7M8Y

CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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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
YTM (Subject of Investigation/LOI)
Query on YTM

Download Ideal Coordinates CCD File 
B [auth A]5-{3-[3-chloro-5-(2-phenylethoxy)phenyl]-2-oxo-2H-[1,3'-bipyridin]-5-yl}pyrimidine-2,4(1H,3H)-dione
C28 H21 Cl N4 O4
JVSFPWJWCIUVJO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.371α = 90
b = 53.545β = 103.2
c = 44.719γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

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

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