0
 10 11  1  0
  8 12  2  0
  9 13  2  0
 11 14  1  1
 14 15  1  0
 10 16  1  0
 16 17  1  0
 15 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 15  1  0
 17 23  2  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  2  0
 27 17  1  0
 25 28  1  0
 28 29  2  0
 28 30  1  0
  1 31  1  0
 30 32  1  0
 32 33  2  0
 33 34  1  0
 34 35  2  0
 35 36  1  0
 36 37  2  0
 37 32  1  0
 24 38  1  0
 35 39  1  0
M  END

Alternative Forms

1. Parent:

   

   ALA4451752

   ---

Molecule Features

Natural Product: No

Oral: No

Chemical Probe: No

Parenteral: No

Molecule Type: Unknown

Topical: No

First In Class: No

Black Box: No

Chirality: No

Availability: No

Prodrug: No

Calculated Properties

Molecular Weight: 541.01

Molecular Weight (Monoisotopic): 540.1677

AlogP: 4.60

#Rotatable Bonds: 6

Polar Surface Area: 117.18

Molecular Species: NEUTRAL

HBA: 6

HBD: 2

#RO5 Violations: 1

HBA (Lipinski): 9

HBD (Lipinski): 2

#RO5 Violations (Lipinski): 1

CX Acidic pKa: 12.23

CX Basic pKa: 4.52

CX LogP: 5.10

CX LogD: 5.10

Aromatic Rings: 4

Heavy Atoms: 39

QED Weighted: 0.37

Np Likeness Score: -1.32

References

1. Letourneau JJ, Stroke IL, Hilbert DW, Cole AG, Sturzenbecker LJ, Marinelli BA, Quintero JG, Sabalski J, Li Y, Ma L, Pechik I, Stein PD, Webb ML..  (2018)  Synthesis and SAR studies of novel benzodiazepinedione-based inhibitors of Clostridium difficile (C. difficile) toxin B (TcdB).,  28  (23-24): [PMID:30392779] [10.1016/j.bmcl.2018.10.047]

Source

Source(1):

• Scientific Literature