3NNW

Crystal structure of P38 alpha in complex with DP802


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  

  • 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: MAPK14 (CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A)
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Go to Gene View: MAPK14
Go to UniProtKB:  Q16539
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDD
Query on EDD

Download SDF File 
Download CCD File 
A
2-[3-(3-tert-butyl-5-{[(2,3-dichlorophenyl)carbamoyl]imino}-2,5-dihydro-1H-pyrazol-1-yl)phenyl]acetamide
C22 H23 Cl2 N5 O2
LLLDJNNXZHGRQO-ZXVVBBHZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EDDIC50: 9 nM BINDINGMOAD
EDDIC50: 9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.551α = 90.00
b = 85.956β = 90.00
c = 126.584γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
StructureStudiodata collection
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description