Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.47 kDa 
• Atom Count: 5354 
• Modelled Residue Count: 611 
• Deposited Residue Count: 624 
• Unique protein chains: 2

6XBG

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW246

• PDB DOI: 10.2210/pdb6XBG/pdb

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


• Deposited: 2020-06-05 Released: 2020-06-17 
• Deposition Author(s): Sacco, M., Ma, C., Wang, J., Chen, Y.
• 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: 1.45 Å
• R-Value Free: 0.206 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L.

Sacco, M.D., Ma, C., Lagarias, P., Gao, A., Townsend, J.A., Meng, X., Dube, P., Zhang, X., Hu, Y., Kitamura, N., Hurst, B., Tarbet, B., Marty, M.T., Kolocouris, A., Xiang, Y., Chen, Y., Wang, J.

(2020) Sci Adv 6

• PubMed: 33158912 
• DOI: 10.1126/sciadv.abe0751
• Primary Citation of Related Structures:  
  6XA4, 6XBG, 6XBH, 6XBI, 6XFN


• PubMed Abstract: 
  

The main protease (M ^pro ) of SARS-CoV-2 is a key antiviral drug target. While most M ^pro inhibitors have a γ-lactam glutamine surrogate at the P1 position, we recently found that several M ^pro inhibitors have hydrophobic moieties at the P1 site, including calpain inhibitors II and XII, which are also active against human cathepsin L, a host protease that is important for viral entry. In this study, we solved x-ray crystal structures of M ^pro in complex with calpain inhibitors II and XII and three analogs of GC-376 The structure of M ^pro with calpain inhibitor II confirmed that the S1 pocket can accommodate a hydrophobic methionine side chain, challenging the idea that a hydrophilic residue is necessary at this position. The structure of calpain inhibitor XII revealed an unexpected, inverted binding pose. Together, the biochemical, computational, structural, and cellular data presented herein provide new directions for the development of dual inhibitors as SARS-CoV-2 antivirals.

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Organizational Affiliation: 

Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA. [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	308	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
inhibitor UAW246	C, D [auth E]	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth B], F [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002392	C, D [auth E]	UAW246	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.206 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.367	α = 90
b = 98.854	β = 108.23
c = 59.215	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-06-05 
• Released Date: 2020-06-17 
Deposition Author(s): Sacco, M., Ma, C., Wang, J., Chen, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI147325

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2020-11-18
  Changes: Database references
• Version 1.2: 2020-12-23
  Changes: Database references
• Version 1.3: 2021-01-27
  Changes: Structure summary