8V4U | pdb_00008v4u

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 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

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 YDLClick on this verticalbar to view details

This is version 1.3 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 67: 13550-13571

  • 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 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
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 

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

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
  • Version 1.1: 2024-09-04
    Changes: Database references
  • Version 1.2: 2024-09-11
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Structure summary