4Y83

Crystal structure of COT kinase domain in complex with 5-(2-amino-5-(quinolin-3-yl)pyridin-3-yl)-1,3,4-oxadiazole-2(3H)-thione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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This is version 1.3 of the entry. See complete history


Literature

The Crystal Structure of Cancer Osaka Thyroid Kinase Reveals an Unexpected Kinase Domain Fold.

Gutmann, S.Hinniger, A.Fendrich, G.Druckes, P.Antz, S.Mattes, H.Mobitz, H.Ofner, S.Schmiedeberg, N.Stojanovic, A.Rieffel, S.Strauss, A.Troxler, T.Glatthar, R.Sparrer, H.

(2015) J Biol Chem 290: 15210-15218

  • DOI: https://doi.org/10.1074/jbc.M115.648097
  • Primary Citation of Related Structures:  
    4Y83, 4Y85

  • PubMed Abstract: 

    Macrophages are important cellular effectors in innate immune responses and play a major role in autoimmune diseases such as rheumatoid arthritis. Cancer Osaka thyroid (COT) kinase, also known as mitogen-activated protein kinase kinase kinase 8 (MAP3K8) and tumor progression locus 2 (Tpl-2), is a serine-threonine (ST) kinase and is a key regulator in the production of pro-inflammatory cytokines in macrophages. Due to its pivotal role in immune biology, COT kinase has been identified as an attractive target for pharmaceutical research that is directed at the discovery of orally available, selective, and potent inhibitors for the treatment of autoimmune disorders and cancer. The production of monomeric, recombinant COT kinase has proven to be very difficult, and issues with solubility and stability of the enzyme have hampered the discovery and optimization of potent and selective inhibitors. We developed a protocol for the production of recombinant human COT kinase that yields pure and highly active enzyme in sufficient yields for biochemical and structural studies. The quality of the enzyme allowed us to establish a robust in vitro phosphorylation assay for the efficient biochemical characterization of COT kinase inhibitors and to determine the x-ray co-crystal structures of the COT kinase domain in complex with two ATP-binding site inhibitors. The structures presented in this study reveal two distinct ligand binding modes and a unique kinase domain architecture that has not been observed previously. The structurally versatile active site significantly impacts the design of potent, low molecular weight COT kinase inhibitors.


  • Organizational Affiliation

    From the Center for Proteomic Chemistry, sascha.gutmann@novartis.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 8
A, B, C
332Homo sapiensMutation(s): 0 
Gene Names: MAP3K8COTESTF
EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for P41279 (Homo sapiens)
Explore P41279 
Go to UniProtKB:  P41279
PHAROS:  P41279
GTEx:  ENSG00000107968 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41279
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.952α = 90
b = 101.952β = 90
c = 108.315γ = 120
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
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: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2015-06-24
    Changes: Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection