8V4U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A Second-Generation Oral SARS-CoV-2 Main Protease Inhibitor Clinical Candidate for the Treatment of COVID-19.

Allerton, C.M.N.Arcari, J.T.Aschenbrenner, L.M.Avery, M.Bechle, B.M.Behzadi, M.A.Boras, B.Buzon, L.M.Cardin, R.D.Catlin, N.R.Carlo, A.A.Coffman, K.J.Dantonio, A.Di, L.Eng, H.Farley, K.A.Ferre, R.A.Gernhardt, S.S.Gibson, S.A.Greasley, S.E.Greenfield, S.R.Hurst, B.L.Kalgutkar, A.S.Kimoto, E.Lanyon, L.F.Lovett, G.H.Lian, Y.Liu, W.Martinez Alsina, L.A.Noell, S.Obach, R.S.Owen, D.R.Patel, N.C.Rai, D.K.Reese, M.R.Rothan, H.A.Sakata, S.Sammons, M.F.Sathish, J.G.Sharma, R.Steppan, C.M.Tuttle, J.B.Verhoest, P.R.Wei, L.Yang, Q.Yurgelonis, I.Zhu, Y.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02469
  • Primary Citation of Related Structures:  
    8V4U

  • PubMed Abstract: 

    Despite the record-breaking discovery, development and approval of vaccines and antiviral therapeutics such as Paxlovid, coronavirus disease 2019 (COVID-19) remained the fourth leading cause of death in the world and third highest in the United States in 2022. Here, we report the discovery and characterization of PF-07817883, a second-generation, orally bioavailable, SARS-CoV-2 main protease inhibitor with improved metabolic stability versus nirmatrelvir, the antiviral component of the ritonavir-boosted therapy Paxlovid. We demonstrate the in vitro pan-human coronavirus antiviral activity and off-target selectivity profile of PF-07817883. PF-07817883 also demonstrated oral efficacy in a mouse-adapted SARS-CoV-2 model at plasma concentrations equivalent to nirmatrelvir. The preclinical in vivo pharmacokinetics and metabolism studies in human matrices are suggestive of improved oral pharmacokinetics for PF-07817883 in humans, relative to nirmatrelvir. In vitro inhibition/induction studies against major human drug metabolizing enzymes/transporters suggest a low potential for perpetrator drug-drug interactions upon single-agent use of PF-07817883.


  • Organizational Affiliation

    Pfizer Research & Development, Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe 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
YDL (Subject of Investigation/LOI)
Query on YDL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-(trifluoromethyl)-L-prolinamide
C21 H32 F3 N5 O5
DTVPKRIYQXLPLE-AIEDFZFUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.407α = 90
b = 54.138β = 101.86
c = 115.15γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling
DIMPLEphasing

Structure Validation

View Full Validation Report



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: 2024-05-15
    Type: Initial release