5ZK3

Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with QNB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the subtype-selective antagonist binding to the M2muscarinic receptor

Suno, R.Lee, S.Maeda, S.Yasuda, S.Yamashita, K.Hirata, K.Horita, S.Tawaramoto, M.S.Tsujimoto, H.Murata, T.Kinoshita, M.Yamamoto, M.Kobilka, B.K.Vaidehi, N.Iwata, S.Kobayashi, T.

(2018) Nat Chem Biol 14: 1150-1158

  • DOI: 10.1038/s41589-018-0152-y
  • Primary Citation of Related Structures:  
    5YC8, 5ZKC, 5ZKB, 5ZK8, 5ZK3

  • PubMed Abstract: 
  • Human muscarinic receptor M 2 is one of the five subtypes of muscarinic receptors belonging to the family of G-protein-coupled receptors. Muscarinic receptors are targets for multiple neurodegenerative diseases. The challenge has been designing subtype-selective ligands against one of the five muscarinic receptors ...

    Human muscarinic receptor M 2 is one of the five subtypes of muscarinic receptors belonging to the family of G-protein-coupled receptors. Muscarinic receptors are targets for multiple neurodegenerative diseases. The challenge has been designing subtype-selective ligands against one of the five muscarinic receptors. We report high-resolution structures of a thermostabilized mutant M 2 receptor bound to a subtype-selective antagonist AF-DX 384 and a nonselective antagonist NMS. The thermostabilizing mutation S110R in M 2 was predicted using a theoretical strategy previously developed in our group. Comparison of the crystal structures and pharmacological properties of the M 2 receptor shows that the Arg in the S110R mutant mimics the stabilizing role of the sodium cation, which is known to allosterically stabilize inactive state(s) of class A GPCRs. Molecular dynamics simulations reveal that tightening of the ligand-residue contacts in M 2 receptors compared to M 3 receptors leads to subtype selectivity of AF-DX 384.


    Organizational Affiliation

    Japan Science and Technology Agency (JST) and Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2A421Homo sapiensMutation(s): 1 
Gene Names: CHRM2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P08172 (Homo sapiens)
Explore P08172 
Go to UniProtKB:  P08172
PHAROS:  P08172
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QNB (Subject of Investigation/LOI)
Query on QNB

Download Ideal Coordinates CCD File 
B [auth A](3R)-1-azabicyclo[2.2.2]oct-3-yl hydroxy(diphenyl)acetate
C21 H23 N O3
HGMITUYOCPPQLE-IBGZPJMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.48α = 90
b = 58.8β = 99
c = 89.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanthe Research Acceleration Program
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanThe Platform Project for Supporting Drug Discovery and Life Science Research
Japan Society for the Promotion of ScienceJapanThe JSPS-NSF International Collaboration in Chemistry
Japan Society for the Promotion of ScienceJapan15K08268, 15H06862
Japan Agency for Medical Research and Development (AMED)JapanThe Platform Project for Supporting Drug Discovery and Life Science Research
National Institutes of Health/National Human Genome Research InstituteUnited StatesNIH R01-GM097261

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references