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 

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

  • 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. ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAC-alpha serine/threonine-protein kinase
A
446Homo sapiensMutation(s): 3 
Gene Names: AKT1 (PKB, RAC)
EC: 2.7.11.1
Find proteins for P31749 (Homo sapiens)
Go to Gene View: AKT1
Go to UniProtKB:  P31749
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SBT
Query on SBT

Download SDF File 
Download CCD File 
A
2-BUTANOL
C4 H10 O
BTANRVKWQNVYAZ-BYPYZUCNSA-N
 Ligand Interaction
0R4
Query on 0R4

Download SDF File 
Download CCD File 
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
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0R4IC50: 5 - 250 nM (99) BINDINGDB
0R4IC50: 5 nM BINDINGMOAD
0R4IC50: 5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.508α = 90.00
b = 88.214β = 90.00
c = 126.936γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-04-06 
  • Released Date: 2012-05-23 
  • Deposition Author(s): Eathiraj, S.

Revision History 

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