7PFM

A SARS-CoV2 major protease non-covalent ligand structure determined to 2.0 A resolution

• PDB DOI: https://doi.org/10.2210/pdb7PFM/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-11 Released: 2022-08-24 
• Deposition Author(s): Moche, M., Moodie, L., Strandback, E., Nyman, T., Sandstrom, A., Akaberi, D., Lennerstrand, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.220 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

The SARS-CoV2 major protease (Mpro) in complex with a non-covalent inhibitory ligand at 2 A resolution

Moche, M., Moodie, L., Strandback, E., Nyman, T., Akaberi, D., Lennerstrand, J.

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: 68.52 kDa 
• Atom Count: 5,082 
• Modelled Residue Count: 610 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7IL (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-[(1R)-2-(tert-butylamino)-2-oxidanylidene-1-pyridin-3-yl-ethyl]-N-(4-tert-butylphenyl)-1H-imidazole-5-carboxamide C25 H31 N5 O2 AJXIAISTEXNTHM-OAQYLSRUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.220 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.233	α = 90
b = 53.947	β = 99.77
c = 115.038	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Moche, M., Moodie, L., Strandback, E., Nyman, T., Sandstrom, A., Akaberi, D., Lennerstrand, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description