3K3J

P38alpha bound to novel DFG-out compound PF-00416121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.995 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1111/j.1747-0285.2009.00884.x
  • Primary Citation of Related Structures:  

  • 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 suc ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14
A
362Homo sapiensMutation(s): 0 
Gene Names: MAPK14 (CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A)
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Go to Gene View: MAPK14
Go to UniProtKB:  Q16539
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F4C
Query on F4C

Download SDF File 
Download CCD File 
A
2-(4-fluorophenyl)-3-oxo-6-pyridin-4-yl-N-[2-(trifluoromethyl)benzyl]-2,3-dihydropyridazine-4-carboxamide
C24 H16 F4 N4 O2
SZWDNHQJXXWUBD-UHFFFAOYSA-N
 Ligand Interaction
I46
Query on I46

Download SDF File 
Download CCD File 
A
2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine
C14 H9 F2 N3
YJCHZVXSPFPKMX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F4CIC50: 2400 - >12500 nM (100) BINDINGDB
F4CIC50: >12500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.995 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.179α = 90.00
b = 74.722β = 90.00
c = 77.733γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance