4X7L

Co-crystal Structure of PERK bound to 4-{2-amino-4-methyl-3-[2-(methylamino)-1,3-benzothiazol-6-yl]benzoyl}-1-methyl-2,5-diphenyl-1,2-dihydro-3H-pyrazol-3-one inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2-alpha kinase 3,Eukaryotic translation initiation factor 2-alpha kinase 3A317Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZJ5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3Z4
Query on 3Z4

Download Ideal Coordinates CCD File 
B [auth A]4-{2-amino-4-methyl-3-[2-(methylamino)-1,3-benzothiazol-6-yl]benzoyl}-1-methyl-2,5-diphenyl-1,2-dihydro-3H-pyrazol-3-one
C32 H27 N5 O2 S
XUIZYNXJUPSUNY-UHFFFAOYSA-N
 Ligand Interaction
TLA
Query on TLA

Download Ideal Coordinates CCD File 
C [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3Z4 BindingDB:  4X7L IC50: min: 9, max: 1300 (nM) from 5 assay(s)
EC50: 200 (nM) from 1 assay(s)
Binding MOAD:  4X7L IC50: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.045α = 90
b = 82.045β = 90
c = 128.371γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references