8UND | pdb_00008und

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

• PDB DOI: https://doi.org/10.2210/pdb8UND/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-18 Released: 2024-10-23 
• Deposition Author(s): Mesecar, A.D., Lendy, E.K., Ghosh, A.K., Center for Structural Biology of Infectious Diseases (CSBID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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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

Literature

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

Mesecar, A.D., Lendy, E.K., Ghosh, A.K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.34 kDa 
• Atom Count: 2,804 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1a polyprotein	A	306	Severe acute respiratory syndrome coronavirus	Mutation(s): 0  Gene Names: ORF1ab
UniProt
Find proteins for A0A6C1F1G5 (Severe acute respiratory syndrome coronavirus 2) Explore A0A6C1F1G5  Go to UniProtKB:  A0A6C1F1G5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X4N (Subject of Investigation/LOI)	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 = 45.848	α = 90
b = 63.968	β = 90
c = 105.24	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Mesecar, A.D., Lendy, E.K., Ghosh, A.K., Center for Structural Biology of Infectious Diseases (CSBID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00035
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI158649

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release