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: 42.43 kDa 
• Atom Count: 2783 
• Modelled Residue Count: 341 
• Deposited Residue Count: 366 
• Unique protein chains: 1

3LHJ

Crystal Structure of p38a Mitogen-Activated Protein Kinase in Complex with a Pyrazolopyridinone Inhibitor.

• PDB DOI: 10.2210/pdb3LHJ/pdb

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


• Deposited: 2010-01-22 Released: 2010-04-14 
• Deposition Author(s): Mohr, C., Jordan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.289 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 

Literature

Discovery and evaluation of 7-alkyl-1,5-bis-aryl-pyrazolopyridinones as highly potent, selective, and orally efficacious inhibitors of p38alpha mitogen-activated protein kinase.

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

(2010) J Med Chem 53: 2973-2985

• PubMed: 20218619 
• DOI: 10.1021/jm100095x
• Primary Citation of Related Structures:  
  3LHJ


• PubMed Abstract: 
  

The p38alpha mitogen-activated protein (MAP) kinase is a central signaling molecule in many proinflammatory pathways, regulating the cellular response to a multitude of external stimuli including heat, ultraviolet radiation, osmotic shock, and a variety of cytokines especially interleukin-1beta and tumor necrosis factor alpha. Thus, inhibitors of this enzyme are postulated to have significant therapeutic potential for the treatment of rheumatoid arthritis, inflammatory bowel disease, and Crohn's disease, as well as other diseases where aberrant cytokine signaling is the driver of disease. In this communication, we describe a novel class of 7-alkyl-1,5-bis-aryl-pyrazolopyridinone-based p38alpha inhibitors. In particular, compound 3f is highly potent in the enzyme and cell-based assays, selective in an Ambit kinase screen, and efficacious (ED(50) < or = 0.01 mg/kg) in the rat collagen induced arthritis (CIA) model.

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Organizational Affiliation: 

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

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, 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
LHJ	B [auth A]	N-cyclopropyl-3-[1-(2,4-difluorophenyl)-7-methyl-6-oxo-6,7-dihydro-1H-pyrazolo[3,4-b]pyridin-5-yl]-4-methylbenzamide C24 H20 F2 N4 O2 XQRUWZMHPKNIDA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LHJ	BindingDB:  3LHJ	Ki: 2.3 (nM) from 1 assay(s)
		Kd: min: 0.3, max: 0.31 (nM) from 2 assay(s)
	PDBBind:  3LHJ	Kd: 0.31 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.289 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.775	α = 90
b = 86.604	β = 90
c = 118.959	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-22 
• Released Date: 2010-04-14 
Deposition Author(s): Mohr, C., Jordan, S.

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance