7RFS

Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4WIClick on this verticalbar to view details

This is version 2.2 of the entry. See complete history


Literature

An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19.

Owen, D.R.Allerton, C.M.N.Anderson, A.S.Aschenbrenner, L.Avery, M.Berritt, S.Boras, B.Cardin, R.D.Carlo, A.Coffman, K.J.Dantonio, A.Di, L.Eng, H.Ferre, R.Gajiwala, K.S.Gibson, S.A.Greasley, S.E.Hurst, B.L.Kadar, E.P.Kalgutkar, A.S.Lee, J.C.Lee, J.Liu, W.Mason, S.W.Noell, S.Novak, J.J.Obach, R.S.Ogilvie, K.Patel, N.C.Pettersson, M.Rai, D.K.Reese, M.R.Sammons, M.F.Sathish, J.G.Singh, R.S.P.Steppan, C.M.Stewart, A.E.Tuttle, J.B.Updyke, L.Verhoest, P.R.Wei, L.Yang, Q.Zhu, Y.

(2021) Science 374: 1586-1593

  • DOI: https://doi.org/10.1126/science.abl4784
  • Primary Citation of Related Structures:  
    7RFR, 7RFS, 7RFU, 7RFW

  • PubMed Abstract: 

    The worldwide outbreak of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic. Alongside vaccines, antiviral therapeutics are an important part of the healthcare response to countering the ongoing threat presented by COVID-19. Here, we report the discovery and characterization of PF-07321332, an orally bioavailable SARS-CoV-2 main protease inhibitor with in vitro pan-human coronavirus antiviral activity and excellent off-target selectivity and in vivo safety profiles. PF-07321332 has demonstrated oral activity in a mouse-adapted SARS-CoV-2 model and has achieved oral plasma concentrations exceeding the in vitro antiviral cell potency in a phase 1 clinical trial in healthy human participants.


  • Organizational Affiliation

    Pfizer Worldwide Research, Development & Medical, Cambridge, MA 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4WI (Subject of Investigation/LOI)
Query on 4WI

Download Ideal Coordinates CCD File 
B [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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.2α = 90
b = 53.03β = 102.52
c = 45.68γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4WIClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references
  • Version 2.0: 2021-12-22
    Changes: Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2022-01-05
    Changes: Database references
  • Version 2.2: 2024-11-06
    Changes: Data collection, Structure summary