Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
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: 71.03 kDa 
• Atom Count: 4952 
• Residue Count: 605 
• Unique protein chains: 1

6W2A

1.65 A resolution structure of SARS-CoV 3CL protease in complex with inhibitor 7j

• DOI: 10.2210/pdb6W2A/pdb

• Classification: HYDROLASE/HYDROLASE Inhibitor
• Organism(s): Severe acute respiratory syndrome-related coronavirus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-03-05 Released: 2020-08-12 
• Deposition Author(s): Kashipathy, M.M., Lovell, S., Battaile, K.P., Rathnayake, A.D., Zheng, J., Kim, Y., Nguyen, H.N., Chang, K.O., Groutas, W.C.
• 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: 1.65 Å
• R-Value Free: 0.203 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice.

Rathnayake, A.D., Zheng, J., Kim, Y., Perera, K.D., Mackin, S., Meyerholz, D.K., Kashipathy, M.M., Battaile, K.P., Lovell, S., Perlman, S., Groutas, W.C., Chang, K.O.

(2020) Sci Transl Med 12

• PubMed: 32747425 
• DOI: 10.1126/scitranslmed.abc5332
• Primary Citation of Related Structures:  
  6XMK, 6W2A, 6VGZ, 6VGY, 6VH1, 6VH0, 6VH3, 6VH2


• PubMed Abstract: 
  

Pathogenic coronaviruses are a major threat to global public health, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the newly emerged SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). We describe herein the structure-guided optimization of a series of inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential for viral replication. The optimized compounds were effective against several human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme assay and in cell-based assays using Huh-7 and Vero E6 cell lines. Two selected compounds showed antiviral effects against SARS-CoV-2 in cultured primary human airway epithelial cells. In a mouse model of MERS-CoV infection, administration of a lead compound 1 day after virus infection increased survival from 0 to 100% and reduced lung viral titers and lung histopathology. These results suggest that this series of compounds has the potential to be developed further as antiviral drugs against human coronaviruses.

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Organizational Affiliation: 

Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA. [e-mail] [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	A, B	310	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: 1a EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus) Explore P0C6U8  Go to UniProtKB:  P0C6U8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VDJ	A, B	[4,4-bis(fluoranyl)cyclohexyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate C21 H35 F2 N3 O8 S BHZBRFONZANPNK-IUVQAAGXSA-N
QYS	A, B	(1S,2S)-2-[(N-{[(4,4-difluorocyclohexyl)methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid C21 H35 F2 N3 O8 S BHZBRFONZANPNK-ZYHFAYPJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.203 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.004	α = 90
b = 99.999	β = 108.31
c = 59.269	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-03-05 
• Released Date: 2020-08-12 
Deposition Author(s): Kashipathy, M.M., Lovell, S., Battaile, K.P., Rathnayake, A.D., Zheng, J., Kim, Y., Nguyen, H.N., Chang, K.O., Groutas, W.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI109039
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110761

Revision History 

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2020-08-19
  Changes: Database references
• Version 1.2: 2020-09-02
  Changes: Database references