8E7N

Crystal structure of beluga whale Gammacoronavirus SW1 Mpro with GC-376 captured in two conformational states


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses.

Zvornicanin, S.N.Shaqra, A.M.Huang, Q.J.Ornelas, E.Moghe, M.Knapp, M.Moquin, S.Dovala, D.Schiffer, C.A.Kurt Yilmaz, N.

(2023) Viruses 15

  • DOI: https://doi.org/10.3390/v15030781
  • Primary Citation of Related Structures:  
    8DSU, 8E7C, 8E7N, 8FWX

  • PubMed Abstract: 

    With the spread of SARS-CoV-2 throughout the globe causing the COVID-19 pandemic, the threat of zoonotic transmissions of coronaviruses (CoV) has become even more evident. As human infections have been caused by alpha- and beta-CoVs, structural characterization and inhibitor design mostly focused on these two genera. However, viruses from the delta and gamma genera also infect mammals and pose a potential zoonotic transmission threat. Here, we determined the inhibitor-bound crystal structures of the main protease (M pro ) from the delta-CoV porcine HKU15 and gamma-CoV SW1 from the beluga whale. A comparison with the apo structure of SW1 M pro , which is also presented here, enabled the identification of structural arrangements upon inhibitor binding at the active site. The cocrystal structures reveal binding modes and interactions of two covalent inhibitors, PF-00835231 (active form of lufotrelvir) bound to HKU15, and GC376 bound to SW1 M pro . These structures may be leveraged to target diverse coronaviruses and toward the structure-based design of pan-CoV inhibitors.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
main protease
A, B
303Beluga whale coronavirus SW1Mutation(s): 0 
UniProt
Find proteins for B2BW31 (Beluga whale coronavirus (strain SW1))
Explore B2BW31 
Go to UniProtKB:  B2BW31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2BW31
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K36 (Subject of Investigation/LOI)
Query on K36

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
(1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
C21 H31 N3 O8 S
BSPZFJDYQHDZNR-HTCLRFROSA-N
B1S
Query on B1S

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
(1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
C21 H31 N3 O8 S
BSPZFJDYQHDZNR-OGNFBWPZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.083α = 90
b = 84.159β = 93.09
c = 68.498γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description