8Z46 | pdb_00008z46

SARS-CoV-2 3CL protease (3CL pro) in complex with a novel inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8Z46/pdb

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


• Deposited: 2024-04-16 Released: 2025-02-26 
• Deposition Author(s): Zhao, W.F., Xiong, L.W., Xu, Y.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Nonstructural Protein Inhibitors.

Wang, X., Xiong, L., Zhu, Y., Liu, S., Zhao, W., Wu, X., Seydimemet, M., Li, L., Ding, P., Lin, X., Liu, J., Wang, X., Duan, Z., Lu, W., Suo, Y., Cui, M., Yue, J., Jin, R., Zheng, M., Xu, Y., Mei, L., Hu, H., Lu, X.

(2024) J Am Chem Soc 146: 33983-33996

• PubMed: 39574309 
• DOI: https://doi.org/10.1021/jacs.4c12992
• Primary Citation Related Structures: 
  8Z46, 8Z4W


• PubMed Abstract: 
  

  The COVID-19 pandemic, exacerbated by persistent viral mutations, underscored the urgent need for diverse inhibitors targeting multiple viral proteins. In this study, we utilized covalent DNA-encoded libraries to discover innovative triazine-based covalent inhibitors for the 3-chymotrypsin-like protease (3CL ^pro , Nsp5) and the papain-like protease (PL ^pro ) domains of Nsp3, as well as novel non-nucleoside covalent inhibitors for the nonstructural protein 12 (Nsp12, RdRp). Optimization through molecular docking and medicinal chemistry led to the development of LU9 , a nonpeptide 3CL ^pro inhibitor with an IC ₅₀ of 0.34 μM, and LU10 , whose crystal structure showed a distinct binding mode within the 3CL ^pro active site. The X-ray cocrystal structure of SARS-CoV-2 PL ^pro in complex with XD5 uncovered a previously unexplored binding site adjacent to the catalytic pocket. Additionally, a non-nucleoside covalent Nsp12 inhibitor XJ5 achieved a potency of 0.12 μM following comprehensive structure-activity relationship analysis and optimization. Molecular dynamics revealed a potential binding mode. These compounds offer valuable chemical probes for target validation and represent promising candidates for the development of SARS-CoV-2 antiviral therapies.

---

Organizational Affiliation: 
• State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China.
University of Chinese Academy of Sciences, Beijing 100049, P. R. China.
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, P. R. China.
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China.
Suzhou Institute of Materia Medica, No. 108 Yuxin Road, Suzhou, Jiangsu 215123, P. R. 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: 34.36 kDa 
• Atom Count: 2,475 
• Modeled Residue Count: 301 
• 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  EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D70 (Subject of Investigation/LOI)	B [auth A]	(2~{S})-~{N}-(3-azanyl-3-oxidanylidene-propyl)-4-[4-[[(1~{S})-1-(2-chlorophenyl)-3-oxidanyl-propyl]amino]-6-(methylamino)-1,3,5-triazin-2-yl]-1-ethanoyl-piperazine-2-carboxamide C23 H32 Cl N9 O4 JPUUFERFUXBQSE-ROUUACIJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.886	α = 90
b = 81.99	β = 114.92
c = 51.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Zhao, W.F., Xiong, L.W., Xu, Y.C.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release