5FOQ

Acetylcholinesterase in complex with C7653


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

The Nature of Activated Non-Classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes.

Berg, L.Mishra, B.K.Andersson, C.D.Ekstrom, F.Linusson, A.

(2016) Chemistry 22: 2672

  • DOI: 10.1002/chem.201503973

  • PubMed Abstract: 
  • Molecular recognition events in biological systems are driven by non-covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CH⋅⋅⋅Y type involving electron-deficient CH donors using dispersion-corrected density ...

    Molecular recognition events in biological systems are driven by non-covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CH⋅⋅⋅Y type involving electron-deficient CH donors using dispersion-corrected density functional theory (DFT) calculations applied to acetylcholinesterase-ligand complexes. The strengths of CH⋅⋅⋅Y interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non-activated CH⋅⋅⋅Y interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CH⋅⋅⋅Y interactions when analysing protein-ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery.


    Organizational Affiliation

    Department of Chemistry, Umeå University, 901 87, Umeå, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACETYLCHOLINESTERASE
A, B
548Mus musculusMutation(s): 0 
Gene Names: Ache
EC: 3.1.1.7
Find proteins for P21836 (Mus musculus)
Go to UniProtKB:  P21836
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P15
Query on P15

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Download CCD File 
B
2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
C13 H28 O7
FHHGCKHKTAJLOM-UHFFFAOYSA-N
 Ligand Interaction
PG0
Query on PG0

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Download CCD File 
A, B
2-(2-METHOXYETHOXY)ETHANOL
PEG 6000
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
GC8
Query on GC8

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Download CCD File 
A, B
2-(2,4-dichlorophenoxy)-N-[4-(1-piperidinylmethyl)phenyl]acetamide
C20 H22 Cl2 N2 O2
KHNVQJDWUHRVDK-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.020α = 90.00
b = 111.770β = 90.00
c = 227.090γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Source and taxonomy
  • Version 2.0: 2018-01-17
    Type: Atomic model, Data collection