Crystal Structure of p38alpha in Complex with Lipid Pocket Ligand 9j

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Structure-based design, synthesis and crystallization of 2-arylquinazolines as lipid pocket ligands of p38 alpha MAPK.

Buhrmann, M.Wiedemann, B.M.Muller, M.P.Hardick, J.Ecke, M.Rauh, D.

(2017) PLoS One 12: e0184627-e0184627

  • DOI: https://doi.org/10.1371/journal.pone.0184627
  • Primary Citation of Related Structures:  
    5N63, 5N64, 5N65, 5N66, 5N67, 5N68

  • PubMed Abstract: 

    In protein kinase research, identifying and addressing small molecule binding sites other than the highly conserved ATP-pocket are of intense interest because this line of investigation extends our understanding of kinase function beyond the catalytic phosphotransfer. Such alternative binding sites may be involved in altering the activation state through subtle conformational changes, control cellular enzyme localization, or in mediating and disrupting protein-protein interactions. Small organic molecules that target these less conserved regions might serve as tools for chemical biology research and to probe alternative strategies in targeting protein kinases in disease settings. Here, we present the structure-based design and synthesis of a focused library of 2-arylquinazoline derivatives to target the lipophilic C-terminal binding pocket in p38α MAPK, for which a clear biological function has yet to be identified. The interactions of the ligands with p38α MAPK was analyzed by SPR measurements and validated by protein X-ray crystallography.

  • Organizational Affiliation

    Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B96

Download Ideal Coordinates CCD File 
C31 H37 N5 O3
Query on BW1

Download Ideal Coordinates CCD File 
B [auth A]~{N}4-[[4-(cyclopropylmethyl)furan-2-yl]methyl]-2-phenyl-quinazoline-4,7-diamine
C23 H22 N4 O
Binding Affinity Annotations 
IDSourceBinding Affinity
B96 BindingDB:  5N66 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)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.75α = 90
b = 74β = 90
c = 79.23γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Federal Ministry for Education and Research (NGFNPlus and e:Med)GermanyBMBF 01GS08104, 01ZX1303C

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description