8E7C

Crystal Structure of Porcine Deltacoronavirus (HKU-15) Mpro with Pfizer Intravenous Inhibitor PF-00835231


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.201 

Starting Model: experimental
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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
307Porcine deltacoronavirusMutation(s): 0 
Gene Names: ORF1ab
UniProt
Find proteins for A0A0E3N825 (Porcine deltacoronavirus)
Explore A0A0E3N825 
Go to UniProtKB:  A0A0E3N825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E3N825
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V2M (Subject of Investigation/LOI)
Query on V2M

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
C24 H34 N4 O6
FDQSUXUTXIGUIA-PRIDNEQBSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
O [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
S [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.201 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.144α = 90
b = 64.144β = 90
c = 261.807γ = 120
Software Package:
Software NamePurpose
CrysalisProdata collection
PHENIXrefinement
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: 2023-10-25
    Changes: Data collection, Refinement description