6CCY

Crystal structure of Akt1 in complex with a selective inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of chiral dihydropyridopyrimidinones as potent, selective and orally bioavailable inhibitors of AKT.

Parthasarathy, S.Henry, K.Pei, H.Clayton, J.Rempala, M.Johns, D.De Frutos, O.Garcia, P.Mateos, C.Pleite, S.Wang, Y.Stout, S.Condon, B.Ashok, S.Lu, Z.Ehlhardt, W.Raub, T.Lai, M.Geeganage, S.Burkholder, T.P.

(2018) Bioorg. Med. Chem. Lett. 28: 1887-1891

  • DOI: 10.1016/j.bmcl.2018.03.092

  • PubMed Abstract: 
  • During the course of our research efforts to develop potent and selective AKT inhibitors, we discovered enatiomerically pure substituted dihydropyridopyrimidinones (DHP) as potent inhibitors of protein kinase B/AKT with excellent selectivity against ...

    During the course of our research efforts to develop potent and selective AKT inhibitors, we discovered enatiomerically pure substituted dihydropyridopyrimidinones (DHP) as potent inhibitors of protein kinase B/AKT with excellent selectivity against ROCK 2 . A key challenge in this program was the poor physicochemical properties of the initial lead compound 5. Integration of structure-based drug design and physical properties-based design resulted in replacement of a highly hydrophobic poly fluorinated aryl ring by a simple trifluoromethyl that led to identification of compound 6 with much improved physicochemical properties. Subsequent SAR studies led to the synthesis of new pyran analog 7 with improved cell potency. Further optimization of pharmacokintetics properties by increasing permeability with appropriate fluorinated alkyl led to compound 8 as a potent, selective AKT inhibitors that blocks the phosphorylation of GSK3β in vivo and had robust, dose and concentration dependent efficacy in the U87MG tumor xenograft model.


    Organizational Affiliation

    Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States.,Lilly S.A., Avda.de la Industria 30, 28108 Alcobendas, Madrid, Spain.,Lilly Research Laboratories, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, United States.,Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN 46285-0150, United States. Electronic address: shakthisarav@gmail.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAC-alpha serine/threonine-protein kinase,PIFtide
A
343Homo sapiensMutation(s): 4 
Gene Names: AKT1 (PKB, RAC), PKN2 (PRK2, PRKCL2)
EC: 2.7.11.1 2.7.11.13
Find proteins for P31749 (Homo sapiens)
Go to Gene View: AKT1
Go to UniProtKB:  P31749
Find proteins for Q16513 (Homo sapiens)
Go to Gene View: PKN2
Go to UniProtKB:  Q16513
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EX4
Query on EX4

Download SDF File 
Download CCD File 
A
(5R)-4-(4-{4-[4-fluoro-3-(trifluoromethyl)phenyl]-1-[2-(pyrrolidin-1-yl)ethyl]-1H-imidazol-2-yl}piperidin-1-yl)-5-methyl-5,8-dihydropyrido[2,3-d]pyrimidin-7(6H)-one
C29 H33 F4 N7 O
XIYKGCYSJCRNDN-GOSISDBHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.664α = 90.00
b = 66.961β = 90.00
c = 109.580γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-02-07 
  • Released Date: 2018-05-02 
  • Deposition Author(s): Wang, Y., Stout, S.

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references