3P7A

p38 inhibitor-bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery of a novel class of non-ATP site DFG-out state p38 inhibitors utilizing computationally assisted virtual fragment-based drug design (vFBDD).

Moffett, K.Konteatis, Z.Nguyen, D.Shetty, R.Ludington, J.Fujimoto, T.Lee, K.J.Chai, X.Namboodiri, H.Karpusas, M.Dorsey, B.Guarnieri, F.Bukhtiyarova, M.Springman, E.Michelotti, E.

(2011) Bioorg.Med.Chem.Lett. 21: 7155-7165

  • DOI: 10.1016/j.bmcl.2011.09.078
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Discovery of a new class of DFG-out p38α kinase inhibitors with no hinge interaction is described. A computationally assisted, virtual fragment-based drug design (vFBDD) platform was utilized to identify novel non-aromatic fragments which make produc ...

    Discovery of a new class of DFG-out p38α kinase inhibitors with no hinge interaction is described. A computationally assisted, virtual fragment-based drug design (vFBDD) platform was utilized to identify novel non-aromatic fragments which make productive hydrogen bond interactions with Arg 70 on the αC-helix. Molecules incorporating these fragments were found to be potent inhibitors of p38 kinase. X-ray co-crystal structures confirmed the predicted binding modes. A lead compound was identified as a potent (p38α IC(50)=22 nM) and highly selective (≥ 150-fold against 150 kinase panel) DFG-out p38 kinase inhibitor.


    Organizational Affiliation

    Ansaris, Four Valley Square, 512 East Township Line Road, Blue Bell, PA 19422, USA. kmistry@earthlink.net




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14
A
366Mus musculusMutation(s): 0 
Gene Names: Mapk14 (Crk1, Csbp1, Csbp2)
EC: 2.7.11.24
Find proteins for P47811 (Mus musculus)
Go to UniProtKB:  P47811
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P7A
Query on P7A

Download SDF File 
Download CCD File 
A
1-[5-tert-butyl-2-(1,1-dioxidothiomorpholin-4-yl)thiophen-3-yl]-3-naphthalen-1-ylurea
C23 H27 N3 O3 S2
VRPGNWGNMYKKMF-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P7AIC50: 520 nM (99) BINDINGDB
P7AIC50: 520 nM BINDINGMOAD
P7AIC50: 520 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.140α = 90.00
b = 74.510β = 90.00
c = 74.410γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
CNSrefinement
HKL-2000data reduction
CNSphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2011-11-09
    Type: Database references
  • Version 1.2: 2012-01-25
    Type: Database references
  • Version 1.3: 2019-07-17
    Type: Data collection, Refinement description