3U8W

Crystal Structure of p38a Mitogen-Activated Protein Kinase in Complex with a Triazolopyridazinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3U8W/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-17 Released: 2012-08-29 
• Deposition Author(s): Mohr, C., Jordan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.255 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 

Literature

Identification of triazolopyridazinones as potent p38alpha inhibitors.

Herberich, B., Jackson, C., Wurz, R.P., Pettus, L.H., Sherman, L., Liu, Q., Henkle, B., Saris, C.J., Wong, L.M., Chmait, S., Lee, M.R., Mohr, C., Hsieh, F., Tasker, A.S.

(2012) Bioorg Med Chem Lett 22: 1226-1229

• PubMed: 22196117 
• DOI: https://doi.org/10.1016/j.bmcl.2011.11.067
• Primary Citation of Related Structures:  
  3U8W


• PubMed Abstract: 
  

  Structure-activity relationship (SAR) investigations of a novel class of triazolopyridazinone p38α mitogen activated protein kinase (MAPK) inhibitors are disclosed. From these studies, increased in vitro potency was observed for 2,6-disubstituted phenyl moieties and N-ethyl triazolopyridazinone cores due to key contacts with Leu108, Ala157 and Val38. Further investigation led to the identification of three compounds, 3g, 3j and 3m that are highly potent inhibitors of LPS-induced MAPKAP kinase 2 (MK2) phosphorylation in 50% human whole blood (hWB), and possess desirable in vivo pharmacokinetic and kinase selectivity profiles.

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Organizational Affiliation: 

Department of Chemistry Research and Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.46 kDa 
• Atom Count: 2,915 
• Modelled Residue Count: 349 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	366	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 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
09J	B [auth A]	3-[3-(2-chloro-6-fluorophenyl)-5-ethyl-6-oxo-5,6-dihydro[1,2,4]triazolo[4,3-b]pyridazin-7-yl]-N-cyclopropyl-4-methylbenzamide C24 H21 Cl F N5 O2 JCOILWGRHHMFON-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
09J	BindingDB:  3U8W	IC50: min: 1, max: 4.9 (nM) from 3 assay(s)
	PDBBind:  3U8W	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.255 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.143	α = 90
b = 85.789	β = 90
c = 120.569	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Mohr, C., Jordan, S.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations