3I6Z

3D Structure of Torpedo californica acetylcholinesterase complexed with N-saccharinohexyl-galanthamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Probing Torpedo californica acetylcholinesterase catalytic gorge with two novel bis-functional galanthamine derivatives.

Bartolucci, C.Haller, L.A.Jordis, U.Fels, G.Lamba, D.

(2010) J.Med.Chem. 53: 745-751

  • DOI: 10.1021/jm901296p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-Piperidinopropyl-galanthamine (2) and N-saccharinohexyl-galanthamine (3) were used to investigate interaction sites along the active site gorge of Torpedo californica actylcholinesterase (TcAChE). The crystal structure of TcAChE-2 solved at 2.3 A s ...

    N-Piperidinopropyl-galanthamine (2) and N-saccharinohexyl-galanthamine (3) were used to investigate interaction sites along the active site gorge of Torpedo californica actylcholinesterase (TcAChE). The crystal structure of TcAChE-2 solved at 2.3 A showed that the N-piperidinopropyl group in 2 is not stretched along the gorge but is folded over the galanthamine moiety. This result was unexpected because the three carbon alkyl chain is just long enough for the bulky piperidine group to be placed above the bottleneck (Tyr121, Phe330) midway down the gorge. The crystal structure of TcAChE-3 at 2.2 A confirmed that a dual interaction with the sites at the bottom, and at the entrance of the gorge, enhances inhibitory activity: a chain of six carbon atoms has, in this class of derivatives, the correct length for optimal interactions with the peripheral anionic site (PAS).


    Related Citations: 
    • Accurate prediction of the bound conformation of galanthamine in the active site of Torpedo californica acetylcholinesterase using molecular docking
      Pilger, C.,Bartolucci, C.,Lamba, D.,Tropsha, A.,Fels, G.
      (2001) J.MOL.GRAPH.MODEL. 19: 288
    • The complex of a bivalent derivative of galanthamine with Torpedo acetylcholinesterase displays drastic deformation of the active-site gorge: implications for structure-based drug design
      Greenblatt, H.M.,Guillou, C.,Guenard, D.,Argaman, A.,Botti, S.,Badet, B.,Thal, C.,Silman, I.,Sussman, J.L.
      (2004) J.Am.Chem.Soc. 126: 15405
    • Galanthamine as bis-functional ligand for the acetylcholinesterase.
      Luttmann, E.,Linnemann, E.,Fels, G.
      (2002) J.Mol.Model. 8: 208
    • Structure of acetylcholinesterase complexed with (-)-galanthamine at 2.3A resolution
      Greenblatt, H.M.,Kryger, G.,Lewis, T.,Silman, I.,Sussman, J.L.
      (1999) FEBS Lett. 463: 321
    • Three-dimensional structure of a complex of galanthamine (Nivalin) with acetylcholinesterase from Torpedo californica: implications for the design of new anti-Alzheimer drugs
      Bartolucci, C.,Perola, E.,Pilger, C.,Fels, G.,Lamba, D.
      (2001) PROTEINS 42: 182
    • A QXP-based multistep docking procedure for accurate prediction of protein-ligand complexes
      Alisaraie, L.,Fels, G.
      (2006) J.Chem.Inf.Model. 46: 1174


    Organizational Affiliation

    Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Area della Ricerca di Roma, P.O. Box 10, I-00016 Monterotondo Stazione(Roma), Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetylcholinesterase
A
534Tetronarce 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
G6X
Query on G6X

Download SDF File 
Download CCD File 
A
2-{6-[(4aS,6R,8aS)-6-hydroxy-3-methoxy-5,6,9,10-tetrahydro-4aH-[1]benzofuro[3a,3,2-ef][2]benzazepin-11(12H)-yl]hexyl}-1,2-benzisothiazol-3(2H)-one 1,1-dioxide
2-[6-[(4aS,6R,8aS)-4a,5,9,10-tetrahydro-6-hydroxy-3-methoxy-6H-benzofuro[3a,3,2-ef][2]benzazepin-11(12H)-yl]hexyl]-1,2-benzisothiazol-3(2H)-one 1,1-dioxide
C29 H34 N2 O6 S
VAEMEXGGRSPJEF-LOMAHXHCSA-N
 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G6XIC50: 50 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.339α = 90.00
b = 111.339β = 90.00
c = 137.207γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
MAR345data collection
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description