3HV3

Human p38 MAP Kinase in Complex with RL49


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Displacement assay for the detection of stabilizers of inactive kinase conformations.

Kluter, S.Grutter, C.Naqvi, T.Rabiller, M.Simard, J.R.Pawar, V.Getlik, M.Rauh, D.

(2010) J Med Chem 53: 357-367

  • DOI: https://doi.org/10.1021/jm901297e
  • Primary Citation of Related Structures:  
    3HV3, 3HV4, 3HV5, 3HV6, 3HV7

  • PubMed Abstract: 

    Targeting protein kinases with small molecules outside the highly conserved ATP pocket to stabilize inactive kinase conformations is becoming a more desirable approach in kinase inhibitor research, since these molecules have advanced pharmacological properties compared to compounds exclusively targeting the ATP pocket. Traditional screening approaches for kinase inhibitors are often based on enzyme activity, but they may miss inhibitors that stabilize inactive kinase conformations by enriching the active state of the kinase. Here we present the development of a kinase binding assay employing a pyrazolourea type III inhibitor and enzyme fragment complementation (EFC) technology that is suitable to screen stabilizers of enzymatically inactive kinases. To validate this assay system, we report the binding characteristics of a series of kinase inhibitors to inactive p38alpha and JNK2. Additionally, we present protein X-ray crystallography studies to examine the binding modes of potent quinoline-based DFG-out binders in p38alpha.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo sapiensMutation(s): 4 
Gene Names: MAPK14CSBPCSBP1CSBP2CSPB1MXI2
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R49
Query on R49

Download Ideal Coordinates CCD File 
B [auth A]1-{4-[(6-aminoquinolin-4-yl)amino]phenyl}-3-[3-tert-butyl-1-(3-methylphenyl)-1H-pyrazol-5-yl]urea
C30 H31 N7 O
MKHUGLZLKVCOGF-UHFFFAOYSA-N
BOG
Query on BOG

Download Ideal Coordinates CCD File 
C [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
R49 PDBBind:  3HV3 IC50: 470 (nM) from 1 assay(s)
BindingDB:  3HV3 IC50: min: 470, max: 900 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.51α = 90
b = 74.52β = 90
c = 76.98γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

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: Non-polymer description, 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: 2021-10-13
    Changes: Database references, Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description