9D75 | pdb_00009d75

Human p38alpha MAP Kinase in complex with 1-(Cyclohexylmethyl)-1H-indazole derivative; OSF346


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.236 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Targeting Neuroinflammation and Cognitive Decline: First-in-Class Dual Butyrylcholinesterase and p38 alpha Mitogen-Activated Protein Kinase Inhibitors.

Ferjancic Benetik, S.Proj, M.Knez, D.Kosak, U.Meden, A.Krajsek, K.Pislar, A.Horvat, S.Svajger, U.Tesic, N.Pulkrabkova, L.Soukup, O.Skarka, A.Andrys, R.Brazzolotto, X.Igert, A.Nachon, F.Dias, J.Detka, J.Gdula-Argasinska, J.Wyska, E.Szafarz, M.Manik, A.Plachtij, N.Musilek, K.Salat, K.Obreza, A.Gobec, S.

(2025) J Med Chem 68: 17378-17411

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00933
  • Primary Citation of Related Structures:  
    9D75, 9D7N, 9I5O, 9I5P, 9I5Q

  • PubMed Abstract: 

    The currently approved drugs for the treatment of Alzheimer's disease (AD) fail to address its interconnected pathological processes. Inhibition of butyrylcholinesterase (BChE) and p38α mitogen-activated protein kinase (p38α MAPK) offers an innovative dual approach to mitigate two major drivers of neurodegeneration in AD: cholinergic deficit and neuroinflammation. Using structure-based drug design and a library of known p38α MAPK inhibitors, we developed first-in-class, selective dual BChE/p38α MAPK inhibitors with balanced activity against both targets. The X-ray crystal structures of the two most promising molecules bound to both enzymes were solved. Those ligands effectively reduced the production of proinflammatory markers in vitro and ex vivo in phytohemagglutinin/lipopolysaccharide neuroinflammation models. Remarkably, these compounds also significantly improved cognition in scopolamine- and lipopolysaccharide-induced models of cognitive dysfunction in mice. Because our dual-acting inhibitors target both the symptoms and the underlying neuropathology, they offer an innovative and comprehensive strategy to combat AD.


  • Organizational Affiliation
    • Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, 1000 Ljubljana, Slovenia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14346Homo sapiensMutation(s): 0 
Gene Names: MAPK14CSBPCSBP1CSBP2CSPB1MXI2SAPK2A
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A2L (Subject of Investigation/LOI)
Query on A1A2L

Download Ideal Coordinates CCD File 
B [auth A]1-(cyclohexylmethyl)-5-[(2,4-difluorophenyl)methyl]-N-[2-(dimethylamino)ethyl]-1H-indazole-6-carboxamide
C26 H32 F2 N4 O
KRBANHWMWFMMPJ-UHFFFAOYSA-N
GG5
Query on GG5

Download Ideal Coordinates CCD File 
C [auth A]4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE
C14 H10 F N3
BILJSHVAAVZERY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.236 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.906α = 90
b = 75.48β = 90
c = 78.923γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release