5O8V

Covalent Inhibitor 4a bound to the Lipid Pocket of p38alpha Mutant S251C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Covalent Lipid Pocket Ligands Targeting p38 alpha MAPK Mutants.

Buhrmann, M.Hardick, J.Weisner, J.Quambusch, L.Rauh, D.

(2017) Angew. Chem. Int. Ed. Engl. 56: 13232-13236

  • DOI: 10.1002/anie.201706345
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A chemical genetic approach is presented to covalently target a unique lipid binding pocket in the protein kinase p38α, whose function is not yet known. Based on a series of cocrystal structures, a library of 2-arylquinazolines that were decorated wi ...

    A chemical genetic approach is presented to covalently target a unique lipid binding pocket in the protein kinase p38α, whose function is not yet known. Based on a series of cocrystal structures, a library of 2-arylquinazolines that were decorated with electrophiles were designed and synthesized to covalently target tailored p38α mutants containing artificially introduced cysteine residues. Matching protein-ligand pairs were identified by MS analysis and further validated by MS/MS studies and protein crystallography. The covalent ligands that emerged from this approach showed excellent selectivity towards a single p38α mutant and will be applicable as suitable probes in future studies of biological systems to dissect the function of the lipid pocket by means of pharmacological perturbations.


    Organizational Affiliation

    Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14
A
360Homo sapiensMutation(s): 1 
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
9O2
Query on 9O2

Download SDF File 
Download CCD File 
A
~{N}-[3-[7-azanyl-4-(2-phenylethylamino)quinazolin-2-yl]phenyl]propanamide
C25 H25 N5 O
VKNJKOQEMPCERA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.200α = 90.00
b = 74.250β = 90.00
c = 77.820γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references
  • Version 1.2: 2018-05-02
    Type: Data collection