7MF0

Co-crystal structure of PERK with inhibitor (R)-2-amino-N-cyclopropyl-5-(4-(2-(3,5-difluorophenyl)-2-hydroxyacetamido)-2-methylphenyl)nicotinamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of 2-amino-3-amido-5-aryl-pyridines as highly potent, orally bioavailable, and efficacious PERK kinase inhibitors.

Calvo, V.Surguladze, D.Li, A.H.Surman, M.D.Malibhatla, S.Bandaru, M.Jonnalagadda, S.K.Adarasandi, R.Velmala, M.Singireddi, D.R.P.Velpuri, M.Nareddy, B.R.Sastry, V.Mandati, C.Guguloth, R.Siddiqui, S.Patil, B.S.Chad, E.Wolfley, J.Gasparek, J.Feldman, K.Betzenhauser, M.Wiens, B.Koszelak-Rosenblum, M.Zhu, G.Du, H.Rigby, A.C.Mulvihill, M.J.

(2021) Bioorg Med Chem Lett 43: 128058-128058

  • DOI: https://doi.org/10.1016/j.bmcl.2021.128058
  • Primary Citation of Related Structures:  
    7MF0

  • PubMed Abstract: 

    The protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK) is one of the three endoplasmic reticulum (ER) transmembrane sensors of the unfolded protein response (UPR) that regulates protein synthesis, alleviates cellular ER stress and has been implicated in tumorigenesis and prolonged cancer cell survival. In this study, we report a series of 2-amino-3-amido-5-aryl-pyridines that we have identified as potent, selective, and orally bioavailable PERK inhibitors. Amongst the series studied herein, compound (28) a (R)-2-Amino-5-(4-(2-(3,5-difluorophenyl)-2-hydroxyacetamido)-2-ethylphenyl)-N-isopropylnicotinamide has demonstrated potent biochemical and cellular activity, robust pharmacokinetics and 70% oral bioavailability in mice. Given these data, this compound (28) was studied in the 786-O renal cell carcinoma xenograft model. We observed dose-dependent, statistically significant tumor growth inhibition, supporting the use of this tool compound in additional mechanistic studies.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2-alpha kinase 3,Eukaryotic translation initiation factor 2-alpha kinase 3A [auth AAA]317Homo sapiensMutation(s): 1 
Gene Names: EIF2AK3PEKPERK
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZJ5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z6P (Subject of Investigation/LOI)
Query on Z6P

Download Ideal Coordinates CCD File 
B [auth AAA]2-amino-N-cyclopropyl-5-(4-{[(2R)-2-(3,5-difluorophenyl)-2-hydroxyacetyl]amino}-2-methylphenyl)pyridine-3-carboxamide
C24 H22 F2 N4 O3
ZAEWPVUVQVUGEE-OAQYLSRUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.827α = 90
b = 84.958β = 90
c = 70.031γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Derived calculations, Refinement description