4E6C

p38a-perifosine Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Lipid Molecules Induce p38 alpha Activation via a Novel Molecular Switch.

Tzarum, N.Eisenberg-Domovich, Y.Gills, J.J.Dennis, P.A.Livnah, O.

(2012) J Mol Biol 424: 339-353

  • DOI: https://doi.org/10.1016/j.jmb.2012.10.007
  • Primary Citation of Related Structures:  
    4E5A, 4E5B, 4E6A, 4E6C, 4E8A

  • PubMed Abstract: 

    p38α mitogen-activated protein kinase (MAPK) is generally activated by dual phosphorylation but has also been shown to exhibit alternative activation modes. One of these modes included a direct interaction with phosphatidylinositol ether lipid analogues (PIA) inducing p38α autoactivation and apoptosis. Perifosine, an Akt inhibitor in phase II clinical trials, also showed p38α activation properties similarly to those of PIAs. The crystal structures of p38α in complex with PIA23, PIA24 and perifosine provide insights into this unique activation mode. The activating molecules bind a unique hydrophobic binding site in the kinase C'-lobe formed in part by the MAPK insert region. In addition, there are conformational changes in the short αEF/αF loop region that acts as an activation switch, inducing autophosphorylation. Structural and biochemical characterization of the αEF/αF loop identified Trp197 as a key residue in the lipid binding and in p38α catalytic activity. The lipid binding site also accommodates hydrophobic inhibitor molecules and, thus, can serve as a novel p38α-target for specific activation or inhibition, with novel therapeutic implications.


  • Organizational Affiliation

    Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences and The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo sapiensMutation(s): 0 
Gene Names: MAPK14CSBPCSBP1CSBP2CSPB1MXI2SAPK2A
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0O8
Query on 0O8

Download Ideal Coordinates CCD File 
B [auth A](1,1-dimethylpiperidin-1-ium-4-yl) octadecyl hydrogen phosphate
C25 H53 N O4 P
SZFPYBIJACMNJV-UHFFFAOYSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
0O8 PDBBind:  4E6C Kd: 1.50e+4 (nM) from 1 assay(s)
Binding MOAD:  4E6C Kd: 1.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.022α = 90
b = 74.031β = 90
c = 74.447γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2013-02-13
    Changes: Non-polymer description
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations