4X7O

Co-crystal Structure of PERK bound to 1-[5-(4-amino-2,7-dimethyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-2,3-dihydro-1H-indol-1-yl]-2-[3-fluoro-5-(trifluoromethyl)phenyl]ethanone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4X7O/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-12-09 Released: 2015-01-28 
• Deposition Author(s): Shaffer, P.L., Long, A.M., Chen, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.226 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Discovery of 1H-Pyrazol-3(2H)-ones as Potent and Selective Inhibitors of Protein Kinase R-like Endoplasmic Reticulum Kinase (PERK).

Smith, A.L., Andrews, K.L., Beckmann, H., Bellon, S.F., Beltran, P.J., Booker, S., Chen, H., Chung, Y.A., D'Angelo, N.D., Dao, J., Dellamaggiore, K.R., Jaeckel, P., Kendall, R., Labitzke, K., Long, A.M., Materna-Reichelt, S., Mitchell, P., Norman, M.H., Powers, D., Rose, M., Shaffer, P.L., Wu, M.M., Lipford, J.R.

(2015) J Med Chem 58: 1426-1441

• PubMed: 25587754 
• DOI: https://doi.org/10.1021/jm5017494
• Primary Citation of Related Structures:  
  4X7H, 4X7J, 4X7K, 4X7L, 4X7N, 4X7O


• PubMed Abstract: 
  

  The structure-based design and optimization of a novel series of selective PERK inhibitors are described resulting in the identification of 44 as a potent, highly selective, and orally active tool compound suitable for PERK pathway biology exploration both in vitro and in vivo.

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Organizational Affiliation: 

Departments of †Medicinal Chemistry, ‡Molecular Structure and Characterization, §Oncology Research, and ∥Pharmacokinetics and Drug Metabolism, Amgen Inc. , One Amgen Center Drive, Thousand Oaks, California 91320-1799, United States.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 37.3 kDa 
• Atom Count: 2,078 
• Modelled Residue Count: 246 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2-alpha kinase 3,Eukaryotic translation initiation factor 2-alpha kinase 3	A	317	Homo sapiens	Mutation(s): 1  Gene Names: EIF2AK3, PEK, PERK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZJ5 (Homo sapiens) Explore Q9NZJ5  Go to UniProtKB:  Q9NZJ5
PHAROS:  Q9NZJ5 GTEx:  ENSG00000172071

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3Z6	B [auth A]	1-[5-(4-amino-2,7-dimethyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-2,3-dihydro-1H-indol-1-yl]-2-[3-fluoro-5-(trifluoromethyl)phenyl]ethanone C25 H21 F4 N5 O MXBMIZHUPORZGB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.226 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.366	α = 90
b = 125.366	β = 90
c = 58.203	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Shaffer, P.L., Long, A.M., Chen, H.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy