5ZHP

M3 muscarinic acetylcholine receptor in complex with a selective antagonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

wwPDB Validation 3D Report Full Report



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
  • Primary Citation of 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 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 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Muscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3AB418Rattus norvegicusEscherichia virus T4Mutation(s): 2 
Gene Names: Chrm3Chrm-3
EC: 3.2.1.17
Find proteins for P08483 (Rattus norvegicus)
Explore P08483 
Go to UniProtKB:  P08483
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C
2 N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9EC
Query on 9EC

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
P6G
Query on P6G

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B
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Calpha-maltoseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.11α = 90
b = 53.05β = 98.7
c = 124.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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
    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