4R3C

Crystal structure of p38 alpha MAP kinase in complex with a novel isoform selective drug candidate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Targeting human central nervous system protein kinases: An isoform selective p38 alpha MAPK inhibitor that attenuates disease progression in Alzheimer's disease mouse models.

Roy, S.M., Grum-Tokars, V.L., Schavocky, J.P., Saeed, F., Staniszewski, A., Teich, A.F., Arancio, O., Bachstetter, A.D., Webster, S.J., Van Eldik, L.J., Minasov, G., Anderson, W.F., Pelletier, J.C., Watterson, D.M.

(2015) ACS Chem Neurosci 6: 666-680

  • DOI: 10.1021/acschemneuro.5b00002
  • Primary Citation of Related Structures:  
    4R3C

  • PubMed Abstract: 

    • The first kinase inhibitor drug approval in 2001 initiated a remarkable decade of tyrosine kinase inhibitor drugs for oncology indications, but a void exists for serine/threonine protein kinase inhibitor drugs and central nervous system indications. ...

    The first kinase inhibitor drug approval in 2001 initiated a remarkable decade of tyrosine kinase inhibitor drugs for oncology indications, but a void exists for serine/threonine protein kinase inhibitor drugs and central nervous system indications. Stress kinases are of special interest in neurological and neuropsychiatric disorders due to their involvement in synaptic dysfunction and complex disease susceptibility. Clinical and preclinical evidence implicates the stress related kinase p38αMAPK as a potential neurotherapeutic target, but isoform selective p38αMAPK inhibitor candidates are lacking and the mixed kinase inhibitor drugs that are promising in peripheral tissue disease indications have limitations for neurologic indications. Therefore, pursuit of the neurotherapeutic hypothesis requires kinase isoform selective inhibitors with appropriate neuropharmacology features. Synaptic dysfunction disorders offer a potential for enhanced pharmacological efficacy due to stress-induced activation of p38αMAPK in both neurons and glia, the interacting cellular components of the synaptic pathophysiological axis, to be modulated. We report a novel isoform selective p38αMAPK inhibitor, MW01-18-150SRM (=MW150), that is efficacious in suppression of hippocampal-dependent associative and spatial memory deficits in two distinct synaptic dysfunction mouse models. A synthetic scheme for biocompatible product and positive outcomes from pharmacological screens are presented. The high-resolution crystallographic structure of the p38αMAPK/MW150 complex documents active site binding, reveals a potential low energy conformation of the bound inhibitor, and suggests a structural explanation for MW150's exquisite target selectivity. As far as we are aware, MW150 is without precedent as an isoform selective p38MAPK inhibitor or as a kinase inhibitor capable of modulating in vivo stress related behavior.

    Organizational Affiliation: 

    †Northwestern University, Chicago, Illinois 60611, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A383Homo sapiensMutation(s): 0 
Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A
EC: 2.7.11.24
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3GF
Query on 3GF
Download CCD File 
A
6-(4-methylpiperazin-1-yl)-3-(naphthalen-2-yl)-4-(pyridin-4-yl)pyridazine
C24 H23 N5
CIIVUDIZZJLXCN-UHFFFAOYSA-N		 Ligand Interaction
GG5
Query on GG5
Download CCD File 
A
4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE
C14 H10 F N3
BILJSHVAAVZERY-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME		AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.85α = 90
b = 74.512β = 90
c = 77.808γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description