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 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 


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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
  • Primary Citation of Related Structures:  
    6CCY

  • 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 ROCK 2 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAC-alpha serine/threonine-protein kinase,PIFtideA343Homo sapiensMutation(s): 4 
Gene Names: AKT1, PKB, RAC, PKN2
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16513 (Homo sapiens)
Explore Q16513 
Go to UniProtKB:  Q16513
PHAROS:  Q16513
GTEx:  ENSG00000065243 
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 GroupsQ16513P31749
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EX4
Query on EX4
Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
EX4 Binding MOAD:  6CCY IC50: 3 (nM) from 1 assay(s)
BindingDB:  6CCY IC50: min: 3, max: 39 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.664α = 90
b = 66.961β = 90
c = 109.58γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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