7VTC

Crystal structure of MERS main protease in complex with PF07321332


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


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Literature

Structural Basis of the Main Proteases of Coronavirus Bound to Drug Candidate PF-07321332.

Li, J.Lin, C.Zhou, X.Zhong, F.Zeng, P.Yang, Y.Zhang, Y.Yu, B.Fan, X.McCormick, P.J.Fu, R.Fu, Y.Jiang, H.Zhang, J.

(2022) J Virol 96: e0201321-e0201321

  • DOI: 10.1128/jvi.02013-21
  • Primary Citation of Related Structures:  
    7VLO, 7VLP, 7VLQ, 7VTC

  • PubMed Abstract: 
  • The high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genera of coronaviruses is the substrate-binding site of the main protease (M pro or 3CL pro ), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses ...

    The high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genera of coronaviruses is the substrate-binding site of the main protease (M pro or 3CL pro ), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses. PF-07321332, developed by Pfizer, is the first orally administered inhibitor targeting the main protease of SARS-CoV-2, which also has shown potency against other coronaviruses. Here, we report three crystal structures of the main protease of SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome (MERS)-CoV bound to the inhibitor PF-07321332. The structures reveal a ligand-binding site that is conserved among SARS-CoV-2, SARS-CoV, and MERS-CoV, providing insights into the mechanism of inhibition of viral replication. The long and narrow cavity in the cleft between domains I and II of the main protease harbors multiple inhibitor-binding sites, where PF-07321332 occupies subsites S1, S2, and S4 and appears more restricted than other inhibitors. A detailed analysis of these structures illuminated key structural determinants essential for inhibition and elucidated the binding mode of action of the main proteases from different coronaviruses. Given the importance of the main protease for the treatment of SARS-CoV-2 infection, insights derived from this study should accelerate the design of safer and more effective antivirals. IMPORTANCE The current pandemic of multiple variants has created an urgent need for effective inhibitors of SARS-CoV-2 to complement vaccine strategies. PF-07321332, developed by Pfizer, is the first orally administered coronavirus-specific main protease inhibitor approved by the FDA. We solved the crystal structures of the main protease of SARS-CoV-2, SARS-CoV, and MERS-CoV that bound to the PF-07321332, suggesting PF-07321332 is a broad-spectrum inhibitor for coronaviruses. Structures of the main protease inhibitor complexes present an opportunity to discover safer and more effective inhibitors for COVID-19.


    Organizational Affiliation

    School of Basic Medical Sciences, Nanchang Universitygrid.260463.5, Nanchang, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA, B322Middle East respiratory syndrome-related coronavirusMutation(s): 0 
EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for T2B9A8 (Middle East respiratory syndrome-related coronavirus)
Explore T2B9A8 
Go to UniProtKB:  T2B9A8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2B9A8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4WI (Subject of Investigation/LOI)
Query on 4WI

Download Ideal Coordinates CCD File 
C [auth A](1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
C23 H34 F3 N5 O4
WDVIRQQKRMIXGS-XIFHJVQQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.422α = 90
b = 93.243β = 90
c = 97.578γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references