5X7D

Structure of beta2 adrenoceptor bound to carazolol and an intracellular allosteric antagonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.703 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of intracellular allosteric beta 2AR antagonist revealed by X-ray crystal structure.

Liu, X.Ahn, S.Kahsai, A.W.Meng, K.C.Latorraca, N.R.Pani, B.Venkatakrishnan, A.J.Masoudi, A.Weis, W.I.Dror, R.O.Chen, X.Lefkowitz, R.J.Kobilka, B.K.

(2017) Nature 548: 480-484

  • DOI: 10.1038/nature23652

  • PubMed Abstract: 
  • G-protein-coupled receptors (GPCRs) pose challenges for drug discovery efforts because of the high degree of structural homology in the orthosteric pocket, particularly for GPCRs within a single subfamily, such as the nine adrenergic receptors. Allos ...

    G-protein-coupled receptors (GPCRs) pose challenges for drug discovery efforts because of the high degree of structural homology in the orthosteric pocket, particularly for GPCRs within a single subfamily, such as the nine adrenergic receptors. Allosteric ligands may bind to less-conserved regions of these receptors and therefore are more likely to be selective. Unlike orthosteric ligands, which tonically activate or inhibit signalling, allosteric ligands modulate physiologic responses to hormones and neurotransmitters, and may therefore have fewer adverse effects. The majority of GPCR crystal structures published to date were obtained with receptors bound to orthosteric antagonists, and only a few structures bound to allosteric ligands have been reported. Compound 15 (Cmpd-15) is an allosteric modulator of the β 2 adrenergic receptor (β 2 AR) that was recently isolated from a DNA-encoded small-molecule library. Orthosteric β-adrenergic receptor antagonists, known as beta-blockers, are amongst the most prescribed drugs in the world and Cmpd-15 is the first allosteric beta-blocker. Cmpd-15 exhibits negative cooperativity with agonists and positive cooperativity with inverse agonists. Here we present the structure of the β 2 AR bound to a polyethylene glycol-carboxylic acid derivative (Cmpd-15PA) of this modulator. Cmpd-15PA binds to a pocket formed primarily by the cytoplasmic ends of transmembrane segments 1, 2, 6 and 7 as well as intracellular loop 1 and helix 8. A comparison of this structure with inactive- and active-state structures of the β 2 AR reveals the mechanism by which Cmpd-15 modulates agonist binding affinity and signalling.


    Organizational Affiliation

    Department of Computer Science, Stanford University, Stanford, California 94305, USA.,Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA.,Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710, USA.,Department of Medicinal Chemistry, School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou 213164, Jiangsu, China.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.,Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chimera protein of Beta-2 adrenergic receptor and Lysozyme
A
500Enterobacteria phage T4Homo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: E, ADRB2 (ADRB2R, B2AR)
EC: 3.2.1.17
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
β2 adrenergic receptor
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Find proteins for P07550 (Homo sapiens)
Go to Gene View: ADRB2
Go to UniProtKB:  P07550
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
BU1
Query on BU1

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Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
ACM
Query on ACM

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Download CCD File 
A
ACETAMIDE
C2 H5 N O
DLFVBJFMPXGRIB-UHFFFAOYSA-N
 Ligand Interaction
CAU
Query on CAU

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Download CCD File 
A
(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
(S)-Carazolol
C18 H22 N2 O2
BQXQGZPYHWWCEB-ZDUSSCGKSA-N
 Ligand Interaction
8VS
Query on 8VS

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Download CCD File 
A
4-carbamoyl-N-[(2R)-2-cyclohexyl-2-phenylacetyl]-L-phenylalanyl-3-bromo-N-methyl-L-phenylalaninamide
C34 H39 Br N4 O4
MZHSBVCCCRUZKX-DTXPUJKBSA-N
 Ligand Interaction
CLR
Query on CLR

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Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.703 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.460α = 90.00
b = 75.710β = 90.00
c = 173.410γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Database references