7M8X

CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.

Deshmukh, M.G.Ippolito, J.A.Zhang, C.H.Stone, E.A.Reilly, R.A.Miller, S.J.Jorgensen, W.L.Anderson, K.S.

(2021) Structure 29: 823

  • DOI: https://doi.org/10.1016/j.str.2021.06.002
  • Primary Citation of Related Structures:  
    7M8M, 7M8N, 7M8O, 7M8P, 7M8X, 7M8Y, 7M8Z, 7M90, 7M91

  • PubMed Abstract: 

    There is a clinical need for direct-acting antivirals targeting SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, to complement current therapeutic strategies. The main protease (M pro ) is an attractive target for antiviral therapy. However, the vast majority of protease inhibitors described thus far are peptidomimetic and bind to the active-site cysteine via a covalent adduct, which is generally pharmacokinetically unfavorable. We have reported the optimization of an existing FDA-approved chemical scaffold, perampanel, to bind to and inhibit M pro noncovalently with IC 50 s in the low-nanomolar range and EC 50 s in the low-micromolar range. Here, we present nine crystal structures of M pro bound to a series of perampanel analogs, providing detailed structural insights into their mechanism of action and structure-activity relationship. These insights further reveal strategies for pursuing rational inhibitor design efforts in the context of considerable active-site flexibility and potential resistance mechanisms.


  • Organizational Affiliation

    Medical Scientist Training Program (MD-PhD), Yale School of Medicine, New Haven, CT, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe 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
YTJ (Subject of Investigation/LOI)
Query on YTJ

Download Ideal Coordinates CCD File 
B [auth A]2-{3-[3-chloro-5-(2-methoxyethoxy)phenyl]-2-oxo-2H-[1,3'-bipyridin]-5-yl}benzonitrile
C26 H20 Cl N3 O3
QRCHFFNDYYKHQM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.766α = 90
b = 81.27β = 116.83
c = 54.519γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAI083146
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM136651
Other privateUnited StatesCoReCT Pilot Grant - Yale University School of Medicine

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2021-08-18
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description