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

Experimental Data Snapshot

  • Resolution: 3.60 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

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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: https://doi.org/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. 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

    Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme,Proteinase-activated receptor 2,Soluble cytochrome b562,Proteinase-activated receptor 2619Tequatrovirus T4Homo sapiensEscherichia coliMutation(s): 10 
Gene Names: eT4Tp126F2RL1GPR11PAR2cybC
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
GTEx:  ENSG00000164251 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P0ABE7P55085
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
Query on NA

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
8UN BindingDB:  5NDZ IC50: min: 2.5, max: 6600 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
XDSdata reduction
Aimlessdata scaling

Structure Validation

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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
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description