3P7B

p38 inhibitor-bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Structures With Same Primary Citation

  • 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 14A366Mus musculusMutation(s): 0 
Gene Names: Mapk14Crk1Csbp1Csbp2
EC: 2.7.11.24
Find proteins for P47811 (Mus musculus)
Explore P47811 
Go to UniProtKB:  P47811
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P7B
Query on P7B

Download CCD File 
A
1-{5-tert-butyl-3-[(5-oxo-1,4-diazepan-1-yl)carbonyl]thiophen-2-yl}-3-naphthalen-1-ylurea
C25 H28 N4 O3 S
SNHWMEWYAPKRQL-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

Download CCD File 
A
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P7BIC50:  18   nM  BindingDB
P7BIC50 :  18   nM  PDBBind
P7BIC50:  18   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.4α = 90
b = 70.99β = 90
c = 75.55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2011-11-09
    Changes: Database references
  • Version 1.2: 2012-01-25
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary