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: 42.45 kDa 
• Atom Count: 2992 
• Modelled Residue Count: 352 
• Deposited Residue Count: 366 
• Unique protein chains: 1

3GFE

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

• PDB DOI: 10.2210/pdb3GFE/pdb

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


• Deposited: 2009-02-26 Released: 2009-07-14 
• Deposition Author(s): Mohr, C., Jordan, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.250 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

Part 1: Structure-Activity Relationship (SAR) investigations of fused pyrazoles as potent, selective and orally available inhibitors of p38alpha mitogen-activated protein kinase.

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

(2009) Bioorg Med Chem Lett 19: 4724-4728

• PubMed: 19574047 
• DOI: 10.1016/j.bmcl.2009.06.058
• Primary Citation of Related Structures:  
  3GFE


• PubMed Abstract: 
  

A novel class of fused pyrazole-derived inhibitors of p38alpha mitogen-activated protein kinase (MAPK) is disclosed. These inhibitors were evaluated for their ability to inhibit the p38alpha enzyme, the secretion of TNFalpha in a LPS-challenged THP1 cell line and TNFalpha-induced production of IL-8 in 50% human whole blood. This series was optimized through a SAR investigation to provide inhibitors with IC(50) values in the low single-digit nanomolar range in whole blood. Further investigation of their pharmacokinetic profiles led to the identification of two potent and orally bioavailable p38 inhibitors 10 m and 10 q. Inhibitor 10 m was found to be efficacious in vivo in the inhibition of TNFalpha production in LPS-stimulated Lewis rats with an ED(50) of 0.1mg/kg while 10 q was found to have an ED(50) of 0.05-0.07 mg/kg.

---

Organizational Affiliation: 

Department of Chemistry Research & Discovery, Amgen Inc, Thousand Oaks, CA 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P37	B [auth A]	N-cyclopropyl-3-{[1-(2,4-difluorophenyl)-7-methyl-6-oxo-6,7-dihydro-1H-pyrazolo[3,4-b]pyridin-4-yl]amino}-4-methylbenzamide C24 H21 F2 N5 O2 WMEYCLAVMZKZCS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P37	BindingDB:  3GFE	IC50: 3.2 (nM) from 1 assay(s)
	PDBBind:  3GFE	IC50: 3.2 (nM) from 1 assay(s)
	Binding MOAD:  3GFE	IC50: 3.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.250 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.419	α = 90
b = 87.708	β = 90
c = 122.332	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-26 
• Released Date: 2009-07-14 
Deposition Author(s): Mohr, C., Jordan, S.

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance