5O8V | pdb_00005o8v

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

• PDB DOI: https://doi.org/10.2210/pdb5O8V/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-06-14 Released: 2017-09-06 
• Deposition Author(s): Buehrmann, M., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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

• PubMed: 28834017 
• DOI: https://doi.org/10.1002/anie.201706345
• Primary Citation Related Structures: 
  5O8U, 5O8V


• 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 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.

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

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.77 kDa 
• Atom Count: 2,708 
• Modeled Residue Count: 328 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 1  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9O2	B [auth A]	~{N}-[3-[7-azanyl-4-(2-phenylethylamino)quinazolin-2-yl]phenyl]propanamide C25 H25 N5 O VKNJKOQEMPCERA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.2	α = 90
b = 74.25	β = 90
c = 77.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Buehrmann, M., Rauh, D.

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2018-05-02
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary