1KV2

Human p38 MAP Kinase in Complex with BIRB 796

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.228 

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.Mol.Biol. 9: 268-272

  • DOI: 10.1038/nsb770
  • Primary Citation of Related Structures:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
p38 MAP kinase
A
360Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B96
Query on B96
Download SDF File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.000α = 90.00
b = 74.000β = 90.00
c = 76.800γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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