3ZDG

Crystal Structure of Ls-AChBP complexed with carbamoylcholine analogue 3-(dimethylamino)butyl dimethylcarbamate (DMABC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Synthesis, Pharmacology, and Biostructural Characterization of Novel Alpha(4)Beta(2) Nicotinic Acetylcholine Receptor Agonists.

Ussing, C.A.Hansen, C.P.Petersen, J.G.Jensen, A.A.Rohde, L.A.H.Ahring, P.K.Nielsen, E.O.Kastrup, J.S.Gajhede, M.Frolund, B.Balle, T.

(2013) J Med Chem 56: 940

  • DOI: https://doi.org/10.1021/jm301409f
  • Primary Citation of Related Structures:  
    3ZDG, 3ZDH

  • PubMed Abstract: 

    In our search for selective agonists for the α(4)β(2) subtype of the nicotinic acetylcholine receptors (nAChRs), we have synthesized and characterized a series of novel heterocyclic analogues of 3-(dimethylamino)butyl dimethylcarbamate (DMABC, 4). All new heterocyclic analogues, especially N,N-dimethyl-4-(1-methyl-1H-imidazol-2-yloxy)butan-2-amine (7), showed an improved binding selectivity profile in favor of α(4)β(2) over other nAChR subtypes, primarily due to impaired binding at β(4) containing receptors. This observation can be rationalized based on cocrystal structures of (R)-4 and (R)-7 bound to acetylcholine binding protein from Lymnaea stagnalis. Functional characterization at both (α(4))(2)(β(2))(3) and (α(4))(3)(β(2))(2) receptors using two-electrode voltage clamp techniques in Xenopus laevis oocytes indicates that the investigated compounds interact differently with the two receptor stoichiometries. Compound 7 is an efficacious agonist at both α(4)-β(2) and α(4)-α(4) binding sites, while the close analogue N,N-dimethyl-4-(1,4-dimethyl-1H-imidazol-2-yloxy)butan-2-amine (9) primarily activates via α(4)-β(2) binding sites. The results suggest that it may be possible to rationally design compounds with specific stoichiometry preferences.


  • Organizational Affiliation

    Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
IB [auth R]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
NAG
Query on NAG

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BB [auth O],
EB [auth P],
VA [auth M]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
XRX
Query on XRX

Download Ideal Coordinates CCD File 
AB [auth O]
BA [auth D]
CA [auth E]
DB [auth P]
FA [auth F]
AB [auth O],
BA [auth D],
CA [auth E],
DB [auth P],
FA [auth F],
FB [auth Q],
HB [auth R],
IA [auth G],
JA [auth H],
LB [auth S],
MA [auth I],
MB [auth T],
NA [auth J],
PA [auth K],
RA [auth L],
U [auth A],
UA [auth M],
W [auth B],
XA [auth N],
Y [auth C]
3-(dimethylamino)butyl dimethylcarbamate
C9 H20 N2 O2
VVGQXMCHKFOTKZ-MRVPVSSYSA-N
PEG
Query on PEG

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WA [auth M]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
CB [auth O]
DA [auth E]
EA [auth E]
GA [auth F]
AA [auth C],
CB [auth O],
DA [auth E],
EA [auth E],
GA [auth F],
GB [auth Q],
HA [auth F],
JB [auth R],
KA [auth H],
KB [auth R],
LA [auth H],
OA [auth J],
QA [auth K],
SA [auth L],
TA [auth L],
V [auth A],
X [auth B],
YA [auth N],
Z [auth C],
ZA [auth N]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
XRX BindingDB:  3ZDG Ki: 79 (nM) from 1 assay(s)
PDBBind:  3ZDG Ki: 79 (nM) from 1 assay(s)
Binding MOAD:  3ZDG Ki: 79 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.73α = 90
b = 144.88β = 107.9
c = 139.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary