6XMK | pdb_00006xmk

1.70 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 7j


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.212 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6XMK

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice.

Rathnayake, A.D.Zheng, J.Kim, Y.Perera, K.D.Mackin, S.Meyerholz, D.K.Kashipathy, M.M.Battaile, K.P.Lovell, S.Perlman, S.Groutas, W.C.Chang, K.O.

(2020) Sci Transl Med 12

  • DOI: https://doi.org/10.1126/scitranslmed.abc5332
  • Primary Citation Related Structures: 
    6VGY, 6VGZ, 6VH0, 6VH1, 6VH2, 6VH3, 6W2A, 6XMK

  • PubMed Abstract: 

    Pathogenic coronaviruses are a major threat to global public health, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the newly emerged SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). We describe herein the structure-guided optimization of a series of inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential for viral replication. The optimized compounds were effective against several human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme assay and in cell-based assays using Huh-7 and Vero E6 cell lines. Two selected compounds showed antiviral effects against SARS-CoV-2 in cultured primary human airway epithelial cells. In a mouse model of MERS-CoV infection, administration of a lead compound 1 day after virus infection increased survival from 0 to 100% and reduced lung viral titers and lung histopathology. These results suggest that this series of compounds has the potential to be developed further as antiviral drugs against human coronaviruses.


  • Organizational Affiliation
    • Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.

Macromolecule Content 

  • Total Structure Weight: 69.39 kDa 
  • Atom Count: 4,873 
  • Modeled Residue Count: 600 
  • Deposited Residue Count: 618 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
309Severe 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QYS
(Subject of Investigation/LOI)

Query on QYS



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
(1S,2S)-2-[(N-{[(4,4-difluorocyclohexyl)methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
C21 H35 F2 N3 O8 S
BHZBRFONZANPNK-ZYHFAYPJSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
E [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.212 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.354α = 90
b = 98.631β = 107.79
c = 58.802γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI130092

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary