P38alpha bound to novel DFG-out compound PF-00416121

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


The Design, Synthesis and Potential Utility of Fluorescence Probes that Target DFG-out Conformation of p38alpha for High Throughput Screening Binding Assay.

Tecle, H.Feru, F.Liu, H.Kuhn, C.Rennie, G.Morris, M.Shao, J.Cheng, A.C.Gikunju, D.Miret, J.Coli, R.Xi, S.H.Clugston, S.L.Low, S.Kazmirski, S.Ding, Y.H.Cao, Q.Johnson, T.L.Deshmukh, G.D.Dinitto, J.P.Wu, J.C.English, J.M.

(2009) Chem Biol Drug Des 74: 547-559

  • DOI: https://doi.org/10.1111/j.1747-0285.2009.00884.x
  • Primary Citation of Related Structures:  
    3K3I, 3K3J

  • PubMed Abstract: 

    The design, synthesis and utility of fluorescence probes that bind to the DFG-out conformation of p38alpha kinase are described. Probes that demonstrate good affinity for p38alpha, have been identified and one of the probes, PF-04438255, has been successfully used in an high throughput screening (HTS) assay to identify two novel non-classical p38alpha inhibitors. In addition, a cascade activity assay was utilized to validate the selective binding of these non-classical kinase inhibitors to the unactive form of the enzyme.

  • Organizational Affiliation

    Pfizer Research Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA. haile.tecle@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14362Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on F4C

Download Ideal Coordinates CCD File 
B [auth A]2-(4-fluorophenyl)-3-oxo-6-pyridin-4-yl-N-[2-(trifluoromethyl)benzyl]-2,3-dihydropyridazine-4-carboxamide
C24 H16 F4 N4 O2
Query on I46

Download Ideal Coordinates CCD File 
C [auth A]2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine
C14 H9 F2 N3
Binding Affinity Annotations 
IDSourceBinding Affinity
F4C BindingDB:  3K3J IC50: min: 2400, max: 1.25e+4 (nM) from 2 assay(s)
PDBBind:  3K3J IC50: 1.25e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.179α = 90
b = 74.722β = 90
c = 77.733γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations