3NNV

Crystal structure of P38 alpha in complex with DP437


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1016/j.bmcl.2010.07.134
  • Structures With Same Primary Citation

  • 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 o ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14
A
354Homo sapiensMutation(s): 0 
Gene Names: MAPK14CSBPCSBP1CSBP2CSPB1MXI2SAPK2A
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
437
Query on 437

Download CCD File 
A
1-{3-tert-butyl-1-[4-(hydroxymethyl)phenyl]-1H-pyrazol-5-yl}-3-naphthalen-1-ylurea
C25 H26 N4 O2
MKYJHFRHAZBFKJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
437IC50 :  27   nM  PDBBind
437IC50:  27   nM  Binding MOAD
437IC50:  27   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-06-24 
  • Released Date: 2010-09-15 
  • Deposition Author(s): Abendroth, J.

Revision History 

  • 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