2BAJ

p38alpha bound to pyrazolourea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Prevention of MKK6-Dependent Activation by Binding to p38alpha MAP Kinase

Sullivan, J.E.Holdgate, G.A.Campbell, D.Timms, D.Gerhardt, S.Breed, J.Breeze, A.L.Bermingham, A.Pauptit, R.A.Norman, R.A.Embrey, K.J.Read, J.Vanscyoc, W.S.Ward, W.H.

(2005) Biochemistry 44: 16475-16490

  • DOI: https://doi.org/10.1021/bi051714v
  • Primary Citation of Related Structures:  
    2BAJ, 2BAK, 2BAL, 2BAQ

  • PubMed Abstract: 

    Inhibition of p38alpha MAP kinase is a potential approach for the treatment of inflammatory disorders. MKK6-dependent phosphorylation on the activation loop of p38alpha increases its catalytic activity and affinity for ATP. An inhibitor, BIRB796, binds at a site used by the purine moiety of ATP and extends into a "selectivity pocket", which is not used by ATP. It displaces the Asp168-Phe169-Gly170 motif at the start of the activation loop, promoting a "DFG-out" conformation. Some other inhibitors bind only in the purine site, with p38alpha remaining in a "DFG-in" conformation. We now demonstrate that selectivity pocket compounds prevent MKK6-dependent activation of p38alpha in addition to inhibiting catalysis by activated p38alpha. Inhibitors using only the purine site do not prevent MKK6-dependent activation. We present kinetic analyses of seven inhibitors, whose crystal structures as complexes with p38alpha have been determined. This work includes four new crystal structures and a novel assay to measure K(d) for nonactivated p38alpha. Selectivity pocket compounds associate with p38alpha over 30-fold more slowly than purine site compounds, apparently due to low abundance of the DFG-out conformation. At concentrations that inhibit cellular production of an inflammatory cytokine, TNFalpha, selectivity pocket compounds decrease levels of phosphorylated p38alpha and beta. Stabilization of a DFG-out conformation appears to interfere with recognition of p38alpha as a substrate by MKK6. ATP competes less effectively for prevention of activation than for inhibition of catalysis. By binding to a different conformation of the enzyme, compounds that prevent activation offer an alternative approach to modulation of p38alpha.


  • Organizational Affiliation

    Molecular Enzymology, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14365Homo sapiensMutation(s): 0 
Gene Names: MAPK14CSBPCSBP1CSBP2MXI2
EC: 2.7.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PP
Query on 1PP

Download Ideal Coordinates CCD File 
B [auth A]1-(3-tert-butyl-1-phenyl-1H-pyrazol-5-yl)-3-(2,3-dichlorophenyl)urea
C20 H20 Cl2 N4 O
ZFJZXGAFKPFNSG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1PP PDBBind:  2BAJ Kd: 4 (nM) from 1 assay(s)
Binding MOAD:  2BAJ Kd: 4 (nM) from 1 assay(s)
BindingDB:  2BAJ IC50: 30 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59α = 90
b = 67.104β = 90
c = 87.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2012-12-05
    Changes: Non-polymer description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations