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 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 2.0 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:  
    3I6M, 3I6Z

  • 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 showed that the N-piperidinopropyl group in 2 is not stretched along the gorge but is folded over the galanthamine moiety ...

    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: 
    • 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
    • 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
    • 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
    • Galanthamine as bis-functional ligand for the acetylcholinesterase.
      Luttmann, E., Linnemann, E., Fels, G.
      (2002) J Mol Model 8: 208
    • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AcetylcholinesteraseA534Tetronarce californicaMutation(s): 0 
Gene Names: ache
EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica)
Explore P04058 
Go to UniProtKB:  P04058
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6X (Subject of Investigation/LOI)
Query on G6X

Download Ideal Coordinates CCD File 
D [auth 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
C29 H34 N2 O6 S
VAEMEXGGRSPJEF-LOMAHXHCSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
G6X PDBBind:  3I6Z IC50: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.339α = 90
b = 111.339β = 90
c = 137.207γ = 120
Software Package:
Software NamePurpose
MAR345data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary