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Two Classes of p38alpha MAP Kinase Inhibitors Having a Common Diphenylether Core but Exhibiting Divergent Binding Modes

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Two classes of p38alpha MAP kinase inhibitors having a common diphenylether core but exhibiting divergent binding modes.

Michelotti, E.L., Moffett, K.K., Nguyen, D., Kelly, M.J., Shetty, R., Chai, X., Northrop, K., Namboodiri, V., Campbell, B., Flynn, G.A., Fujimoto, T., Hollinger, F.P., Bukhtiyarova, M., Springman, E.B., Karpusas, M.

(2005) Bioorg Med Chem Lett 15: 5274-5279

  • DOI: 10.1016/j.bmcl.2005.08.038
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Two new classes of diphenylether inhibitors of p38alpha MAP kinase are described. Both chemical classes are based on a common diphenylether core that is identified by simulated fragment annealing as one of the most favored chemotypes within a promine ...

    Two new classes of diphenylether inhibitors of p38alpha MAP kinase are described. Both chemical classes are based on a common diphenylether core that is identified by simulated fragment annealing as one of the most favored chemotypes within a prominent hydrophobic pocket of the p38alpha ATP-binding site. In the fully elaborated molecules, the diphenylether moiety acts as an anchor occupying the deep pocket, while polar extensions make specific interactions with either the adenine binding site or the phosphate binding site of ATP. The synthesis, crystallographic analysis, and biological activity of these p38alpha inhibitors are discussed.

    Organizational Affiliation: 

    Department of Chemistry, Locus Pharmaceuticals, Inc., Four Valley Square, 512 Township Line Rd, Blue Bell, PA 19422, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14A360Homo sapiensMutation(s): 0 
Gene Names: MAPK14, CSBP, CSBP1, CSBP2, MXI2, CSPB1, SAPK2A
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539
GTEx  ENSG00000112062
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B11
Query on B11
Download CCD File 
A
N-[3-(4-FLUOROPHENOXY)PHENYL]-4-[(2-HYDROXYBENZYL)AMINO]PIPERIDINE-1-SULFONAMIDE
C24 H26 F N3 O4 S
JHHBGNIRSUTQAS-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 %)
B11IC50:  6000   nM  Binding MOAD
B11IC50:  6000   nM  BindingDB
B11IC50 :  6000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.262 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.29α = 90
b = 74.23β = 90
c = 74.42γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary