6T9R

Aplysia californica AChBP in complex with a cytisine derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The thermodynamic profile and molecular interactions of a C(9)-cytisine derivative-binding acetylcholine-binding protein from Aplysia californica.

Davis, S.Rego Campello, H.Gallagher, T.Hunter, W.N.

(2020) Acta Crystallogr F Struct Biol Commun 76: 74-80

  • DOI: https://doi.org/10.1107/S2053230X20001168
  • Primary Citation of Related Structures:  
    6T9R

  • PubMed Abstract: 

    Cytisine, a natural product with high affinity for clinically relevant nicotinic acetylcholine receptors (nAChRs), is used as a smoking-cessation agent. The compound displays an excellent clinical profile and hence there is an interest in derivatives that may be further improved or find use in the treatment of other conditions. Here, the binding of a cytisine derivative modified by the addition of a 3-(hydroxypropyl) moiety (ligand 4) to Aplysia californica acetylcholine-binding protein (AcAChBP), a surrogate for nAChR orthosteric binding sites, was investigated. Isothermal titration calorimetry revealed that the favorable binding of cytisine and its derivative to AcAChBP is driven by the enthalpic contribution, which dominates an unfavorable entropic component. Although ligand 4 had a less unfavorable entropic contribution compared with cytisine, the affinity for AcAChBP was significantly diminished owing to the magnitude of the reduction in the enthalpic component. The high-resolution crystal structure of the AcAChBP-4 complex indicated close similarities in the protein-ligand interactions involving the parts of 4 common to cytisine. The point of difference, the 3-(hydroxypropyl) substituent, appears to influence the conformation of the Met133 side chain and helps to form an ordered solvent structure at the edge of the orthosteric binding site.


  • Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholine binding protein249Aplysia californicaMutation(s): 0 
UniProt
Find proteins for Q8WSF8 (Aplysia californica)
Explore Q8WSF8 
Go to UniProtKB:  Q8WSF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WSF8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MXQ (Subject of Investigation/LOI)
Query on MXQ

Download Ideal Coordinates CCD File 
CA [auth CCC]
EB [auth FFF]
GC [auth III]
K [auth AAA]
NA [auth DDD]
CA [auth CCC],
EB [auth FFF],
GC [auth III],
K [auth AAA],
NA [auth DDD],
NB [auth GGG],
PC [auth JJJ],
R [auth BBB],
VA [auth EEE],
WB [auth HHH]
(1~{R},9~{S})-5-(3-oxidanylpropyl)-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one
C14 H20 N2 O2
JXEXVCIRYVIYEW-CMPLNLGQSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
DA [auth CCC]
FB [auth FFF]
HC [auth III]
L [auth AAA]
OA [auth DDD]
DA [auth CCC],
FB [auth FFF],
HC [auth III],
L [auth AAA],
OA [auth DDD],
OB [auth GGG],
QC [auth JJJ],
S [auth BBB],
WA [auth EEE],
XB [auth HHH]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AC [auth HHH]
HA [auth CCC]
IB [auth FFF]
JC [auth III]
N [auth AAA]
AC [auth HHH],
HA [auth CCC],
IB [auth FFF],
JC [auth III],
N [auth AAA],
PA [auth DDD],
SB [auth GGG],
TC [auth JJJ],
W [auth BBB],
ZA [auth EEE]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth EEE]
BB [auth EEE]
BC [auth HHH]
CC [auth HHH]
DC [auth HHH]
AB [auth EEE],
BB [auth EEE],
BC [auth HHH],
CC [auth HHH],
DC [auth HHH],
EA [auth CCC],
FA [auth CCC],
GA [auth CCC],
GB [auth FFF],
HB [auth FFF],
IA [auth CCC],
IC [auth III],
JB [auth FFF],
KC [auth III],
LA [auth DDD],
LC [auth III],
M [auth AAA],
MA [auth DDD],
MB [auth GGG],
MC [auth III],
O [auth AAA],
PB [auth GGG],
QA [auth DDD],
QB [auth GGG],
RA [auth DDD],
RB [auth GGG],
RC [auth JJJ],
SC [auth JJJ],
T [auth BBB],
U [auth BBB],
UA [auth EEE],
UC [auth JJJ],
V [auth BBB],
VB [auth HHH],
X [auth BBB],
XA [auth EEE],
Y [auth BBB],
YA [auth EEE],
YB [auth HHH],
Z [auth BBB],
ZB [auth HHH]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth BBB]
DB [auth EEE]
FC [auth HHH]
KA [auth CCC]
LB [auth FFF]
BA [auth BBB],
DB [auth EEE],
FC [auth HHH],
KA [auth CCC],
LB [auth FFF],
OC [auth III],
Q [auth AAA],
TA [auth DDD],
UB [auth GGG],
WC [auth JJJ]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth BBB]
CB [auth EEE]
EC [auth HHH]
JA [auth CCC]
KB [auth FFF]
AA [auth BBB],
CB [auth EEE],
EC [auth HHH],
JA [auth CCC],
KB [auth FFF],
NC [auth III],
P [auth AAA],
SA [auth DDD],
TB [auth GGG],
VC [auth JJJ]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.466α = 90
b = 132.874β = 102.524
c = 131.086γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description, Structure summary