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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.01 kDa 
• Atom Count: 2909 
• Modelled Residue Count: 326 
• Deposited Residue Count: 359 
• Unique protein chains: 1

2YIW

triazolopyridine inhibitors of p38 kinase

• PDB DOI: 10.2210/pdb2YIW/pdb

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


• Deposited: 2011-05-17 Released: 2011-11-30 
• Deposition Author(s): Millan, D.S., Anderson, M., Bunnage, M.E., Burrows, J.L., Butcher, K.J., Dodd, P.G., Evans, T.J., Fairman, D.A., Hughes, S.J., Irving, S.L., Kilty, I.C., Lemaitre, A., Lewthwaite, R.A., Mahnke, A., Mathais, J.P., Philip, J., Phillips, C., Smith, R.T., Stefamiak, M.H., Yeadon, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Design and Synthesis of Inhaled P38 Inhibitors for the Treatment of Chronic Obstructive Pulmonary Disease.

Millan, D.S., Bunnage, M.E., Burrows, J.L., Butcher, K.J., Dodd, P.G., Evans, T.J., Fairman, D.A., Hughes, S.J., Kilty, I.C., Lemaitre, A., Lewthwaite, R.A., Mahnke, A., Mathias, J.P., Philip, J., Smith, R.T., Stefaniak, M.H., Yeadon, M., Phillips, C.

(2011) J Med Chem 54: 7797

• PubMed: 21888439 
• DOI: 10.1021/jm200677b
• Primary Citation of Related Structures:  
  2YIS, 2YIW, 2YIX


• PubMed Abstract: 
  

This paper describes the identification and optimization of a novel series of DFG-out binding p38 inhibitors as inhaled agents for the treatment of chronic obstructive pulmonary disease. Structure based drug design and "inhalation by design" principles have been applied to the optimization of the lead series exemplied by compound 1a. Analogues have been designed to be potent and selective for p38, with an emphasis on slow enzyme dissociation kinetics to deliver prolonged lung p38 inhibition. Pharmacokinetic properties were tuned with high intrinsic clearance and low oral bioavailability in mind, to minimize systemic exposure and reduce systemically driven adverse events. High CYP mediated clearance and glucuronidation were targeted to achieve high intrinsic clearance coupled with multiple routes of clearance to minimize drug-drug interactions. Furthermore, pharmaceutical properties such as stability, crystallinity, and solubility were considered to ensure compatibility with a dry powder inhaler. 1ab (PF-03715455) was subsequently identified as a clinical candidate from this series with efficacy and safety profiles confirming its potential as an inhaled agent for the treatment of COPD.

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Organizational Affiliation: 

Worldwide Medicinal Chemistry, Pfizer Global Research and Development , Sandwich Laboratories, Ramsgate Road, Sandwich, Kent, CT13 9NJ, U.K. [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
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YIW	B [auth A]	1-(3-tert-butyl-1-phenyl-1H-pyrazol-5-yl)-3-(2-{[3-(1-methylethyl)[1,2,4]triazolo[4,3-a]pyridin-6-yl]sulfanyl}benzyl)urea C30 H33 N7 O S GQJUPNKTYNFBRZ-UHFFFAOYSA-N
I46	C [auth A]	2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine C14 H9 F2 N3 YJCHZVXSPFPKMX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YIW	BindingDB:  2YIW	Kd: 0.4 (nM) from 1 assay(s)
	PDBBind:  2YIW	IC50: 0.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.58	α = 90
b = 74.32	β = 90
c = 76.82	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-17 
• Released Date: 2011-11-30 
Deposition Author(s): Millan, D.S., Anderson, M., Bunnage, M.E., Burrows, J.L., Butcher, K.J., Dodd, P.G., Evans, T.J., Fairman, D.A., Hughes, S.J., Irving, S.L., Kilty, I.C., Lemaitre, A., Lewthwaite, R.A., Mahnke, A., Mathais, J.P., Philip, J., Phillips, C., Smith, R.T., Stefamiak, M.H., Yeadon, M.

Revision History  

• Version 1.0: 2011-11-30
  Type: Initial release