7MAZ

SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139

• PDB DOI: https://doi.org/10.2210/pdb7MAZ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-03-31 Released: 2022-10-12 
• Deposition Author(s): Lockbaum, G.J., Schiffer, C.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.207 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Starting Model: experimental

Literature

SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139

Lockbaum, G.J., Schiffer, C.A.

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: 68.77 kDa 
• Atom Count: 5,159 
• Modelled Residue Count: 610 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YVD (Subject of Investigation/LOI)	C [auth A], D [auth B]	4-fluoro-D-phenylalanyl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-4-fluoro-L-phenylalaninamide C29 H36 F2 N4 O5 WOTTZMBQRDTTCI-KTJVCJKDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.207 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.823	α = 90
b = 105.273	β = 104.05
c = 52.894	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Lockbaum, G.J., Schiffer, C.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01-GM109767

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary