Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 113.85 kDa 
• Atom Count: 7372 
• Modelled Residue Count: 916 
• Deposited Residue Count: 996 
• Unique protein chains: 1

4Y85

Crystal structure of COT kinase domain in complex with 5-(5-(1H-indol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-1,3,4-oxadiazol-2-amine

• PDB DOI: 10.2210/pdb4Y85/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-02-16 Released: 2015-05-06 
• Deposition Author(s): Gutmann, S., Hinniger, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.207 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

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

• PubMed: 25918157 
• DOI: 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: 

Autoimmunity Transplantation Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase 8	A, B, C	332	Homo sapiens	Mutation(s): 0  Gene Names: MAP3K8, COT, ESTF 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
499	D [auth A], E [auth B], F [auth C]	5-[5-(1H-indol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-1,3,4-oxadiazol-2-amine C17 H12 N6 O UQPVGCWCXPFUTD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
499	Binding MOAD:  4Y85	IC50: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.207 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.978	α = 90
b = 85.113	β = 91.06
c = 85.964	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-02-16 
• Released Date: 2015-05-06 
Deposition Author(s): Gutmann, S., Hinniger, A.

Revision History  

• 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: 2018-06-27
  Changes: Data collection, Derived calculations
• Version 1.4: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.5: 2019-05-29
  Changes: Data collection, Derived calculations