8Y42 | pdb_00008y42

Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 51

• PDB DOI: https://doi.org/10.2210/pdb8Y42/pdb

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


• Deposited: 2024-01-30 Released: 2025-02-12 
• Deposition Author(s): Nie, T.Q., Su, H.X., Li, M.J., Xu, Y.C.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.274 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Discovery of Novel Nonpeptidic and Noncovalent Small Molecule 3CL pro Inhibitors as anti-SARS-CoV-2 Drug Candidate.

Jiang, Z., Feng, B., Chen, L., Nie, T., Chen, S., Wang, L., Liu, H., Yu, T., Zhang, Y., Zheng, M., Xu, Y., Liu, H., Zang, Y., Su, H., Zhang, L., Li, J., Zhou, Y.

(2024) J Med Chem 67: 12760-12783

• PubMed: 39072488 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c00739
• Primary Citation Related Structures: 
  8GTV, 8GTW, 8Y42, 8Y44


• PubMed Abstract: 
  

  SARS-CoV-2 has still been threatening global public health with its emerging variants. Our previous work reported lead compound JZD-07 that displayed good 3CL ^pro inhibitory activity. Here, an in-depth structural optimization for JZD-07 was launched to obtain more desirable drug candidates for the therapy of SARS-CoV-2 infection, in which 54 novel derivatives were designed and synthesized by a structure-based drug design strategy. Among them, 24 compounds show significantly enhanced 3CL ^pro inhibitory potencies with IC ₅₀ values less than 100 nM, and 11 compounds dose-dependently inhibit the replication of the SARS-CoV-2 delta variant. In particular, compound 49 has the most desirable antiviral activity with EC ₅₀ of 0.272 ± 0.013 μM against the delta variant, which was more than 20 times stronger than JZD-07 . Oral administration of 49 could significantly reduce the lung viral copies of mice, exhibiting a more favorable therapeutic potential. Overall, this investigation presents a promising drug candidate for further development to treat SARS-CoV-2 infection.

---

Organizational Affiliation: 
• Lingang Laboratory, Shanghai 200031, China.
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Shenyang Pharmaceutical University, Shenyang 110016, China.
College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China.
State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
Pharmaceutical College of Henan University, Kaifeng 475004, China.
Hubei Jiangxia Laboratory, Wuhan 430200, China.
Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, 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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 137.32 kDa 
• Atom Count: 9,172 
• Modeled Residue Count: 1,208 
• Deposited Residue Count: 1,224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B, C, D	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
A1D51 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	~{N}-[(1~{S},2~{R})-2-[[4-cyclopropyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]-2-oxidanylidene-1~{H}-quinoline-4-carboxamide C27 H29 N5 O5 MVXGEYVENMHUPC-YADHBBJMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.274 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.49	α = 90
b = 107.84	β = 101.08
c = 116.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
xia2	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Nie, T.Q., Su, H.X., Li, M.J., Xu, Y.C.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Database references, Structure summary