Structure of acetylcholinesterase (E.C. complexed with (S,S)-(-)-bis(12)-hupyridone at 2.15A resolution

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report

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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

  • DOI: 10.1021/ja021111w
  • Primary Citation of Related Structures:  
  • Also Cited By: 1ODC, 1UT6, 1ZGB, 1ZGC

  • PubMed Abstract: 
  • Acetylcholinesterase (AChE) inhibitors improve the cognitive abilities of Alzheimer patients. (-)-Huperzine A [(-)-HupA], an alkaloid isolated from the club moss, Huperzia serrata, is one such inhibitor, but the search for more potent and selective d ...

    Acetylcholinesterase (AChE) inhibitors improve the cognitive abilities of Alzheimer patients. (-)-Huperzine A [(-)-HupA], an alkaloid isolated from the club moss, Huperzia serrata, is one such inhibitor, but the search for more potent and selective drugs continues. Recently, alkylene-linked dimers of 5-amino-5,6,7,8-tetrahydroquinolinone (hupyridone, 1a), a fragment of HupA, were shown to serve as more potent inhibitors of AChE than (-)-HupA and monomeric 1a. We soaked two such dimers, (S,S)-(-)-bis(10)-hupyridone [(S,S)-(-)-2a] and (S,S)-(-)-bis(12)-hupyridone [(S,S)-(-)-2b] containing, respectively, 10 and 12 methylenes in the spacer, into trigonal TcAChE crystals, and solved the X-ray structures of the resulting complexes using the difference Fourier technique, both to 2.15 A resolution. The structures revealed one HupA-like 1a unit bound to the "anionic" subsite of the active-site, near the bottom of the active-site gorge, adjacent to Trp84, as seen for the TcAChE/(-)-HupA complex, and the second 1a unit near Trp279 in the "peripheral" anionic site at the top of the gorge, both bivalent molecules thus spanning the active-site gorge. The results confirm that the increased affinity of the dimeric HupA analogues for AChE is conferred by binding to the two "anionic" sites of the enzyme. Inhibition data show that (-)-2a binds to TcAChE approximately 6-7- and > 170-fold more tightly than (-)-2b and (-)-HupA, respectively. In contrast, previous data for rat AChE show that (-)-2b binds approximately 3- and approximately 2-fold more tightly than (-)-2a and (-)-HupA, respectively. Structural comparison of TcAChE with rat AChE, as represented by the closely related mouse AChE structure (1maa.pdb), reveals a narrower gorge for rat AChE, a perpendicular alignment of the Tyr337 ring to the gorge axis, and its conformational rigidity, as a result of hydrogen bonding between its hydroxyl group and that of Tyr341, relative to TcAChE Phe330. These structural differences in the active-site gorge explain the switch in inhibitory potency of (-)-2a and 2b and the larger dimer/(-)-HupA potency ratios observed for TcAChE relative to rat AChE. The results offer new insights into factors affecting protein-ligand complementarity within the gorge and should assist the further development of improved AChE inhibitors.

    Related Citations: 
    • 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
    • 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
    • Dimerization of an Inactive Fragment of Huperzine a Produces a Drug with Twice the Potency of the Natural Product
      Carlier, P.R.,Du, D.-M.,Han, Y.-F.,Liu, J.,Perola, E.,Williams, I.D.,Pang, Y.-P.
      (2000) Angew.Chem.Int.Ed.Engl. 39: 1775
    • Structure of Acetylcholinesterase Complexed with the Nootropic Alkaloid, (-)-Huperzine A
      Raves, M.L.,Harel, M.,Pang, Y.-P.,Silman, I.,Kozikowski, A.P.,Sussman, J.L.
      (1997) Nat.Struct.Mol.Biol. 4: 57

    Organizational Affiliation

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


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
543Tetronarce californicaGene Names: ache
Find proteins for P04058 (Tetronarce californica)
Go to UniProtKB:  P04058
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on E12

Download SDF File 
Download CCD File 
C30 H46 N4 O2
 Ligand Interaction
Query on NAG

Download SDF File 
Download CCD File 
C8 H15 N O6
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
E12Ki: 4.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.794α = 90.00
b = 111.794β = 90.00
c = 137.775γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-23
    Type: Initial release
  • Version 1.1: 2011-08-31
    Type: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2014-01-22
    Type: Database references