Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.87 kDa 
• Atom Count: 2656 
• Residue Count: 325 
• Unique protein chains: 1

1KV2

Human p38 MAP Kinase in Complex with BIRB 796

• DOI: 10.2210/pdb1KV2/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-01-23 Released: 2002-03-27 
• Deposition Author(s): 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.

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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 

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

• PubMed: 11896401 
• DOI: 10.1038/nsb770
• Structures With Same Primary Citation


• 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 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.

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Organizational Affiliation: 

Department of Biology, Boehringer Ingelheim Pharmaceuticals, Research and Development Center, 900 Ridgebury Road, Ridgefield, Connecticut 06877, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
p38 MAP kinase	A	360	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.1 (PDB Primary Data), 2.7.11.24 (UniProt)
Find proteins for Q16539 (Homo sapiens) Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539 GTEx  ENSG00000112062

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B96	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
B96	IC50:  8   nM  BindingDB
B96	Kd:  0.11999999731779099   nM  BindingDB
B96	Kd:  12   nM  BindingDB
B96	Kd:  0.1599999964237213   nM  BindingDB
B96	IC50:  12   nM  BindingDB
B96	Kd :  0.10000000149011612   nM  PDBBind
B96	IC50:  10   nM  BindingDB
B96	IC50:  17   nM  BindingDB
B96	IC50:  250   nM  BindingDB
B96	IC50:  220   nM  BindingDB
B96	Ki:  6.400000095367432   nM  BindingDB
B96	Kd:  1   nM  BindingDB
B96	IC50:  20   nM  BindingDB
B96	Ki:  22   nM  BindingDB
B96	Kd:  0.3700000047683716   nM  BindingDB
B96	Kd:  0.05000000074505806   nM  BindingDB
B96	IC50:  47   nM  BindingDB
B96	Kd:  0.44999998807907104   nM  BindingDB
B96	IC50:  44   nM  BindingDB
B96	IC50:  4   nM  BindingDB
B96	Kd:  0.23999999463558197   nM  BindingDB
B96	Kd:  7.5   nM  BindingDB
B96	IC50:  89   nM  BindingDB
B96	Ki:  0.10000000149011612   nM  BindingDB
B96	Kd:  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 = 64	α = 90
b = 74	β = 90
c = 76.8	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-01-23 
• Released Date: 2002-03-27 
Deposition Author(s): 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.

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