7K6D

SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Determined from Crystals Grown with 40 nL Acoustically Ejected Mpro Droplets at 1.48 A Resolution (Cryo-protected)

• PDB DOI:  https://doi.org/10.2210/pdb7K6D/pdb

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


• Deposited: 2020-09-19 Released: 2020-09-30 
• Deposition Author(s): Kreitler, D.F., Andi, B., Kumaran, D., Soares, A.S., Shi, W., Jakoncic, J., Fuchs, M.R., Keereetaweep, J., Shanklin, J., McSweeney, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), Brookhaven National Laboratory (BNL), National Virtual Biotechnology Laboratory (NVBL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.215 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Literature

Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.

Andi, B., Kumaran, D., Kreitler, D.F., Soares, A.S., Keereetaweep, J., Jakoncic, J., Lazo, E.O., Shi, W., Fuchs, M.R., Sweet, R.M., Shanklin, J., Adams, P.D., Schmidt, J.G., Head, M.S., McSweeney, S.

(2022) Sci Rep 12: 12197-12197

• PubMed: 35842458 
• DOI: https://doi.org/10.1038/s41598-022-15930-z
• Primary Citation of Related Structures:  
  7JYC, 7K3T, 7K40, 7K6D, 7K6E, 7MNG, 7MRR


• PubMed Abstract: 
  

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (M ^pro also known as 3CL ^pro ) is a primary drug target, due to its essential role in maturation of the viral polyproteins. In this study, we provide crystallographic evidence, along with some binding assay data, that three clinically approved anti hepatitis C virus drugs and two other drug-like compounds covalently bind to the M ^pro Cys145 catalytic residue in the active site. Also, molecular docking studies can provide additional insight for the design of new antiviral inhibitors for SARS-CoV-2 using these drugs as lead compounds. One might consider derivatives of these lead compounds with higher affinity to the M ^pro as potential COVID-19 therapeutics for further testing and possibly clinical trials.

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Organizational Affiliation: 

National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.59 kDa 
• Atom Count: 2,438 
• Modelled Residue Count: 305 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SV6 (Subject of Investigation/LOI)	C [auth A]	(1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide C36 H55 N7 O6 FTZGWEAUHOMNIG-FJRGXGLZSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002448 (SV6)	C [auth A]	TELAPREVIR, bound form	Peptide-like / Antiviral		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.215 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.76	α = 90
b = 54.82	β = 101.233
c = 48.24	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
AutoProcess	data reduction
Aimless	data reduction
pointless	data processing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Kreitler, D.F., Andi, B., Kumaran, D., Soares, A.S., Shi, W., Jakoncic, J., Fuchs, M.R., Keereetaweep, J., Shanklin, J., McSweeney, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133893
Department of Energy (DOE, United States)	United States	KP1605010
Brookhaven National Laboratory (BNL)	United States	LDRD 20-042
National Virtual Biotechnology Laboratory (NVBL)	United States	Coronavirus CARES Act

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2020-10-14
  Changes: Author supporting evidence, Structure summary
• Version 1.2: 2021-01-27
  Changes: Structure summary
• Version 1.3: 2021-09-01
  Changes: Data collection, Database references
• Version 1.4: 2022-07-27
  Changes: Database references