Crystal Structure of the Human Coronavirus 229E HR1 motif in complex with pan-CoVs inhibitor EK1

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike.

Xia, S.Yan, L.Xu, W.Agrawal, A.S.Algaissi, A.Tseng, C.K.Wang, Q.Du, L.Tan, W.Wilson, I.A.Jiang, S.Yang, B.Lu, L.

(2019) Sci Adv 5: eaav4580-eaav4580

  • DOI: https://doi.org/10.1126/sciadv.aav4580
  • Primary Citation of Related Structures:  
    5ZUV, 5ZVK, 5ZVM

  • PubMed Abstract: 

    Continuously emerging highly pathogenic human coronaviruses (HCoVs) remain a major threat to human health, as illustrated in past SARS-CoV and MERS-CoV outbreaks. The development of a drug with broad-spectrum HCoV inhibitory activity would address this urgent unmet medical need. Although previous studies have suggested that the HR1 of HCoV spike (S) protein is an important target site for inhibition against specific HCoVs, whether this conserved region could serve as a target for the development of broad-spectrum pan-CoV inhibitor remains controversial. Here, we found that peptide OC43-HR2P, derived from the HR2 domain of HCoV-OC43, exhibited broad fusion inhibitory activity against multiple HCoVs. EK1, the optimized form of OC43-HR2P, showed substantially improved pan-CoV fusion inhibitory activity and pharmaceutical properties. Crystal structures indicated that EK1 can form a stable six-helix bundle structure with both short α-HCoV and long β-HCoV HR1s, further supporting the role of HR1 region as a viable pan-CoV target site.

  • Organizational Affiliation

    Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein,Spike glycoprotein,inhibitor EK1
A, B, C
133Human coronavirus 229Esynthetic construct
This entity is chimeric
Mutation(s): 0 
Gene Names: S2
Find proteins for P15423 (Human coronavirus 229E)
Explore P15423 
Go to UniProtKB:  P15423
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15423
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.21 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.515α = 90
b = 45.548β = 96.33
c = 94.737γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (China)China31600619

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.2: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description