4EJN

Crystal structure of autoinhibited form of AKT1 in complex with N-(4-(5-(3-acetamidophenyl)-2-(2-aminopyridin-3-yl)-3H-imidazo[4,5-b]pyridin-3-yl)benzyl)-3-fluorobenzamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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Literature

Discovery and optimization of a series of 3-(3-phenyl-3H-imidazo[4,5-b]pyridin-2-yl)pyridin-2-amines: orally bioavailable, selective, and potent ATP-independent Akt inhibitors.

Ashwell, M.A., Lapierre, J.M., Brassard, C., Bresciano, K., Bull, C., Cornell-Kennon, S., Eathiraj, S., France, D.S., Hall, T., Hill, J., Kelleher, E., Khanapurkar, S., Kizer, D., Koerner, S., Link, J., Liu, Y., Makhija, S., Moussa, M., Namdev, N., Nguyen, K., Nicewonger, R., Palma, R., Szwaya, J., Tandon, M., Uppalapati, U., Vensel, D., Volak, L.P., Volckova, E., Westlund, N., Wu, H., Yang, R.Y., Chan, T.C.

(2012) J Med Chem 55: 5291-5310

  • DOI: https://doi.org/10.1021/jm300276x
  • Primary Citation of Related Structures:  
    4EJN

  • PubMed Abstract: 

    • This paper describes the implementation of a biochemical and biophysical screening strategy to identify and optimize small molecule Akt1 inhibitors that act through a mechanism distinct from that observed for kinase domain ATP-competitive inhibitors. With the aid of an unphosphorylated Akt1 cocrystal structure of 12j solved at 2 ...

    This paper describes the implementation of a biochemical and biophysical screening strategy to identify and optimize small molecule Akt1 inhibitors that act through a mechanism distinct from that observed for kinase domain ATP-competitive inhibitors. With the aid of an unphosphorylated Akt1 cocrystal structure of 12j solved at 2.25 Å, it was possible to confirm that as a consequence of binding these novel inhibitors, the ATP binding cleft contained a number of hydrophobic residues that occlude ATP binding as expected. These Akt inhibitors potently inhibit intracellular Akt activation and its downstream target (PRAS40) in vitro. In vivo pharmacodynamic and pharmacokinetic studies with two examples, 12e and 12j, showed the series to be similarly effective at inhibiting the activation of Akt and an additional downstream effector (p70S6) following oral dosing in mice.

    Organizational Affiliation: 

    ArQule Inc., 19 Presidential Way, Woburn, Massachusetts 01801, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAC-alpha serine/threonine-protein kinaseA446Homo sapiensMutation(s): 3 
Gene Names: AKT1, PKB, RAC
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P31749 (Homo sapiens)
Explore P31749 
Go to UniProtKB:  P31749
PHAROS:  P31749
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31749
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0R4
Query on 0R4
Download Ideal Coordinates CCD File 
B [auth A]N-(4-{5-[3-(acetylamino)phenyl]-2-(2-aminopyridin-3-yl)-3H-imidazo[4,5-b]pyridin-3-yl}benzyl)-3-fluorobenzamide
C33 H26 F N7 O2
WFDHLKUQFQCHKF-UHFFFAOYSA-N		 Ligand Interaction
SBT
Query on SBT
Download Ideal Coordinates CCD File 
C [auth A]2-BUTANOL
C4 H10 O
BTANRVKWQNVYAZ-BYPYZUCNSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0R4 BindingDB:  4EJN IC50: min: 5, max: 250 (nM) from 7 assay(s)
PDBBind:  4EJN IC50: 5 (nM) from 1 assay(s)
Binding MOAD:  4EJN IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.508α = 90
b = 88.214β = 90
c = 126.936γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2012-05-23 
    • Deposition Author(s): Eathiraj, S.

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references