8ZQ8 | pdb_00008zq8

SARS-Cov-2 3CL protease in complex with macrocyclic inhibitor CG-1039

• PDB DOI: https://doi.org/10.2210/pdb8ZQ8/pdb

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


• Deposited: 2024-06-01 Released: 2025-06-11 
• Deposition Author(s): Chen, X., Hou, K., Tang, X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.223 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Discovery of macrocyclic covalent inhibitors for severe acute respiratory syndrome coronavirus 2 3CL protease.

Tang, X., Hou, K., Chen, X., Fan, W., Wu, H., Lu, C., He, G.X.

(2024) Bioorg Med Chem 111: 117846-117846

• PubMed: 39106653 
• DOI: https://doi.org/10.1016/j.bmc.2024.117846
• Primary Citation Related Structures: 
  8ZQ8


• PubMed Abstract: 
  

  The coronavirus disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spread worldwide for more than 3 years. Although the hospitalization rate and mortality have decreased dramatically due to wide vaccination effort and improved treatment options, the disease is still a global health issue due to constant viral mutations, causing negative impact on social and economic activities. In addition, long COVID and complications arising from COVID-19 weeks after infection have become a concern for public health experts. Therefore, better treatments for COVID-19 are still needed. Herein, we describe a class of macrocyclic peptidomimetic compounds that are potent inhibitors of SARS-Cov-2 3CL protease (3CL ^pro ). Significantly, some of the compounds showed a higher stability against human liver microsomes (HLM t _1/2  > 180 min) and may be suitable for oral administration without the need for a pharmacokinetic (PK) boosting agent such as ritonavir.

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Organizational Affiliation: 
• Shanghai CureGene Pharmaceutical Co., Ltd, 2nd floor, Building C1, No. 1976 middle Gaoke Road, ZhangJiang Hitech Park, Pudong, Shanghai 201210, China. Electronic address: [e-mail].
Shanghai CureGene Pharmaceutical Co., Ltd, 2nd floor, Building C1, No. 1976 middle Gaoke Road, ZhangJiang Hitech Park, Pudong, Shanghai 201210, China.

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: 35.32 kDa 
• Atom Count: 2,811 
• Modeled Residue Count: 305 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	316	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
A1D8T (Subject of Investigation/LOI)	B [auth A]	CG-1039 C30 H40 N6 O6 DJPAHHWHKANOFU-BXRCACEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.223 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.39	α = 90
b = 52.95	β = 103.51
c = 45.42	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Chen, X., Hou, K., Tang, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release
  
• Version 1.1: 2026-06-24
  Changes: Database references