3U8N

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3950 (1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1074/jbc.M111.292243
  • Primary Citation of Related Structures:  
    3U8J, 3U8K, 3U8L, 3U8M, 3U8N

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholine-binding protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
210Lymnaea stagnalisMutation(s): 0 
UniProt
Find proteins for P58154 (Lymnaea stagnalis)
Explore P58154 
Go to UniProtKB:  P58154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58154
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
09S
Query on 09S

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth F]
DA [auth G]
EA [auth H]
GA [auth I]
AA [auth E],
BA [auth F],
DA [auth G],
EA [auth H],
GA [auth I],
HA [auth J],
IA [auth K],
JA [auth L],
KA [auth M],
LA [auth N],
NA [auth O],
OA [auth P],
RA [auth Q],
SA [auth R],
TA [auth S],
U [auth A],
VA [auth T],
W [auth B],
Y [auth C],
Z [auth D]
1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane
C12 H18 Br N3 O
UGNNTIXQGYYUAP-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CA [auth G],
WA [auth T],
X [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
FA [auth H]
MA [auth N]
PA [auth P]
QA [auth P]
UA [auth S]
FA [auth H],
MA [auth N],
PA [auth P],
QA [auth P],
UA [auth S],
V [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
09S PDBBind:  3U8N Ki: 0.07 (nM) from 1 assay(s)
BindingDB:  3U8N Ki: 0.07 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 239.12α = 90
b = 73.11β = 97.45
c = 271.84γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2013-09-18
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Data collection, Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-06
    Changes: Structure summary