4M7I

Crystal Structure of GSK6157 Bound to PERK (R587-R1092, delete A660-T867) at 2.34A Resolution

• PDB DOI: https://doi.org/10.2210/pdb4M7I/pdb

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


• Deposited: 2013-08-12 Released: 2014-09-03 
• Deposition Author(s): Gampe, R.T., Axten, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.282 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Discovery of 5-{4-fluoro-1-[(6-methyl-2-pyridinyl)acetyl]-2,3-dihydro-1H-indol-5-yl}-7-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine (GSK2656157), a Potent and Selective PERK Inhibitor Selected for Preclinical Development

Axten, J.M., Romeril, S.P., Shu, A., Ralph, J., Medina, J.R., Feng, Y., Li, W.H.H., Grant, S.W., Heerding, D.A., Minthorn, E., Mencken, T., Gaul, N., Goetz, A., Stanley, T., Hassell, A.M., Gampe, R.T., Atkins, C., Kumar, R.

To be published.

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: 35.21 kDa 
• Atom Count: 2,129 
• Modelled Residue Count: 247 
• Deposited Residue Count: 299 
• Unique protein chains: 1

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 (PDB Primary Data), 2.7.10.2 (UniProt)
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
27D	B [auth A]	1-[5-(4-amino-7-methyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-4-fluoro-1H-indol-1-yl]-2-(6-methylpyridin-2-yl)ethanone C23 H19 F N6 O YGEJQNSKXJFIJF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.282 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.06	α = 90
b = 101.06	β = 90
c = 158.028	γ = 120

Software Package:

Software Name	Purpose
MD2	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Gampe, R.T., Axten, J.M.

Revision History  

• Version 1.0: 2014-09-03
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Source and taxonomy
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description