Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | 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 
• Modelled Residue Count: 325 
• Deposited Residue Count: 360 
• Unique protein chains: 1

1KV2

Human p38 MAP Kinase in Complex with BIRB 796

• PDB 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
• Primary Citation of Related Structures:  
  1KV1, 1KV2


• 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	Image
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)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539 GTEx:  ENSG00000112062

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
B96	BindingDB:  1KV2	Ki: min: 0.1, max: 22 (nM) from 3 assay(s)
		Kd: min: 0.05, max: 12 (nM) from 11 assay(s)
		IC50: min: 0.1, max: 250 (nM) from 13 assay(s)
	PDBBind:  1KV2	Kd: 0.1 (nM) from 1 assay(s)

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