9L13 | pdb_00009l13

The crystal structure of SARS-CoV-2 Main protease in complex with an iso-quinoline-derived inhibitor FD6-31

• PDB DOI: https://doi.org/10.2210/pdb9L13/pdb

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


• Deposited: 2024-12-13 Released: 2025-12-17 
• Deposition Author(s): Zhong, B.S., Luo, G., Wang, G., Lu, W.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.233 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Next-generation inhibitors of SARS-CoV-2 M pro overcome the deficiencies of Paxlovid.

Luo, G., Wang, G., Liao, C., Zhong, B., Fan, L., Zhang, J., Rao, J., Zhang, J., Wang, Z., Luo, M., Yan, Y., Lu, L., Xu, W., Wu, F., Gao, X., Lu, W.

(2026) Nat Commun 17

• PubMed: 41935038 
• DOI: https://doi.org/10.1038/s41467-026-71436-6
• Primary Citation Related Structures: 
  9L13


• PubMed Abstract: 
  

  It remains elusive to design peptidomimetic inhibitors of SARS-CoV-2 main protease (M ^pro ) refractory to multiple deficiencies of Paxlovid (ritonavir-boosted nirmatrelvir), pertaining mainly to E166X mutations-conferred drug resistance and inherent pharmacokinetic limitations to nirmatrelvir. We identify via virtual screening an iso-quinoline P1 moiety in place of the traditional γ-lactam and design iso-quinoline-containing inhibitors with high affinity for M ^pro and its nirmatrelvir-resistant E166X mutants. Further optimization at P4 cultivates distinctive peptidomimetic inhibitors with drastically improved pharmacokinetic properties and significantly enhanced antiviral efficacy independent of ritonavir. Two such inhibitors, FD3-32 and FD3-36, also potent against SARS-CoV-1 and MERS-CoV M ^pro , are more effective as a monotherapy regimen than Paxlovid in reducing viral loads in vivo and protecting infected male mice from acute lung injury. Here, we report the discovery of next-generation SARS-CoV-2 M ^pro inhibitors that overcome the deficiencies of Paxlovid, promising efficacious antivirals critical for mitigating the current and future pandemics of coronaviruses.

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Organizational Affiliation: 
• Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China. [e-mail].
Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China. [e-mail].
Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China. [e-mail].
Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China. [e-mail].

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: 33.67 kDa 
• Atom Count: 2,379 
• Modeled Residue Count: 301 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	301	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
A1EH0 (Subject of Investigation/LOI)	B [auth A]	(5-chloranylspiro[1~{H}-2-benzofuran-3,4'-piperidine]-1'-yl)-isoquinolin-4-yl-methanone C22 H19 Cl N2 O2 RJTPGFSJXJKVJI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.233 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.15	α = 90
b = 80.9	β = 114.67
c = 51.55	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Zhong, B.S., Luo, G., Wang, G., Lu, W.Y.

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

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release
  
• Version 1.1: 2026-07-01
  Changes: Database references