3U8K

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3573 (1-(5-ethoxypyridin-3-yl)-1,4-diazepane)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Intersubunit bridge formation governs agonist efficacy at nicotinic acetylcholine alpha 4 beta 2 receptors: unique role of halogen bonding revealed.

Rohde, L.A.Ahring, P.K.Jensen, M.L.Nielsen, E.Peters, D.Helgstrand, C.Krintel, C.Harpse, K.Gajhede, M.Kastrup, J.S.Balle, T.

(2012) J.Biol.Chem. 287: 4248-4259

  • DOI: 10.1074/jbc.M111.292243
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The α4β2 subtype of the nicotinic acetylcholine receptor has been pursued as a drug target for treatment of psychiatric and neurodegenerative disorders and smoking cessation aids for decades. Still, a thorough understanding of structure-function rela ...

    The α4β2 subtype of the nicotinic acetylcholine receptor has been pursued as a drug target for treatment of psychiatric and neurodegenerative disorders and smoking cessation aids for decades. Still, a thorough understanding of structure-function relationships of α4β2 agonists is lacking. Using binding experiments, electrophysiology and x-ray crystallography we have investigated a consecutive series of five prototypical pyridine-containing agonists derived from 1-(pyridin-3-yl)-1,4-diazepane. A correlation between binding affinities at α4β2 and the acetylcholine-binding protein from Lymnaea stagnalis (Ls-AChBP) confirms Ls-AChBP as structural surrogate for α4β2 receptors. Crystal structures of five agonists with efficacies at α4β2 from 21-76% were determined in complex with Ls-AChBP. No variation in closure of loop C is observed despite large efficacy variations. Instead, the efficacy of a compound appears tightly coupled to its ability to form a strong intersubunit bridge linking the primary and complementary binding interfaces. For the tested agonists, a specific halogen bond was observed to play a large role in establishing such strong intersubunit anchoring.


    Organizational Affiliation

    Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Copenhagen 2100, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetylcholine-binding protein
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
210Lymnaea stagnalisMutation(s): 0 
Find proteins for P58154 (Lymnaea stagnalis)
Go to UniProtKB:  P58154
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C, D, H, I, K, M, N, O, P, T
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
09P
Query on 09P

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
1-(5-ethoxypyridin-3-yl)-1,4-diazepane
C12 H19 N3 O
RQXFSCANOMMTFZ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, G, R
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
09PKi: 2.2 nM (100) BINDINGDB
09PKi: 2.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 235.410α = 90.00
b = 273.160β = 90.00
c = 73.580γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2013-09-18
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Data collection