Crystal structure of P38 alpha in complex with DP437

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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This is version 1.4 of the entry. See complete history


Switch control pocket inhibitors of p38-MAP kinase. Durable type II inhibitors that do not require binding into the canonical ATP hinge region

Ahn, Y.M.Clare, M.Ensinger, C.L.Hood, M.M.Lord, J.W.Lu, W.P.Miller, D.F.Patt, W.C.Smith, B.D.Vogeti, L.Kaufman, M.D.Petillo, P.A.Wise, S.C.Abendroth, J.Chun, L.Clark, R.Feese, M.Kim, H.Stewart, L.Flynn, D.L.

(2010) Bioorg Med Chem Lett 20: 5793-5798

  • DOI: https://doi.org/10.1016/j.bmcl.2010.07.134
  • Primary Citation of Related Structures:  
    3NNU, 3NNV, 3NNW, 3NNX

  • PubMed Abstract: 

    Switch control pocket inhibitors of p38-alpha kinase are described. Durable type II inhibitors were designed which bind to arginines (Arg67 or Arg70) that function as key residues for mediating phospho-threonine 180 dependant conformational fluxing of p38-alpha from an inactive type II state to an active type I state. Binding to Arg70 in particular led to potent inhibitors, exemplified by DP-802, which also exhibited high kinase selectivity. Binding to Arg70 obviated the requirement for binding into the ATP Hinge region. X-ray crystallography revealed that DP-802 and analogs induce an enhanced type II conformation upon binding to either the unphosphorylated or the doubly phosphorylated form of p38-alpha kinase.

  • Organizational Affiliation

    Deciphera Pharmaceuticals LLC, 643 Massachusetts St, Lawrence, KS 66044, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14354Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 437

Download Ideal Coordinates CCD File 
B [auth A]1-{3-tert-butyl-1-[4-(hydroxymethyl)phenyl]-1H-pyrazol-5-yl}-3-naphthalen-1-ylurea
C25 H26 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
437 BindingDB:  3NNV IC50: 27 (nM) from 1 assay(s)
Binding MOAD:  3NNV IC50: 27 (nM) from 1 assay(s)
PDBBind:  3NNV IC50: 27 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.561α = 90
b = 86.334β = 90
c = 125.774γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data 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: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-05
    Changes: Non-polymer description
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations