4G31

Crystal Structure of GSK6414 Bound to PERK (R587-R1092, delete A660-T867) at 2.28 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery of 7-Methyl-5-(1-{[3-(trifluoromethyl)phenyl]acetyl}-2,3-dihydro-1H-indol-5-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (GSK2606414), a Potent and Selective First-in-Class Inhibitor of Protein Kinase R (PKR)-like Endoplasmic Reticulum Kinase (PERK).

Axten, J.M.Medina, J.R.Feng, Y.Shu, A.Romeril, S.P.Grant, S.W.Li, W.H.Heerding, D.A.Minthorn, E.Mencken, T.Atkins, C.Liu, Q.Rabindran, S.Kumar, R.Hong, X.Goetz, A.Stanley, T.Taylor, J.D.Sigethy, S.D.Tomberlin, G.H.Hassell, A.M.Kahler, K.M.Shewchuk, L.M.Gampe, R.T.

(2012) J.Med.Chem. 55: 7193-7207

  • DOI: 10.1021/jm300713s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK) is activated in response to a variety of endoplasmic reticulum stresses implicated in numerous disease states. Evidence that PERK is implicated in tumorigenesis and cancer cell survival ...

    Protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK) is activated in response to a variety of endoplasmic reticulum stresses implicated in numerous disease states. Evidence that PERK is implicated in tumorigenesis and cancer cell survival stimulated our search for small molecule inhibitors. Through screening and lead optimization using the human PERK crystal structure, we discovered compound 38 (GSK2606414), an orally available, potent, and selective PERK inhibitor. Compound 38 inhibits PERK activation in cells and inhibits the growth of a human tumor xenograft in mice.


    Organizational Affiliation

    Oncology Research, Protein Dynamics DPU, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania 19426, United States. Jeffrey.M.Axten@gsk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2-alpha kinase 3
A
299Homo sapiensMutation(s): 0 
Gene Names: EIF2AK3 (PEK, PERK)
EC: 2.7.11.1
Find proteins for Q9NZJ5 (Homo sapiens)
Go to Gene View: EIF2AK3
Go to UniProtKB:  Q9NZJ5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0WH
Query on 0WH

Download SDF File 
Download CCD File 
A
1-[5-(4-amino-7-methyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-2,3-dihydro-1H-indol-1-yl]-2-[3-(trifluoromethyl)phenyl]ethanone
C24 H20 F3 N5 O
SIXVRXARNAVBTC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0WHIC50: 0.4 nM BINDINGMOAD
0WHIC50: 0.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.204 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 101.119α = 90.00
b = 101.119β = 90.00
c = 158.831γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
MD2data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2012-09-05
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Source and taxonomy
  • Version 1.3: 2017-11-15
    Type: Refinement description