7UUA

Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NOLClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

A Novel Y-Shaped, S-O-N-O-S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease.

Yang, K.S.Blankenship, L.R.Kuo, S.A.Sheng, Y.J.Li, P.Fierke, C.A.Russell, D.H.Yan, X.Xu, S.Liu, W.R.

(2023) ACS Chem Biol 18: 449-455

  • DOI: https://doi.org/10.1021/acschembio.2c00695
  • Primary Citation of Related Structures:  
    7UU6, 7UU7, 7UU8, 7UU9, 7UUA, 7UUB, 7UUC, 7UUD, 7UUE

  • PubMed Abstract: 

    As the COVID-19 pathogen, SARS-CoV-2 relies on its main protease (M Pro ) for pathogenesis and replication. During crystallographic analyses of M Pro crystals that were exposed to the air, a uniquely Y-shaped, S-O-N-O-S-bridged post-translational cross-link that connects three residues C22, C44, and K61 at their side chains was frequently observed. As a novel covalent modification, this cross-link serves potentially as a redox switch to regulate the catalytic activity of M Pro , a demonstrated drug target of COVID-19. The formation of this linkage leads to a much more open active site that can potentially be targeted for the development of novel SARS-CoV-2 antivirals. The structural rearrangement of M Pro by this cross-link indicates that small molecules that lock M Pro in the cross-linked form can potentially be used with other active-site-targeting molecules such as paxlovid for synergistic effects in inhibiting SARS-CoV-2 viral replication.


  • Organizational Affiliation

    Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NOL (Subject of Investigation/LOI)
Query on NOL

Download Ideal Coordinates CCD File 
B [auth A]N-[(BENZYLOXY)CARBONYL]-O-(TERT-BUTYL)-L-THREONYL-3-CYCLOHEXYL-N-[(1S)-2-HYDROXY-1-{[(3S)-2-OXOPYRROLIDIN-3-YL]METHYL}ETHYL]-L-ALANINAMIDE
C32 H50 N4 O7
YIWYOEOSWRXENJ-FFXRMZKPSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.247α = 90
b = 80.818β = 96.92
c = 85.722γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NOLClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Welch FoundationUnited StatesA1715

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 1.4: 2024-11-20
    Changes: Structure summary