Crystal Structure of JNK1-alpha1 isoform complex with a biaryl tetrazol (A-82118)

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

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Discovery and characterization of non-ATP site inhibitors of the mitogen activated protein (MAP) kinases.

Comess, K.M.Sun, C.Abad-Zapatero, C.Goedken, E.R.Gum, R.J.Borhani, D.W.Argiriadi, M.Groebe, D.R.Jia, Y.Clampit, J.E.Haasch, D.L.Smith, H.T.Wang, S.Song, D.Coen, M.L.Cloutier, T.E.Tang, H.Cheng, X.Quinn, C.Liu, B.Xin, Z.Liu, G.Fry, E.H.Stoll, V.Ng, T.I.Banach, D.Marcotte, D.Burns, D.J.Calderwood, D.J.Hajduk, P.J.

(2011) ACS Chem Biol 6: 234-244

  • DOI: https://doi.org/10.1021/cb1002619
  • Primary Citation of Related Structures:  
    3NEW, 3O2M

  • PubMed Abstract: 

    Inhibition of protein kinases has validated therapeutic utility for cancer, with at least seven kinase inhibitor drugs on the market. Protein kinase inhibition also has significant potential for a variety of other diseases, including diabetes, pain, cognition, and chronic inflammatory and immunologic diseases. However, as the vast majority of current approaches to kinase inhibition target the highly conserved ATP-binding site, the use of kinase inhibitors in treating nononcology diseases may require great selectivity for the target kinase. As protein kinases are signal transducers that are involved in binding to a variety of other proteins, targeting alternative, less conserved sites on the protein may provide an avenue for greater selectivity. Here we report an affinity-based, high-throughput screening technique that allows nonbiased interrogation of small molecule libraries for binding to all exposed sites on a protein surface. This approach was used to screen both the c-Jun N-terminal protein kinase Jnk-1 (involved in insulin signaling) and p38α (involved in the formation of TNFα and other cytokines). In addition to canonical ATP-site ligands, compounds were identified that bind to novel allosteric sites. The nature, biological relevance, and mode of binding of these ligands were extensively characterized using two-dimensional (1)H/(13)C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38α both belong to the MAP kinase family, and the allosteric ligands for both targets bind similarly on a ledge of the protein surface exposed by the MAP insertion present in the CMGC family of protein kinases and distant from the active site. Medicinal chemistry studies resulted in an improved Jnk-1 ligand able to increase adiponectin secretion in human adipocytes and increase insulin-induced protein kinase PKB phosphorylation in human hepatocytes, in similar fashion to Jnk-1 siRNA and to rosiglitazone treatment. Together, the data suggest that these new ligand series bind to a novel, allosteric, and physiologically relevant site and therefore represent a unique approach to identify kinase inhibitors.

  • Organizational Affiliation

    Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States. kenneth.m.comess@abbott.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 8A,
C [auth B]
370Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for P45983 (Homo sapiens)
Explore P45983 
Go to UniProtKB:  P45983
PHAROS:  P45983
GTEx:  ENSG00000107643 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45983
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-Jun-amino-terminal kinase-interacting protein 1, JIP1, 10MER PEPTIDEB [auth F],
D [auth G]
10Mus musculusMutation(s): 0 
Find proteins for Q9WVI9 (Mus musculus)
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Go to UniProtKB:  Q9WVI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WVI9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.379α = 90
b = 158.379β = 90
c = 123.959γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-14
    Changes: Database references
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations