1UT6

Structure of acetylcholinesterase (E.C. 3.1.1.7) complexed with N-9-(1',2',3',4'-Tetrahydroacridinyl)-1,8- diaminooctane at 2.4 angstroms resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Complexes of Alkylene-Linked Tacrine Dimers with Torpedo Californica Acetylcholinesterase: Binding of Bis(5)-Tacrine Produces a Dramatic Rearrangement in the Active-Site Gorge.

Rydberg, E.H.Brumshtein, B.Greenblatt, H.M.Wong, D.M.Shaya, D.Williams, L.D.Carlier, P.R.Pang, Y.-P.Silman, I.Sussman, J.L.

(2006) J.Med.Chem. 49: 5491

  • DOI: 10.1021/jm060164b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The X-ray crystal structures were solved for complexes with Torpedo californica acetylcholinesterase of two bivalent tacrine derivative compounds in which the two tacrine rings were separated by 5- and 7-carbon spacers. The derivative with the 7-carb ...

    The X-ray crystal structures were solved for complexes with Torpedo californica acetylcholinesterase of two bivalent tacrine derivative compounds in which the two tacrine rings were separated by 5- and 7-carbon spacers. The derivative with the 7-carbon spacer spans the length of the active-site gorge, making sandwich interactions with aromatic residues both in the catalytic anionic site (Trp84 and Phe330) at the bottom of the gorge and at the peripheral anionic site near its mouth (Tyr70 and Trp279). The derivative with the 5-carbon spacer interacts in a similar manner at the bottom of the gorge, but the shorter tether precludes a sandwich interaction at the peripheral anionic site. Although the upper tacrine group does interact with Trp279, it displaces the phenyl residue of Phe331, thus causing a major rearrangement in the Trp279-Ser291 loop. The ability of this inhibitor to induce large-scale structural changes in the active-site gorge of acetylcholinesterase has significant implications for structure-based drug design because such conformational changes in the target enzyme are difficult to predict and to model.


    Related Citations: 
    • Heterodimeric Tacrine-Based Acetylcholinesterase Inhibitors: Investigating Ligand-Peripheral Site Interactions
      Carlier, P.R.,Chow, E.S.-H.,Han, Y.-F.,Liu, J.,El Yazal, J.,Pang, Y.-P.
      (1999) J.Med.Chem. 42: 4225
    • Quaternary Ligand Binding to Aromatic Residues in the Active-Site Gorge of Acetylcholinesterase
      Harel, M.,Schalk, I.,Ehret-Sabatier, L.,Bouet, F.,Goeldner, M.,Hirth, C.,Axelsen, P.H.,Silman, I.,Sussman, J.L.
      (1993) Proc.Natl.Acad.Sci.USA 90: 9031
    • Atomic Structure of Acetylcholinesterase from Torpedo Californica: A Prototypic Acetylcholine-Binding Protein
      Sussman, J.L.,Harel, M.,Frolow, F.,Oefner, C.,Goldman, A.,Toker, L.,Silman, I.
      (1991) Science 253: 872
    • Acetylcholinesterase Complexed with Bivalent Ligands Related to Huperzine A: Experimental Evidence for Species-Dependent Protein-Ligand Complementarity
      Wong, D.M.,Greenblatt, H.M.,Dvir, H.,Carlier, P.R.,Han, Y.-F.,Pang, Y.-P.,Silman, I.,Sussman, J.L.
      (2003) J.Am.Chem.Soc. 125: 363
    • Prediction of the Binding Sites of Huperzine a in Acetylcholinesterase by Docking Studies
      Pang, Y.-P.,Kozikowski, A.P.
      (1994) J. Comput. Aided Mol. Des. 8: 669


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACETYLCHOLINESTERASE
A
537Tetronarce californicaMutation(s): 0 
Gene Names: ache
EC: 3.1.1.7
Find proteins for P04058 (Tetronarce californica)
Go to UniProtKB:  P04058
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A8N
Query on A8N

Download SDF File 
Download CCD File 
A
N-9-(1',2',3',4'-TETRAHYDROACRIDINYL)-1,8-DIAMINOOCTANE
(9S)-9-[(8-AMMONIOOCTYL)AMINO]-1,2,3,4,9,10-HEXAHYDROACRIDINIUM
C21 H33 N3
LFBAUYQQFKFFCF-UHFFFAOYSA-P
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.194 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.193α = 90.00
b = 111.193β = 90.00
c = 136.853γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-21
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-04-03
    Type: Data collection, Database references, Derived calculations, Experimental preparation, Other