4B80 | pdb_00004b80

Mus musculus Acetylcholinesterase in complex with N-(2-Diethylamino-ethyl)-1-(4-fluoro-phenyl)-methanesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.223 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4B80

Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

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.Linusson, A.

(2013) J Med Chem 56: 7615-7624

  • 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.


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

Macromolecule Content 

  • Total Structure Weight: 123.53 kDa 
  • Atom Count: 8,861 
  • Modeled Residue Count: 1,071 
  • Deposited Residue Count: 1,096 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACETYLCHOLINESTERASE
A, B
548Mus musculusMutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21836
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P21836-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P4C

Query on P4C



Download:Ideal Coordinates CCD File
X [auth B]O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
C14 H28 O8
CTLLATPOKUEFSQ-UHFFFAOYSA-N
A36

Query on A36



Download:Ideal Coordinates CCD File
C [auth A],
M [auth B]
N-[2-(diethylamino)ethyl]-1-(4-fluorophenyl)methanesulfonamide
C13 H21 F N2 O2 S
UKOZIEJMLUYTMK-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A],
I [auth A],
R [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
K [auth A],
Q [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
J [auth A]
P [auth B]
U [auth B]
G [auth A],
H [auth A],
J [auth A],
P [auth B],
U [auth B],
W [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]
L [auth A]
N [auth B]
S [auth B]
T [auth B]
D [auth A],
L [auth A],
N [auth B],
S [auth B],
T [auth B],
V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
A36 BindingDB:  4B80 IC50: 4.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.223 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.867α = 90
b = 111.543β = 90
c = 227.589γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2013-10-30
    Changes: Database references
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 2.0: 2018-07-11
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 2.2: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.3: 2024-10-16
    Changes: Structure summary