Crystal Structure of GSK6924 Bound to PERK (R587-R1092, delete A660-T867) at 2.70 A Resolution

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/jm300713s
  • Primary Citation of Related Structures:  
    4G31, 4G34

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2-alpha kinase 3299Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZJ5 (Homo sapiens)
Explore Q9NZJ5 
Go to UniProtKB:  Q9NZJ5
GTEx:  ENSG00000172071 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZJ5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 924

Download Ideal Coordinates CCD File 
B [auth A]1-[5-(4-aminothieno[3,2-c]pyridin-3-yl)-2,3-dihydro-1H-indol-1-yl]-2-phenylethanone
C23 H19 N3 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
924 BindingDB:  4G34 IC50: min: 12, max: 300 (nM) from 2 assay(s)
PDBBind:  4G34 IC50: 11.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.46α = 90
b = 101.46β = 90
c = 158.312γ = 120
Software Package:
Software NamePurpose
MD2data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2012-09-05
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description