8W1V

The beta2 adrenergic receptor bound to a bitopic ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

Starting Model: experimental
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Literature

Bitopic Ligands Support the Presence of a Metastable Binding Site at the beta 2 Adrenergic Receptor.

Gaiser, B.I.Danielsen, M.Xu, X.Ropke Jorgensen, K.Fronik, P.Marcher-Rorsted, E.Wrobel, T.M.Liu, X.Mosolff Mathiesen, J.Sejer Pedersen, D.

(2024) J Med Chem 67: 11053-11068

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00578
  • Primary Citation of Related Structures:  
    8W1V

  • PubMed Abstract: 

    Metastable binding sites (MBS) have been observed in a multitude of molecular dynamics simulations and can be considered low affinity allosteric binding sites (ABS) that function as stepping stones as the ligand moves toward the orthosteric binding site (OBS). Herein, we show that MBS can be utilized as ABS in ligand design, resulting in ligands with improved binding kinetics. Four homobivalent bitopic ligands ( 1 - 4 ) were designed by molecular docking of ( S )-alprenolol (( S )-ALP) in the cocrystal structure of the β 2 adrenergic receptor (β 2 AR) bound to the antagonist ALP. Ligand 4 displayed a potency and affinity similar to ( S )-ALP, but with a >4-fold increase in residence time. The proposed binding mode was confirmed by X-ray crystallography of ligand 4 in complex with the β 2 AR. This ligand design principle can find applications beyond the β 2 AR and G protein-coupled receptors (GPCRs) as a general approach for improving the pharmacological profile of orthosteric ligands by targeting the OBS and an MBS simultaneously.


  • Organizational Affiliation

    Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2 adrenergic receptor,Endolysin
A, B
549Homo sapiensMutation(s): 3 
Gene Names: ADRB2ADRB2RB2AR
EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P07550 (Homo sapiens)
Explore P07550 
Go to UniProtKB:  P07550
PHAROS:  P07550
GTEx:  ENSG00000169252 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P07550
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody60C [auth D],
D [auth F]
125Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AV0 (Subject of Investigation/LOI)
Query on AV0

Download Ideal Coordinates CCD File 
G [auth B]Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-VWHTXWAPSA-N
A1AE2
Query on A1AE2

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
(2S)-1-[(3-{1-[4-(4-{(2S)-2-hydroxy-3-[(propan-2-yl)amino]propoxy}phenyl)butyl]-1H-1,2,3-triazol-4-yl}propyl)amino]-3-(2-propylphenoxy)propan-2-ol
C33 H51 N5 O4
YQSRDTSIHACZCZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.68α = 90
b = 146.77β = 107.06
c = 91.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaGrant 32122041

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references