Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.54 kDa 
• Atom Count: 5,036 
• Modelled Residue Count: 612 
• Deposited Residue Count: 612 
• Unique protein chains: 1

 7LDL

Improved Feline Drugs as SARS-CoV-2 Mpro Inhibitors: Structure-Activity Studies & Micellar Solubilization for Enhanced Bioavailability

• PDB DOI:  https://doi.org/10.2210/pdb7LDL/pdb

• Classification: VIRAL PROTEIN,HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli O103:H2 str. 12009
• Mutation(s): No 


• Deposited: 2021-01-13 Released: 2021-07-07 
• Deposition Author(s): Khan, M.B., Lu, J., Arutyunova, E., Young, H.S., Lemieux, M.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

Improved SARS-CoV-2 M pro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies.

Vuong, W., Fischer, C., Khan, M.B., van Belkum, M.J., Lamer, T., Willoughby, K.D., Lu, J., Arutyunova, E., Joyce, M.A., Saffran, H.A., Shields, J.A., Young, H.S., Nieman, J.A., Tyrrell, D.L., Lemieux, M.J., Vederas, J.C.

(2021) Eur J Med Chem 222: 113584-113584

• PubMed: 34118724 
• DOI: https://doi.org/10.1016/j.ejmech.2021.113584
• Primary Citation of Related Structures:  
  7LCO, 7LCR, 7LCS, 7LCT, 7LDL


• PubMed Abstract: 
  

Replication of SARS-CoV-2, the coronavirus causing COVID-19, requires a main protease (M ^pro ) to cleave viral proteins. Consequently, M ^pro is a target for antiviral agents. We and others previously demonstrated that GC376, a bisulfite prodrug with efficacy as an anti-coronaviral agent in animals, is an effective inhibitor of M ^pro in SARS-CoV-2. Here, we report structure-activity studies of improved GC376 derivatives with nanomolar affinities and therapeutic indices >200. Crystallographic structures of inhibitor-M ^pro complexes reveal that an alternative binding pocket in M ^pro , S4, accommodates the P3 position. Alternative binding is induced by polar P3 groups or a nearby methyl. NMR and solubility studies with GC376 show that it exists as a mixture of stereoisomers and forms colloids in aqueous media at higher concentrations, a property not previously reported. Replacement of its Na ⁺ counter ion with choline greatly increases solubility. The physical, biochemical, crystallographic, and cellular data reveal new avenues for M ^pro inhibitor design.

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Organizational Affiliation: 

Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada. Electronic address: [e-mail].

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 (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), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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
XV4 (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide C23 H32 N4 O5 WHTWOUANZWYZGR-MPGHIAIKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.07	α = 79.846
b = 60.86	β = 68.236
c = 63.67	γ = 70.402

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Khan, M.B., Lu, J., Arutyunova, E., Young, H.S., Lemieux, M.J.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	549297-2019

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release