7END

Crystal structure of SARS-CoV 3CLpro in complex with the non-covalent inhibitor WU-04


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro.

Hou, N.Shuai, L.Zhang, L.Xie, X.Tang, K.Zhu, Y.Yu, Y.Zhang, W.Tan, Q.Zhong, G.Wen, Z.Wang, C.He, X.Huo, H.Gao, H.Xu, Y.Xue, J.Peng, C.Zou, J.Schindewolf, C.Menachery, V.Su, W.Yuan, Y.Shen, Z.Zhang, R.Yuan, S.Yu, H.Shi, P.Y.Bu, Z.Huang, J.Hu, Q.

(2023) ACS Cent Sci 9: 217-227

  • DOI: https://doi.org/10.1021/acscentsci.2c01359
  • Primary Citation of Related Structures:  
    7EN8, 7EN9, 7END, 7ENE

  • PubMed Abstract: 

    The 3C-like protease (3CLpro) is an essential enzyme for the replication of SARS-CoV-2 and other coronaviruses and thus is a target for coronavirus drug discovery. Nearly all inhibitors of coronavirus 3CLpro reported so far are covalent inhibitors. Here, we report the development of specific, noncovalent inhibitors of 3CLpro. The most potent one, WU-04, effectively blocks SARS-CoV-2 replications in human cells with EC 50 values in the 10-nM range. WU-04 also inhibits the 3CLpro of SARS-CoV and MERS-CoV with high potency, indicating that it is a pan-inhibitor of coronavirus 3CLpro. WU-04 showed anti-SARS-CoV-2 activity similar to that of PF-07321332 (Nirmatrelvir) in K18-hACE2 mice when the same dose was administered orally. Thus, WU-04 is a promising drug candidate for coronavirus treatment.


  • Organizational Affiliation

    Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replicase polyprotein 1a306Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: 1a
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J7R (Subject of Investigation/LOI)
Query on J7R

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[(1~{S},2~{R})-2-[[4-bromanyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]isoquinoline-4-carboxamide
C24 H24 Br N5 O4
BPLNOSFMIIASSJ-UXHICEINSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.496α = 90
b = 82.677β = 103.64
c = 107.454γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Database references
  • Version 1.2: 2023-03-15
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description