8HHU

Crystal structure of the SARS-CoV-2 main protease in complex with SY110


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A new generation M pro inhibitor with potent activity against SARS-CoV-2 Omicron variants.

Huang, C.Shuai, H.Qiao, J.Hou, Y.Zeng, R.Xia, A.Xie, L.Fang, Z.Li, Y.Yoon, C.Huang, Q.Hu, B.You, J.Quan, B.Zhao, X.Guo, N.Zhang, S.Ma, R.Zhang, J.Wang, Y.Yang, R.Zhang, S.Nan, J.Xu, H.Wang, F.Lei, J.Chu, H.Yang, S.

(2023) Signal Transduct Target Ther 8: 128-128

  • DOI: https://doi.org/10.1038/s41392-023-01392-w
  • Primary Citation of Related Structures:  
    8HHT, 8HHU

  • PubMed Abstract: 

    Emerging SARS-CoV-2 variants, particularly the Omicron variant and its sublineages, continually threaten the global public health. Small molecule antivirals are an effective treatment strategy to fight against the virus. However, the first-generation antivirals either show limited clinical efficacy and/or have some defects in pharmacokinetic (PK) properties. Moreover, with increased use of these drugs across the globe, they face great pressure of drug resistance. We herein present the discovery and characterization of a new generation antiviral drug candidate (SY110), which is a potent and selective inhibitor of SARS-CoV-2 main protease (M pro ). This compound displayed potent in vitro antiviral activity against not only the predominant SARS-CoV-2 Omicron sublineage BA.5, but also other highly pathogenic human coronaviruses including SARS-CoV-1 and MERS-CoV. In the Omicron-infected K18-hACE2 mouse model, oral treatment with SY110 significantly lowered the viral burdens in lung and alleviated the virus-induced pathology. Importantly, SY110 possesses favorable PK properties with high oral drug exposure and oral bioavailability, and also an outstanding safety profile. Furthermore, SY110 exhibited sensitivity to several drug-resistance M pro mutations. Collectively, this investigation provides a promising new drug candidate against Omicron and other variants of SARS-CoV-2.


  • Organizational Affiliation

    State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
Molecule Chains  Sequence Length Organism Details Image
3C-like proteinase nsp5
A
306 Severe acute respiratory syndrome coronavirus 2 Mutation(s): 1 
EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group P0DTC1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
ID Chains  Name / Formula / InChI Key 2D Diagram 3D Interactions
LVX (Subject of Investigation/LOI)
Query on LVX

Download Ideal Coordinates CCD File 
B [auth A] (1~{R})-3,3-bis(fluoranyl)-~{N}-[(2~{R})-3-methoxy-1-oxidanylidene-1-[[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(1,3-thiazol-2-ylmethylamino)butan-2-yl]amino]propan-2-yl]cyclohexane-1-carboxamide
C25 H32 F2 N4 O5 S
PYEYIJGOSSTTFY-XCJLJZCSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å ) Angle ( ˚ )
a = 98.704 α = 90
b = 82.411 β = 114.69
c = 51.946 γ = 90
Software Package:
Software Name Purpose
BUSTER refinement
MOLREP phasing
Aimless data scaling
XDS data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding Organization Location Grant Number
National Natural Science Foundation of China (NSFC) China 2021YFF0702004

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description