1KV2

Human p38 MAP Kinase in Complex with BIRB 796


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site.

Pargellis, C.Tong, L.Churchill, L.Cirillo, P.F.Gilmore, T.Graham, A.G.Grob, P.M.Hickey, E.R.Moss, N.Pav, S.Regan, J.

(2002) Nat Struct Biol 9: 268-272

  • DOI: 10.1038/nsb770
  • Primary Citation of Related Structures:  
    1KV2, 1KV1

  • PubMed Abstract: 
  • The p38 MAP kinase plays a crucial role in regulating the production of proinflammatory cytokines, such as tumor necrosis factor and interleukin-1. Blocking this kinase may offer an effective therapy for treating many inflammatory diseases. Here we r ...

    The p38 MAP kinase plays a crucial role in regulating the production of proinflammatory cytokines, such as tumor necrosis factor and interleukin-1. Blocking this kinase may offer an effective therapy for treating many inflammatory diseases. Here we report a new allosteric binding site for a diaryl urea class of highly potent and selective inhibitors against human p38 MAP kinase. The formation of this binding site requires a large conformational change not observed previously for any of the protein Ser/Thr kinases. This change is in the highly conserved Asp-Phe-Gly motif within the active site of the kinase. Solution studies demonstrate that this class of compounds has slow binding kinetics, consistent with the requirement for conformational change. Improving interactions in this allosteric pocket, as well as establishing binding interactions in the ATP pocket, enhanced the affinity of the inhibitors by 12,000-fold. One of the most potent compounds in this series, BIRB 796, has picomolar affinity for the kinase and low nanomolar inhibitory activity in cell culture.


    Organizational Affiliation

    Department of Biology, Boehringer Ingelheim Pharmaceuticals, Research and Development Center, 900 Ridgebury Road, Ridgefield, Connecticut 06877, USA. cpargel@rdg.boehringer-ingelheim.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
p38 MAP kinaseA360Homo sapiensMutation(s): 0 
Gene Names: MAPK14CSBPCSBP1CSBP2CSPB1MXI2SAPK2A
EC: 2.7.1 (PDB Primary Data), 2.7.11.24 (UniProt)
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B96
Query on B96

Download CCD File 
A
1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA
C31 H37 N5 O3
MVCOAUNKQVWQHZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B96IC50:  8   nM  BindingDB
B96Kd:  0.11999999731779099   nM  BindingDB
B96Kd:  12   nM  BindingDB
B96Kd:  0.1599999964237213   nM  BindingDB
B96IC50:  12   nM  BindingDB
B96Kd :  0.10000000149011612   nM  PDBBind
B96IC50:  10   nM  BindingDB
B96IC50:  17   nM  BindingDB
B96IC50:  250   nM  BindingDB
B96IC50:  220   nM  BindingDB
B96Ki:  6.400000095367432   nM  BindingDB
B96Kd:  1   nM  BindingDB
B96IC50:  20   nM  BindingDB
B96Ki:  22   nM  BindingDB
B96Kd:  0.3700000047683716   nM  BindingDB
B96Kd:  0.05000000074505806   nM  BindingDB
B96IC50:  47   nM  BindingDB
B96Kd:  0.44999998807907104   nM  BindingDB
B96IC50:  44   nM  BindingDB
B96IC50:  4   nM  BindingDB
B96Kd:  0.23999999463558197   nM  BindingDB
B96Kd:  7.5   nM  BindingDB
B96IC50:  89   nM  BindingDB
B96Ki:  0.10000000149011612   nM  BindingDB
B96Kd:  0.10000000149011612   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64α = 90
b = 74β = 90
c = 76.8γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance