8QDC

Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalent inhibitor GUE-3642 (compound 1 in publication)

• PDB DOI: https://doi.org/10.2210/pdb8QDC/pdb

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


• Deposited: 2023-08-28 Released: 2024-07-03 
• Deposition Author(s): Strater, N., Claff, T., Sylvester, K., Mueller, C.E., Guetschow, M.
• Funding Organization(s): Volkswagen Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.239 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Development of an active-site titrant for SARS-CoV-2 main protease as an indispensable tool for evaluating enzyme kinetics.

Voget, R., Breidenbach, J., Claff, T., Hingst, A., Sylvester, K., Steinebach, C., Vu, L.P., Weisse, R.H., Bartz, U., Strater, N., Muller, C.E., Gutschow, M.

(2024) Acta Pharm Sin B 14: 2349-2357

• PubMed: 38799620 
• DOI: https://doi.org/10.1016/j.apsb.2024.03.001
• Primary Citation of Related Structures:  
  8QDC


• PubMed Abstract: 
  

  A titrant for the SARS-CoV-2 main protease (M ^pro ) was developed that enables, for the first time, the exact determination of the concentration of the enzymatically active M ^pro by active-site titration. The covalent binding mode of the tetrapeptidic titrant was elucidated by the determination of the crystal structure of the enzyme-titrant complex. Four fluorogenic substrates of M ^pro , including a prototypical, internally quenched Dabcyl-EDANS peptide, were compared in terms of solubility under typical assay conditions. By exploiting the new titrant, key kinetic parameters for the M ^pro -catalyzed cleavage of these substrates were determined.

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Organizational Affiliation: 

Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.05 kDa 
• Atom Count: 5,185 
• Modelled Residue Count: 600 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
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
XV9 (Subject of Investigation/LOI)	C [auth A], D [auth B]	(phenylmethyl) ~{N}-[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-1-[[iminomethyl-(phenylmethyl)amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate C36 H46 N6 O5 NHQUTJQVPJWESZ-YEPDJPBYSA-N
DMS	E [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.239 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.006	α = 90
b = 98.647	β = 104.42
c = 67.525	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Strater, N., Claff, T., Sylvester, K., Mueller, C.E., Guetschow, M.

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Funding Organization	Location	Grant Number
Volkswagen Foundation	Germany	9A894

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release