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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.17 kDa 
• Atom Count: 3160 
• Modelled Residue Count: 338 
• Deposited Residue Count: 365 
• Unique protein chains: 1

5WJJ

Structure-based Design, Synthesis, and Biological Evaluation of Imidazo[1,2-b]pyridazine-based p38 MAP Kinase Inhibitors

• PDB DOI: 10.2210/pdb5WJJ/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2017-07-23 Released: 2018-01-17 
• Deposition Author(s): Snell, G.P., Okada, K., Bragstad, K., Sang, B.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Structure-based design, synthesis, and biological evaluation of imidazo[1,2-b]pyridazine-based p38 MAP kinase inhibitors.

Kaieda, A., Takahashi, M., Takai, T., Goto, M., Miyazaki, T., Hori, Y., Unno, S., Kawamoto, T., Tanaka, T., Itono, S., Takagi, T., Hamada, T., Shirasaki, M., Okada, K., Snell, G., Bragstad, K., Sang, B.C., Uchikawa, O., Miwatashi, S.

(2018) Bioorg Med Chem 26: 647-660

• PubMed: 29291937 
• DOI: 10.1016/j.bmc.2017.12.031
• Primary Citation of Related Structures:  
  5WJJ, 6ANL


• PubMed Abstract: 
  

We identified novel potent inhibitors of p38 MAP kinase using structure-based design strategy. X-ray crystallography showed that when p38 MAP kinase is complexed with TAK-715 (1) in a co-crystal structure, Phe169 adopts two conformations, where one interacts with 1 and the other shows no interaction with 1. Our structure-based design strategy shows that these two conformations converge into one via enhanced protein-ligand hydrophobic interactions. According to the strategy, we focused on scaffold transformation to identify imidazo[1,2-b]pyridazine derivatives as potent inhibitors of p38 MAP kinase. Among the herein described and evaluated compounds, N-oxide 16 exhibited potent inhibition of p38 MAP kinase and LPS-induced TNF-α production in human monocytic THP-1 cells, and significant in vivo efficacy in rat collagen-induced arthritis models. In this article, we report the discovery of potent, selective and orally bioavailable imidazo[1,2-b]pyridazine-based p38 MAP kinase inhibitors with pyridine N-oxide group.

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Organizational Affiliation: 

Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	365	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539 GTEx:  ENSG00000112062

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AQY (Subject of Investigation/LOI)	B [auth A]	N-{4-[2-(4-fluoro-3-methylphenyl)imidazo[1,2-b]pyridazin-3-yl]pyridin-2-yl}-2-methyl-1-oxo-1lambda~5~-pyridine-4-carboxamide C25 H19 F N6 O2 RNPHICWBCUQEML-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AQY	Binding MOAD:  5WJJ	IC50: 5.4 (nM) from 1 assay(s)
	BindingDB:  5WJJ	IC50: 5.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.813	α = 90
b = 69.974	β = 90
c = 73.878	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-07-23 
• Released Date: 2018-01-17 
Deposition Author(s): Snell, G.P., Okada, K., Bragstad, K., Sang, B.-C.

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Database references