1ZZ2

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 

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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
  • Primary Citation of Related Structures:  
    1ZYJ, 1ZZ2

  • 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 prominent hydrophobic pocket of the p38alpha ATP-binding site ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
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)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B11
Query on B11
Download Ideal Coordinates CCD File 
C [auth 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 Ideal Coordinates CCD File 
B [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B11 BindingDB:  1ZZ2 IC50: 6000 (nM) from 1 assay(s)
PDBBind:  1ZZ2 IC50: 6000 (nM) from 1 assay(s)
Binding MOAD:  1ZZ2 IC50: 6000 (nM) from 1 assay(s)
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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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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