Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.18 kDa 
• Atom Count: 2102 
• Residue Count: 248 
• Unique protein chains: 1

4G34

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

• DOI: 10.2210/pdb4G34/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-13 Released: 2012-08-08 
• Deposition Author(s): Gampe, R.T., Axten, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.258 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

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

• PubMed: 22827572 
• DOI: 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.

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Organizational Affiliation: 

Oncology Research, Protein Dynamics DPU, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania 19426, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2-alpha kinase 3	A	299	Homo sapiens	Mutation(s): 0  Gene Names: EIF2AK3, PEK, PERK EC: 2.7.11.1
Find proteins for Q9NZJ5 (Homo sapiens) Explore Q9NZJ5  Go to UniProtKB:  Q9NZJ5
NIH Common Fund Data Resources
PHAROS:  Q9NZJ5 GTEx:  ENSG00000172071

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
924	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 ZDMNFWRMUCKWCS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
924	IC50 :  11.699999809265137   nM  PDBBind
924	IC50:  12   nM  BindingDB
924	IC50:  300   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 101.46	α = 90
b = 101.46	β = 90
c = 158.312	γ = 120

Software Package:

Software Name	Purpose
MD2	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-13 
• Released Date: 2012-08-08 
Deposition Author(s): Gampe, R.T., Axten, J.M.

Revision History 

• 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