Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.62 kDa 
• Atom Count: 2819 
• Residue Count: 334 
• Unique protein chains: 1

2BAK

p38alpha MAP kinase bound to MPAQ

• DOI: 10.2210/pdb2BAK/pdb

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


• Deposited: 2005-10-14 Released: 2005-12-06 
• Deposition Author(s): Gerhardt, S., Breed, J., Pauptit, R.A., Read, J., Norman, R.A., Ward, W.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.250 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

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

• PubMed: 16342939 
• DOI: 10.1021/bi051714v
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Mitogen-activated protein kinase 14	A	365	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, MXI2, CSPB1, SAPK2A EC: 2.7.1.37 (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
AQZ	A	N-(3-{[7-METHOXY-6-(2-PYRROLIDIN-1-YLETHOXY)QUINAZOLIN-4-YL]AMINO}-4-METHYLPHENYL)-2-MORPHOLIN-4-YLISONICOTINAMIDE C32 H37 N7 O4 LGTPGGBSDIEHKM-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AQZ	Kd:  37   nM  Binding MOAD
AQZ	Kd :  37   nM  PDBBind
AQZ	IC50:  39   nM  BindingDB
AQZ	IC50:  30   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.250 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.332	α = 90
b = 75.84	β = 90
c = 78.112	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-14 
• Released Date: 2005-12-06 
Deposition Author(s): Gerhardt, S., Breed, J., Pauptit, R.A., Read, J., Norman, R.A., Ward, W.H.

Revision History 

• 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