3O2M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1021/cb1002619
  • Primary Citation of Related Structures:  
    3O2M, 3NEW

  • 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 8 AB370Homo sapiensMutation(s): 3 
Gene Names: JNK1MAPK8PRKM8SAPK1SAPK1C
EC: 2.7.11.24
Find proteins for P45983 (Homo sapiens)
Explore P45983 
Go to UniProtKB:  P45983
NIH Common Fund Data Resources
PHAROS:  P45983
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
C-Jun-amino-terminal kinase-interacting protein 1, JIP1, 10MER PEPTIDE FG10Mus musculusMutation(s): 0 
Gene Names: Mapk8ip1Ib1Jip1Mapk8ipPrkm8ip
Find proteins for Q9WVI9 (Mus musculus)
Explore Q9WVI9 
Go to UniProtKB:  Q9WVI9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
46A
Query on 46A

Download Ideal Coordinates CCD File 
A, B
N-butyl-4,6-dimethyl-N-{[2'-(2H-tetrazol-5-yl)biphenyl-4-yl]methyl}pyrimidin-2-amine
C24 H27 N7
ZSQBWJVNWXAGKO-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
46AKd :  16000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-07-22 
  • Released Date: 2011-01-12 
  • Deposition Author(s): Abad-Zapatero, C.

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