39KL | pdb_000039kl

SARS-CoV-2 Main Protease with Zevotrelvir

• PDB DOI: https://doi.org/10.2210/pdb39KL/pdb

• Classification: VIRAL PROTEIN, Hydrolase/Inhibitor
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2026-10-14 Released: 2026-11-11 
• Deposition Author(s): Al-Homoudi, A.I., Brunzelle, J.S., Kovari, L.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Molecular Determinants of Differential Resistance Across Approved and Next-Generation SARS-CoV-2 Main Protease Inhibitors

Al-Homoudi, A.I., Brunzelle, J.S., Kovari, L.C.

To be published.

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)

Biological Assembly Evidence: fluorescence resonance energy transfer

Macromolecule Content 

• Total Structure Weight: 34.24 kDa 
• Atom Count: 2,572 
• Modeled Residue Count: 300 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	305	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
A1AA0 (Subject of Investigation/LOI)	B [auth A]	4,6,7-trifluoro-N-{(2S)-1-[(3R,5'R)-5'-(iminomethyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidin]-1'-yl]-4-methyl-1-oxopentan-2-yl}-N-methyl-1H-indole-2-carboxamide C28 H28 F3 N5 O3 HTIJRVKDMBVLCG-RAAJOXOESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.761	α = 90
b = 81.564	β = 114.879
c = 51.917	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-11 
Deposition Author(s): Al-Homoudi, A.I., Brunzelle, J.S., Kovari, L.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI173229
Other private	United States	085P1000817

Revision History  

• Version 1.0: 2026-11-11
  Type: Initial release