1H23

Structure of acetylcholinesterase (E.C. 3.1.1.7) complexed with (S,S)-(-)-bis(12)-hupyridone at 2.15A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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
  • Structures With Same Primary Citation

  • 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: 
    • 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 Biol 4: 57
    • 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
    • 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

    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
543Tetronarce 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
E12
Query on E12

Download CCD File 
A
(S,S)-(-)-N,N'-DI-5'-[5',6',7',8'-TETRAHYDRO- 2'(1'H)-QUINOLYNYL]-1,12-DIAMINODODECANE DIHYDROCHLORIDE
C30 H46 N4 O2
VFFGYPZORQBRNM-UIOOFZCWSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
E12Ki:  4.5   nM  BindingDB
E12IC50:  16   nM  BindingDB
E12Ki :  4.5   nM  PDBBind
E12Ki:  4.5   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.794α = 90
b = 111.794β = 90
c = 137.775γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-23
    Type: Initial release
  • Version 1.1: 2011-08-31
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2014-01-22
    Changes: Database references
  • Version 1.3: 2019-04-03
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other