8EQD

Co-crystal structure of PERK with compound 24

• PDB DOI: https://doi.org/10.2210/pdb8EQD/pdb

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


• Deposited: 2022-10-07 Released: 2022-11-30 
• Deposition Author(s): Zhu, G., Surman, M.D., Mulvihill, M.J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.280 
• R-Value Work: 0.246 

Literature

Optimization of a Novel Mandelamide-Derived Pyrrolopyrimidine Series of PERK Inhibitors.

Stokes, M.E., Surman, M.D., Calvo, V., Surguladze, D., Li, A.H., Gasparek, J., Betzenhauser, M., Zhu, G., Du, H., Rigby, A.C., Mulvihill, M.J.

(2022) Pharmaceutics 14

• PubMed: 36297668 
• DOI: https://doi.org/10.3390/pharmaceutics14102233
• Primary Citation of Related Structures:  
  8EQ9, 8EQD, 8EQE


• PubMed Abstract: 
  

  The protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK) is one of three endoplasmic reticulum (ER) transmembrane sensors of the unfolded protein response (UPR) responsible for regulating protein synthesis and alleviating ER stress. PERK has been implicated in tumorigenesis, cancer cell survival as well metabolic diseases such as diabetes. The structure-based design and optimization of a novel mandelamide-derived pyrrolopyrimidine series of PERK inhibitors as described herein, resulted in the identification of compound 26 , a potent, selective, and orally bioavailable compound suitable for interrogating PERK pathway biology in vitro and in vivo, with pharmacokinetics suitable for once-a-day oral dosing in mice.

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Organizational Affiliation: 

HiberCell Inc., 619 West 54th Street, New York, NY 10019, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 37.24 kDa 
• Atom Count: 2,137 
• Modelled Residue Count: 256 
• 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	A [auth AAA]	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
WPX (Subject of Investigation/LOI)	B [auth AAA]	(2R)-N-[(4M)-4-(4-amino-2,7-dimethyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-3-methylphenyl]-2-(3-fluorophenyl)-2-hydroxyacetamide C23 H22 F N5 O2 NZUZHCPIKAILKT-HXUWFJFHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.280 
• R-Value Work: 0.246 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.9	α = 90
b = 125.9	β = 90
c = 55.216	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-30 
Deposition Author(s): Zhu, G., Surman, M.D., Mulvihill, M.J.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2022-11-30
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description