Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 41.55 kDa 
• Atom Count: 2971 
• Residue Count: 344 
• Unique protein chains: 1

3HRB

p38 kinase Crystal structure in complex with small molecule inhibitor

• DOI: 10.2210/pdb3HRB/pdb

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


• Deposited: 2009-06-09 Released: 2009-09-01 
• Deposition Author(s): Segarra, V., Lumeras, W., Vidal, B., Leonard, P., Fisher, M., Lamers, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.260 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Design, synthesis, and structure-activity relationships of aminopyridine N-oxides, a novel scaffold for the potent and selective inhibition of p38 mitogen activated protein kinase

Lumeras, W., Caturla, F., Vidal, L., Esteve, C., Balague, C., Orellana, A., Dominguez, M., Roca, R., Huerta, J.M., Godessart, N., Vidal, B.

(2009) J Med Chem 52: 5531-5545

• PubMed: 19678708 
• DOI: 10.1021/jm9008604
• Primary Citation of Related Structures:  
  3HRB


• PubMed Abstract: 
  

A novel series of aminopyridine N-oxides were designed, synthesized, and tested for their ability to inhibit p38alpha MAP kinase. Some of these compounds showed a significant reduction in the LPS-induced TNFalpha production in human whole blood. Structure-activity relationship studies revealed that N-oxide oxygen was essential for activity and was probably a determinant factor for a marked selectivity against other related kinases. Compound 45 was identified as a potent and selective p38alpha inhibitor with an appropriate balance between potency and pharmacokinetics. In vivo efficacy of 45 was demonstrated in reducing TNFalpha levels in an acute murine model of inflammation (ED(50) = 1 mg/kg in LPS-induced TNFalpha production when dosed orally 1.5 h prior to LPS administration). The oral efficacy of 45 was further demonstrated in a chronic model of adjuvant arthritis in rats with established disease when administered orally (ED(50) = 4.5 mg/kg).

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Organizational Affiliation: 

Department of Medicinal Chemistry, Almirall Research Center, Almirall SA, Barcelona, Spain. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	359	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539 GTEx  ENSG00000112062

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I39	A	[3-amino-2-(2-methylphenyl)-1-oxidopyridin-4-yl](2,4-difluorophenyl)methanone C19 H14 F2 N2 O2 LTGBWAXSDFOJNJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
I39	IC50 :  21   nM  PDBBind
I39	IC50:  21   nM  Binding MOAD
I39	IC50:  21   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.260 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.22	α = 90
b = 86.75	β = 90
c = 122.23	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-09 
• Released Date: 2009-09-01 
Deposition Author(s): Segarra, V., Lumeras, W., Vidal, B., Leonard, P., Fisher, M., Lamers, M.

Revision History 

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance