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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 70.61 kDa 
• Atom Count: 5085 
• Modelled Residue Count: 597 
• Deposited Residue Count: 618 
• Unique protein chains: 1

7T44

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 4c

• PDB DOI: 10.2210/pdb7T44/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-12-09 Released: 2021-12-22 
• Deposition Author(s): Liu, L., Lovell, S., Battaile, K.P., Chamandi, S.D., Kim, Y., Groutas, W.C., Chang, K.O.
• 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: 0.226 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.

Dampalla, C.S., Rathnayake, A.D., Galasiti Kankanamalage, A.C., Kim, Y., Perera, K.D., Nguyen, H.N., Miller, M.J., Madden, T.K., Picard, H.R., Thurman, H.A., Kashipathy, M.M., Liu, L., Battaile, K.P., Lovell, S., Chang, K.O., Groutas, W.C.

(2022) J Med Chem 65: 7818-7832

• PubMed: 35638577 
• DOI: 10.1021/acs.jmedchem.2c00224
• Primary Citation of Related Structures:  
  7T3Y, 7T3Z, 7T40, 7T41, 7T42, 7T43, 7T44, 7T45, 7T46, 7T48, 7T49, 7T4A, 7T4B


• PubMed Abstract: 
  

The worldwide impact of the ongoing COVID-19 pandemic on public health has made imperative the discovery and development of direct-acting antivirals aimed at targeting viral and/or host targets. SARS-CoV-2 3C-like protease (3CL ^pro ) has emerged as a validated target for the discovery of SARS-CoV-2 therapeutics because of the pivotal role it plays in viral replication. We describe herein the structure-guided design of highly potent inhibitors of SARS-CoV-2 3CL ^pro that incorporate in their structure novel spirocyclic design elements aimed at optimizing potency by accessing new chemical space. Inhibitors of both SARS-CoV-2 3CL ^pro and MERS-CoV 3CL ^pro that exhibit nM potency and high safety indices have been identified. The mechanism of action of the inhibitors and the structural determinants associated with binding were established using high-resolution cocrystal structures.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	309	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ET6	D [auth A], F [auth B]	(1S,2S)-1-hydroxy-2-{[N-({[2-(methanesulfonyl)-2-azaspiro[3.3]heptan-6-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid C21 H36 N4 O10 S2 MQSKUPXMBXNALP-FJXLLPKBSA-N
ESS	C [auth A], E [auth B]	(1R,2S)-2-[(N-{[(2-azaspiro[3.3]heptan-6-yl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid C21 H36 N4 O10 S2 MQSKUPXMBXNALP-QBWPOKONSA-N
PG4	G [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.226 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.546	α = 90
b = 98.752	β = 108.34
c = 59.317	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: 2021-12-09 
• Released Date: 2021-12-22 
Deposition Author(s): Liu, L., Lovell, S., Battaile, K.P., Chamandi, S.D., Kim, Y., Groutas, W.C., Chang, K.O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI161085

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2022-06-08
  Changes: Database references
• Version 1.2: 2022-06-15
  Changes: Database references
• Version 1.3: 2022-06-22
  Changes: Database references