4BTL | pdb_00004btl

Aromatic interactions in acetylcholinesterase-inhibitor complexes

• PDB DOI: https://doi.org/10.2210/pdb4BTL/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2013-06-18 Released: 2013-09-11 
• Deposition Author(s): Andersson, C.D., Forsgren, N., Akfur, C., Allgardsson, A., Qian, W., Engdahl, C., Berg, L., Ekstrom, F., Linusson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.232 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Divergent Structure-Activity Relationships of Structurally Similar Acetylcholinesterase Inhibitors.

Andersson, C.D., Forsgren, N., Akfur, C., Allgardsson, A., Berg, L., Engdahl, C., Qian, W., Ekstrom, F.J., Linusson, A.

(2013) J Med Chem 56: 7615

• PubMed: 23984975 
• DOI: https://doi.org/10.1021/jm400990p
• Primary Citation Related Structures: 
  4B7Z, 4B80, 4B81, 4B82, 4B83, 4B84, 4B85, 4BTL


• PubMed Abstract: 
  

  The molecular interactions between the enzyme acetylcholinesterase (AChE) and two compound classes consisting of N-[2-(diethylamino)ethyl]benzenesulfonamides and N-[2-(diethylamino)ethyl]benzenemethanesulfonamides have been investigated using organic synthesis, enzymatic assays, X-ray crystallography, and thermodynamic profiling. The inhibitors' aromatic properties were varied to establish structure-activity relationships (SAR) between the inhibitors and the peripheral anionic site (PAS) of AChE. The two structurally similar compound classes proved to have distinctly divergent SARs in terms of their inhibition capacity of AChE. Eight X-ray structures revealed that the two sets have different conformations in PAS. Furthermore, thermodynamic profiles of the binding between compounds and AChE revealed class-dependent differences of the entropy/enthalpy contributions to the free energy of binding. Further development of the entropy-favored compound class resulted in the synthesis of the most potent inhibitor and an extension beyond the established SARs. The divergent SARs will be utilized to develop reversible inhibitors of AChE into reactivators of nerve agent-inhibited AChE.

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Organizational Affiliation: 
• Department of Chemistry, Umeå University , SE-901 87 Umeå, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 129.36 kDa 
• Atom Count: 8,961 
• Modeled Residue Count: 1,069 
• Deposited Residue Count: 1,086 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYLCHOLINESTERASE	A, B	543	Mus musculus	Mutation(s): 0  EC: 3.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P21836 (Mus musculus) Explore P21836  Go to UniProtKB:  P21836
IMPC:  MGI:87876
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P21836-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE3	E [auth A], F [auth A], J [auth A], L [auth A], M [auth A], O [auth B], Q [auth B], T [auth B], U [auth B], W [auth B], Y [auth B]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C28 H58 O15 ILLKMACMBHTSHP-UHFFFAOYSA-N
5GZ	C [auth A], I [auth A], N [auth B], V [auth B]	4-(2-chloro-6-nitrophenoxy)-N-[2-(diethylamino)ethyl]benzenesulfonamide C18 H22 Cl N3 O5 S NBPRMWUQGSKNES-UHFFFAOYSA-N
NAG	D [auth A], G [auth A], P [auth B], R [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	H [auth A], K [auth A], S [auth B], X [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5GZ	BindingDB:  4BTL	IC50: 2500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.232 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.671	α = 90
b = 110.824	β = 90
c = 227.112	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Andersson, C.D., Forsgren, N., Akfur, C., Allgardsson, A., Qian, W., Engdahl, C., Berg, L., Ekstrom, F., Linusson, A.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-10-16
  Changes: Structure summary