5ZHP

M3 muscarinic acetylcholine receptor in complex with a selective antagonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists

Liu, H.Hofmann, J.Fish, I.Schaake, B.Eitel, K.Bartuschat, A.Kaindl, J.Rampp, H.Banerjee, A.Hubner, H.Clark, M.J.Vincent, S.G.Fisher, J.T.Heinrich, M.R.Hirata, K.Liu, X.Sunahara, R.K.Shoichet, B.K.Kobilka, B.K.Gmeiner, P.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 12046-12050

  • DOI: 10.1073/pnas.1813988115

  • PubMed Abstract: 
  • Drugs that treat chronic obstructive pulmonary disease by antagonizing the M3 muscarinic acetylcholine receptor (M3R) have had a significant effect on health, but can suffer from their lack of selectivity against the M2R subtype, which modulates hear ...

    Drugs that treat chronic obstructive pulmonary disease by antagonizing the M3 muscarinic acetylcholine receptor (M3R) have had a significant effect on health, but can suffer from their lack of selectivity against the M2R subtype, which modulates heart rate. Beginning with the crystal structures of M2R and M3R, we exploited a single amino acid difference in their orthosteric binding pockets using molecular docking and structure-based design. The resulting M3R antagonists had up to 100-fold selectivity over M2R in affinity and over 1,000-fold selectivity in vivo. The crystal structure of the M3R-selective antagonist in complex with M3R corresponded closely to the docking-predicted geometry, providing a template for further optimization.


    Organizational Affiliation

    Department of Biomedical & Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6.,Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801 Ramat Aviv, Israel.,Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany; liu_xy@mail.tsinghua.edu.cn bshoichet@gmail.com kobilka@stanford.edu peter.gmeiner@fau.de.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158.,Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, 100084 Beijing, China.,Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA 92093.,Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158; liu_xy@mail.tsinghua.edu.cn bshoichet@gmail.com kobilka@stanford.edu peter.gmeiner@fau.de.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305.,Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, 100084 Beijing, China; liu_xy@mail.tsinghua.edu.cn bshoichet@gmail.com kobilka@stanford.edu peter.gmeiner@fau.de.,Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany.,Division of Respirology, Department of Medicine, Queen's University, Kingston, ON, Canada K7L 3N6.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Muscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3
A, B
418Rattus norvegicusEnterobacteria phage T4
This entity is chimeric
Mutation(s): 2 
Gene Names: Chrm3 (Chrm-3), E
EC: 3.2.1.17
Find proteins for P08483 (Rattus norvegicus)
Go to UniProtKB:  P08483
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
CIT
Query on CIT

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Download CCD File 
B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
9EC
Query on 9EC

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Download CCD File 
A, B
(1R,2R,4S,5S,7s)-7-({[4-fluoro-2-(thiophen-2-yl)phenyl]carbamoyl}oxy)-9,9-dimethyl-3-oxa-9-azatricyclo[3.3.1.0~2,4~]nonan-9-ium
C20 H22 F N2 O3 S
YBYUWXNCRPKGOH-ADYDWEGLSA-O
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
B
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 122.110α = 90.00
b = 53.050β = 98.70
c = 124.720γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
US National Institutes of HealthUnited StatesGM106990
German Research FoundationGermanyGm 13/10 and GRK 1910

Revision History 

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2018-12-05
    Type: Data collection, Database references