9HD8 | pdb_00009hd8

SARS-CoV-2 Main Protease in complex with with (1R)-N-(3-chlorophenyl)-N-[4-(2,4-dioxo-1H-pyrimidin-5-yl)phenyl]-3-oxo-indane-1-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb9HD8/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-12 Released: 2024-11-27 
• Deposition Author(s): Hanoulle, X., Charton, J., Deprez, B.
• Funding Organization(s): European Union (EU), Centre National de la Recherche Scientifique (CNRS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.169 (DCC) 

Starting Model: experimental

Literature

SARS-CoV-2 Main Protease in complex with with (1R)-N-(3-chlorophenyl)-N-[4-(2,4-dioxo-1H-pyrimidin-5-yl)phenyl]-3-oxo-indane-1-carboxamide

Hanoulle, X., Charton, J., Deprez, B.

To be published.

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 PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.34 kDa 
• Atom Count: 2,826 
• Modeled 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 nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ITV (Subject of Investigation/LOI)	B [auth A]	(1~{R})-~{N}-[4-[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-5-yl]phenyl]-~{N}-(3-chlorophenyl)-3-oxidanylidene-1,2-dihydroindene-1-carboxamide C26 H18 Cl N3 O4 WUIFAQSQLPAHRA-OAQYLSRUSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.169 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.41	α = 90
b = 53.825	β = 100.805
c = 44.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
Aimless	data scaling
MOLREP	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Hanoulle, X., Charton, J., Deprez, B.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	REACT-EU 22003061
Centre National de la Recherche Scientifique (CNRS)	France	COVID and ViroCrib programs

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release