Structure of Inactive Human p38 MAP Kinase in Complex with a Thiazole-Urea

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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This is version 1.4 of the entry. See complete history


High-Throughput Screening To Identify Inhibitors Which Stabilize Inactive Kinase Conformations in p38alpha

Simard, J.R.Gruetter, C.Pawar, V.Aust, B.Wolf, A.Rabiller, M.Wulfert, S.Robubi, A.Kluter, S.Ottmann, C.Rauh, D.

(2009) J Am Chem Soc 131: 18478-18488

  • DOI: https://doi.org/10.1021/ja907795q
  • Primary Citation of Related Structures:  
    3IW5, 3IW6, 3IW7, 3IW8

  • PubMed Abstract: 

    Small molecule kinase inhibitors are an attractive means to modulate kinase activities in medicinal chemistry and chemical biology research. In the physiological setting of a cell, kinase function is orchestrated by a plethora of regulatory processes involving the structural transition of kinases between inactive and enzymatically competent conformations and vice versa. The development of novel kinase inhibitors is mainly fostered by high-throughput screening initiatives where the small molecule perturbation of the phosphorylation reaction is measured to identify inhibitors. Such setups require enzymatically active kinase preparations and present a risk of solely identifying classical ATP-competitive Type I inhibitors. Here we report the high-throughput screening of a library of approximately 35000 small organic molecules with an assay system that utilizes enzymatically inactive human p38alpha MAP kinase to detect stabilizers of the pharmacologically more desirable DFG-out conformation. We used protein X-ray crystallography to characterize the binding mode of hit compounds and reveal structural features which explain how these ligands stabilize and/or induce the DFG-out conformation. Lastly, we show that although some of the hit compounds were confirmed by protein X-ray crystallography, they were not detected in classic phosphorylation assays, thus validating the unique sensitivity of the assay system used in this study and highlighting the potential of screening with inactive kinase preparations.

  • Organizational Affiliation

    Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo sapiensMutation(s): 4 
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 HIZ

Download Ideal Coordinates CCD File 
B [auth A]1-{4-[(1S)-1-amino-2-(benzyloxy)ethyl]-1,3-thiazol-2-yl}-3-(3-chloro-4-fluorophenyl)urea
C19 H18 Cl F N4 O2 S
Query on BOG

Download Ideal Coordinates CCD File 
C [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
Binding Affinity Annotations 
IDSourceBinding Affinity
HIZ PDBBind:  3IW8 Kd: 1.34e+4 (nM) from 1 assay(s)
Binding MOAD:  3IW8 Kd: 1.34e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.37α = 90
b = 69.84β = 90
c = 74.7γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2021-11-10
    Changes: Database references, Structure summary
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description