9OIX | pdb_00009oix

Co-Structure of Main Protease of SARS-CoV-2 with NVP-EGT710

• PDB DOI: https://doi.org/10.2210/pdb9OIX/pdb

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


• Deposited: 2025-05-06 Released: 2025-12-24 
• Deposition Author(s): Knapp, M.S., Ornelas, E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Preclinical characterization of EGT710, an oral non-peptidomimetic reversible covalent SARS-CoV-2 main protease inhibitor

Moquin, S.A., Lakshminarayana, S.B., Balavenkatraman, K.K., Schiller, H., Claas, A., Bhhatarai, B., Loisios-Konstantinidis, I., Vulic, K., Kurhade, C., Kalveram, B.K., Chen, J.Y.C., Zou, J., Xie, X., Tandeske, L., Dovala, D., Ornelas, E., Knapp, M.S., Fuller, D., Nguyen, Z., Barkan, D.T., Bebrevska, L., Wright, S.K., Busby, S.A., Blais, J., Shi, P.Y., Gaudet, S., Bergeron, R., Yu, H., Zack, J., Sarko, C., Gu, F., Bradner, J.E., Tallarico, J.A., Diagana, T.T., Papillon, J.P.N.

(2025) NPJ Drug Discov 2: 28

• DOI: https://doi.org/10.1038/s44386-025-00030-5

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.21 kDa 
• Atom Count: 2,544 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	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
A1CBU (Subject of Investigation/LOI)	B [auth A]	(4S)-4-(iminomethyl)-3-(isoquinolin-4-yl)-1-[6-(trifluoromethyl)pyridin-3-yl]imidazolidin-2-one C19 H14 F3 N5 O XZYITQWBMBTCLK-BUTILUPYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.159	α = 90
b = 54.47	β = 100.568
c = 45.109	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Knapp, M.S., Ornelas, E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release