2W6C | pdb_00002w6c

ACHE IN COMPLEX WITH A BIS-(-)-NOR-MEPTAZINOL DERIVATIVE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.235 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.185 (Depositor) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

The Crystal Structure of a Complex of Acetylcholinesterase with a Bis-(-)-Nor-Meptazinol Derivative Reveals Disruption of the Catalytic Triad.

Paz, A.Xie, Q.Greenblatt, H.M.Fu, W.Tang, Y.Silman, I.Qiu, Z.Sussman, J.L.

(2009) J Med Chem 52: 2543

  • DOI: https://doi.org/10.1021/jm801657v
  • Primary Citation Related Structures: 
    2W6C

  • PubMed Abstract: 

    A bis-(-)-nor-meptazinol derivative in which the two meptazinol rings are linked by a nonamethylene spacer is a novel acetylcholinesterase inhibitor that inhibits both catalytic activity and Abeta peptide aggregation. The crystal structure of its complex with Torpedo californica acetylcholinesterase was determined to 2.7 A resolution. The ligand spans the active-site gorge, with one nor-meptazinol moiety bound at the "anionic" subsite of the active site, disrupting the catalytic triad by forming a hydrogen bond with His440N(epsilon2), which is hydrogen-bonded to Ser200O(gamma) in the native enzyme. The second nor-meptazinol binds at the peripheral "anionic" site at the gorge entrance. A number of GOLD models of the complex, using both native TcAChE and the protein template from the crystal structure of the bis-(-)-nor-meptazinol/TcAChE complex, bear higher similarity to the X-ray structure than a previous model obtained using the mouse enzyme structure. These findings may facilitate rational design of new meptazinol-based acetylcholinesterase inhibitors.


  • Organizational Affiliation
    • Department of Structural Biology and Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel.

Macromolecule Content 

  • Total Structure Weight: 67.4 kDa 
  • Atom Count: 4,368 
  • Modeled Residue Count: 528 
  • Deposited Residue Count: 586 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACETYLCHOLINESTERASEA [auth X]586Tetronarce californicaMutation(s): 0 
EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica)
Explore P04058 
Go to UniProtKB:  P04058
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04058
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BM4

Query on BM4



Download:Ideal Coordinates CCD File
C [auth X]3-[(3R)-3-ethyl-1-{9-[(3S)-3-ethyl-3-(3-hydroxyphenyl)azepan-1-yl]nonyl}azepan-3-yl]phenol
C37 H58 N2 O2
ZZKZUUMHRSWLQQ-JXLNJXQWSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth X],
E [auth X]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.235 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.185 (Depositor) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.172α = 90
b = 112.172β = 90
c = 137.568γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Advisory
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-23
    Changes: Structure summary