7SFI

SARS-CoV-2 Main Protease (Mpro) in Complex with ML104

• PDB DOI: https://doi.org/10.2210/pdb7SFI/pdb

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


• Deposited: 2021-10-03 Released: 2022-10-05 
• Deposition Author(s): Westberg, M., Fernandez, D., Lin, M.Z.
• Funding Organization(s): Novo Nordisk Foundation, Other private

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.239 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases

Westberg, M., Su, Y., Zou, X., Rustagi, A., Beck, A., Ning, L., Fernandez, D., Blish, C., Lin, M.Z.

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: 34.43 kDa 
• Atom Count: 2,630 
• Modelled 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	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
91Z (Subject of Investigation/LOI)	B [auth A]	(1R,2S,5S)-N-{(2S,3R)-4-amino-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[N-(2,4,6-trifluorophenyl)glycyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C24 H30 F3 N5 O5 YNUIIZLFVOREIR-NZIQIWATSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.239 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.49	α = 90
b = 63.586	β = 90
c = 105.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-05 
Deposition Author(s): Westberg, M., Fernandez, D., Lin, M.Z.

---

Funding Organization	Location	Grant Number
Novo Nordisk Foundation		NNF18OC0031816
Other private		--

Revision History  

• Version 1.0: 2022-10-05
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary