9MLJ | pdb_00009mlj

X-ray structure of SARS-CoV-2 main protease covalently bound to compound GRL-050-23 at 1.6 A

• PDB DOI: https://doi.org/10.2210/pdb9MLJ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-19 Released: 2025-11-26 
• Deposition Author(s): Beechboard, S.N., Mesecar, A.D., 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), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of SARS-CoV-2 main protease covalently bound to compound GRL-050-23 at 1.6 A

Beechboard, S.N., Mesecar, A.D., Ghosh, A.K., Center for Structural Biology of Infectious Diseases (CSBID)

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.65 kDa 
• Atom Count: 2,896 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BMU (Subject of Investigation/LOI)	C [auth A]	(3S)-N-{(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopiperidin-3-yl]propan-2-yl}-7-fluoro-2-[3-methyl-N-(trifluoroacetyl)-L-valyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide C33 H37 F4 N5 O5 S OPEOCXRIOYYAID-OKGCJIDBSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.335	α = 90
b = 82.903	β = 117.306
c = 54.373	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Beechboard, S.N., Mesecar, A.D., 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	HHSN272201700060C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1RO1 AI158649
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM132024
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	S10 OD030507

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release