8UND | pdb_00008und

X-ray Structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-190-21 at 1.90 A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.203 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Exploration of P1 and P4 modifications of nirmatrelvir: Design, synthesis, biological evaluation, and X-ray structural studies of SARS-CoV-2 Mpro inhibitors.

Ghosh, A.K.Yadav, M.Iddum, S.Ghazi, S.Lendy, E.K.Jayashankar, U.Beechboard, S.N.Takamatsu, Y.Hattori, S.I.Amano, M.Higashi-Kuwata, N.Mitsuya, H.Mesecar, A.D.

(2024) Eur J Med Chem 267: 116132-116132

  • DOI: https://doi.org/10.1016/j.ejmech.2024.116132
  • Primary Citation of Related Structures:  
    8UND

  • PubMed Abstract: 

    We report the synthesis, biological evaluation, and X-ray structural studies of a series of SARS-CoV-2 Mpro inhibitors based upon the X-ray crystal structure of nirmatrelvir, an FDA approved drug that targets the main protease of SARS-CoV-2. The studies involved examination of various P4 moieties, P1 five- and six-membered lactam rings to improve potency. In particular, the six-membered P1 lactam ring analogs exhibited high SARS-CoV-2 Mpro inhibitory activity. Several compounds effectively blocked SARS-CoV-2 replication in VeroE6 cells. One of these compounds maintained good antiviral activity against variants of concern including Delta and Omicron variants. A high-resolution X-ray crystal structure of an inhibitor bound to SARS-CoV-2 Mpro was determined to gain insight into the ligand-binding properties in the Mpro active site.


  • Organizational Affiliation
    • Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA. Electronic address: akghosh@purdue.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF1a polyprotein306Severe acute respiratory syndrome coronavirusMutation(s): 0 
Gene Names: ORF1ab
UniProt
Find proteins for A0A6C1F1G5 (Severe acute respiratory syndrome coronavirus 2)
Explore A0A6C1F1G5 
Go to UniProtKB:  A0A6C1F1G5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6C1F1G5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X4N (Subject of Investigation/LOI)
Query on X4N

Download Ideal Coordinates CCD File 
B [auth A](1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopiperidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
C24 H36 F3 N5 O4
ANWPXQGZBIGAAL-OMYRVQQUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.203 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.848α = 90
b = 63.968β = 90
c = 105.24γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data 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 Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00035
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI158649

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references