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 


This is version 2.1 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 


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