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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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: 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAC-alpha serine/threonine-protein kinaseA446Homo sapiensMutation(s): 3 
Gene Names: AKT1PKBRAC
EC: 2.7.11.1
Find proteins for P31749 (Homo sapiens)
Explore P31749 
Go to UniProtKB:  P31749
NIH Common Fund Data Resources
PHAROS:  P31749
Protein Feature View
Expand
  • 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0R4IC50 :  5   nM  PDBBind
0R4IC50:  250   nM  BindingDB
0R4IC50:  32   nM  BindingDB
0R4IC50:  5   nM  Binding MOAD
0R4IC50:  5   nM  BindingDB
0R4IC50:  44   nM  BindingDB
0R4IC50:  45   nM  BindingDB
0R4IC50:  27   nM  BindingDB
0R4IC50:  220   nM  BindingDB
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

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-04-06 
  • 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