8V4U | pdb_00008v4u

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

• PDB DOI: https://doi.org/10.2210/pdb8V4U/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-29 Released: 2024-05-15 
• Deposition Author(s): Greasley, S.E., Ferre, R.A., Liu, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.264 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

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

• PubMed: 38687966 
• DOI: https://doi.org/10.1021/acs.jmedchem.3c02469
• Primary Citation 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.

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Organizational Affiliation: 
• Pfizer Research & Development, Cambridge, Massachusetts 02139, United States.
Pfizer Research & Development, Groton, Connecticut 06340, United States.
Pfizer Research & Development, Pearl River, New York 10965, United States.
Pfizer Research & Development, La Jolla, California 92121, United States.
Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah 84322, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.63 kDa 
• Atom Count: 4,996 
• Modeled Residue Count: 605 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YDL (Subject of Investigation/LOI)	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), 0.255 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.407	α = 90
b = 54.138	β = 101.86
c = 115.15	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
DIMPLE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Greasley, S.E., Ferre, R.A., Liu, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• 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