5ZHP | pdb_00005zhp

M3 muscarinic acetylcholine receptor in complex with a selective antagonist

• PDB DOI: https://doi.org/10.2210/pdb5ZHP/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus, Tequatrovirus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-03-13 Released: 2018-11-28 
• Deposition Author(s): 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., Heinrich, M., Hirata, K., Liu, X., Sunahara, R.K., Shoichet, B.K., Kobilka, B.K., Gmeiner, P.
• Funding Organization(s): US National Institutes of Health, German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.267 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

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

• PubMed: 30404914 
• DOI: https://doi.org/10.1073/pnas.1813988115
• Primary Citation Related Structures: 
  5ZHP


• 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 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.

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Organizational Affiliation: 
• Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, 100084 Beijing, China.
Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany.
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158.
Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801 Ramat Aviv, Israel.
Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA 92093.
Department of Biomedical & Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6.
Division of Respirology, Department of Medicine, Queen's University, Kingston, ON, Canada K7L 3N6.
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.
Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, 100084 Beijing, China; [e-mail] [e-mail] [e-mail] [e-mail].
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158; [e-mail] [e-mail] [e-mail] [e-mail].
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305.
Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany; [e-mail] [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.65 kDa 
• Atom Count: 6,324 
• Modeled Residue Count: 788 
• Deposited Residue Count: 836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Muscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3	A, B	418	Rattus norvegicus, Tequatrovirus T4	Mutation(s): 2  Gene Names: Chrm3, Chrm-3, e EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for P08483 (Rattus norvegicus) Explore P08483  Go to UniProtKB:  P08483
UniProt Groups	P00720P08483

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9EC	E [auth A], F [auth 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
P6G	G [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
CIT	H [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.267 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.11	α = 90
b = 53.05	β = 98.7
c = 124.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-28 
Deposition Author(s): 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., Heinrich, M., Hirata, K., Liu, X., Sunahara, R.K., Shoichet, B.K., Kobilka, B.K., Gmeiner, P.

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Funding Organization	Location	Grant Number
US National Institutes of Health	United States	GM106990
German Research Foundation	Germany	Gm 13/10 and GRK 1910

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2018-12-05
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary