9I5Q | pdb_00009i5q

Recombinant human butyrylcholinesterase in complex with 2-(cyclohexylmethyl)-5-(2,4-difluorophenoxy)-N-(2-(3-(methoxymethyl)piperidin-1-yl)ethyl)-2H-indazole-6-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.222 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.184 (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 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00933
  • Primary Citation of Related Structures:  
    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
Cholinesterase529Homo sapiensMutation(s): 4 
Gene Names: BCHECHE1
EC: 3.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P06276 (Homo sapiens)
Explore P06276 
Go to UniProtKB:  P06276
PHAROS:  P06276
GTEx:  ENSG00000114200 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06276
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P06276-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
3N-Glycosylation
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IZ3 (Subject of Investigation/LOI)
Query on A1IZ3

Download Ideal Coordinates CCD File 
I [auth A]5-[2,4-bis(fluoranyl)phenoxy]-2-(cyclohexylmethyl)-~{N}-[2-[(3~{R})-3-(methoxymethyl)piperidin-1-yl]ethyl]indazole-6-carboxamide
C30 H38 F2 N4 O3
OJJHRKPNNTZEQJ-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
J [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
O [auth A],
P [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A],
S [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.222 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.391α = 90
b = 155.391β = 90
c = 126.766γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Ministry of Armed ForcesFranceNBC-5-C-2316

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release