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

  • Resolution: 2.19 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


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:  

  • 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 2.25 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RAC-alpha serine/threonine-protein kinase446Homo sapiensMutation(s): 3 
Gene Names: AKT1PKBRAC
UniProt & NIH Common Fund Data Resources
Find proteins for P31749 (Homo sapiens)
Explore P31749 
Go to UniProtKB:  P31749
PHAROS:  P31749
GTEx:  ENSG00000142208 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31749
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
Query on SBT

Download Ideal Coordinates CCD File 
C [auth A]2-BUTANOL
C4 H10 O
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
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)
Experimental Data & Validation

Experimental Data

  • 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
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

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