8WTI

Crystal structure of the SARS-CoV-2 main protease in complex with 20j


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

Starting Model: experimental
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Literature

Discovery of alpha-Ketoamide inhibitors of SARS-CoV-2 main protease derived from quaternized P1 groups.

Huang, Q.Quan, B.Chen, Y.Zhao, X.Zhou, Y.Huang, C.Qiao, J.Wang, Y.Li, Y.Yang, S.Lei, J.Li, L.

(2024) Bioorg Chem 143: 107001-107001

  • DOI: https://doi.org/10.1016/j.bioorg.2023.107001
  • Primary Citation of Related Structures:  
    8WTI

  • PubMed Abstract: 

    Although the SARS-CoV-2 pandemic has ended, multiple sporadic cases still exist, posing a request for more antivirals. The main protease (M pro ) of SARS-CoV-2, a key enzyme for viral replication, is an attractive target for drug development. Here, we report the discovery of a new potent α-ketoamide-containing M pro inhibitor, N-((R)-1-cyclohexyl-2-(((R)-3-methoxy-1-oxo-1-((1-(2-oxo-2-((thiazol-2-ylmethyl)amino)acetyl)cyclobutyl)amino)propan-2-yl)amino)-2-oxoethyl)-4,4-difluorocyclohexane-1-carboxamide (20j). This compound presented promising enzymatic inhibitory activity against SARS-CoV-2 M pro with an IC 50 value of 19.0 nM, and an excellent antiviral activity in cell-based assay with an EC 50 value of 138.1 nM. This novel covalent inhibitor may be used as a lead compound for subsequent drug discovery against SARS-CoV-2.


  • Organizational Affiliation

    Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X1Z (Subject of Investigation/LOI)
Query on X1Z

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
~{N}-[(1~{R})-1-cyclohexyl-2-[[(2~{R})-3-methoxy-1-oxidanylidene-1-[[1-[(1~{S})-1-oxidanyl-2-oxidanylidene-2-(1,3-thiazol-2-ylmethylamino)ethyl]cyclobutyl]amino]propan-2-yl]amino]-2-oxidanylidene-ethyl]-4,4-bis(fluoranyl)cyclohexane-1-carboxamide
C29 H43 F2 N5 O6 S
UHHQICGXTSMHIU-YMPZKCBVSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.57α = 90
b = 106.37β = 103.03
c = 54.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
Aimlessdata scaling
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2021YFF0702004

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release