5NDZ

Crystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in complex with AZ3451 at 3.6 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insight into allosteric modulation of protease-activated receptor 2.

Cheng, R.K.Y.Fiez-Vandal, C.Schlenker, O.Edman, K.Aggeler, B.Brown, D.G.Brown, G.A.Cooke, R.M.Dumelin, C.E.Dore, A.S.Geschwindner, S.Grebner, C.Hermansson, N.O.Jazayeri, A.Johansson, P.Leong, L.Prihandoko, R.Rappas, M.Soutter, H.Snijder, A.Sundstrom, L.Tehan, B.Thornton, P.Troast, D.Wiggin, G.Zhukov, A.Marshall, F.H.Dekker, N.

(2017) Nature 545: 112-115

  • DOI: 10.1038/nature22309
  • Primary Citation of Related Structures:  
    5NDD, 5NDZ, 5NJ6

  • PubMed Abstract: 
  • Protease-activated receptors (PARs) are a family of G-protein-coupled receptors (GPCRs) that are irreversibly activated by proteolytic cleavage of the N terminus, which unmasks a tethered peptide ligand that binds and activates the transmembrane receptor domain, eliciting a cellular cascade in response to inflammatory signals and other stimuli ...

    Protease-activated receptors (PARs) are a family of G-protein-coupled receptors (GPCRs) that are irreversibly activated by proteolytic cleavage of the N terminus, which unmasks a tethered peptide ligand that binds and activates the transmembrane receptor domain, eliciting a cellular cascade in response to inflammatory signals and other stimuli. PARs are implicated in a wide range of diseases, such as cancer and inflammation. PARs have been the subject of major pharmaceutical research efforts but the discovery of small-molecule antagonists that effectively bind them has proved challenging. The only marketed drug targeting a PAR is vorapaxar, a selective antagonist of PAR1 used to prevent thrombosis. The structure of PAR1 in complex with vorapaxar has been reported previously. Despite sequence homology across the PAR isoforms, discovery of PAR2 antagonists has been less successful, although GB88 has been described as a weak antagonist. Here we report crystal structures of PAR2 in complex with two distinct antagonists and a blocking antibody. The antagonist AZ8838 binds in a fully occluded pocket near the extracellular surface. Functional and binding studies reveal that AZ8838 exhibits slow binding kinetics, which is an attractive feature for a PAR2 antagonist competing against a tethered ligand. Antagonist AZ3451 binds to a remote allosteric site outside the helical bundle. We propose that antagonist binding prevents structural rearrangements required for receptor activation and signalling. We also show that a blocking antibody antigen-binding fragment binds to the extracellular surface of PAR2, preventing access of the tethered ligand to the peptide-binding site. These structures provide a basis for the development of selective PAR2 antagonists for a range of therapeutic uses.


    Organizational Affiliation

    Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme,Proteinase-activated receptor 2,Soluble cytochrome b562,Proteinase-activated receptor 2A619Escherichia virus T4Homo sapiensEscherichia coliMutation(s): 10 
Gene Names: ET4Tp126F2RL1GPR11PAR2cybC
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P55085 (Homo sapiens)
Explore P55085 
Go to UniProtKB:  P55085
PHAROS:  P55085
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8UN (Subject of Investigation/LOI)
Query on 8UN

Download Ideal Coordinates CCD File 
B [auth A]2-(6-bromanyl-1,3-benzodioxol-5-yl)-~{N}-(4-cyanophenyl)-1-[(1~{S})-1-cyclohexylethyl]benzimidazole-5-carboxamide
C30 H27 Br N4 O3
FJAOGFGHTPYADT-SFHVURJKSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
8UN BindingDB:  5NDZ IC50: min: 2.5, max: 6600 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.099α = 104.38
b = 62.599β = 91.66
c = 86.467γ = 96.4
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Database references