9HDC | pdb_00009hdc

SARS-CoV-2 Main Protease in complex with (3S)-3-[(3R)-3-phenylpiperidine-1-carbonyl]indan-1-one

• PDB DOI: https://doi.org/10.2210/pdb9HDC/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: 1.79 Å
• R-Value Free: 
  0.229 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.168 (DCC) 

Starting Model: experimental

Literature

SARS-CoV-2 Main Protease in complex with (3S)-3-[(3R)-3-phenylpiperidine-1-carbonyl]indan-1-one

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: 34.35 kDa 
• Atom Count: 2,546 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ITW (Subject of Investigation/LOI)	D [auth A]	(3~{S})-3-[(3~{R})-3-phenylpiperidin-1-yl]carbonyl-2,3-dihydroinden-1-one C21 H21 N O2 SIVSQHBZCSYPQG-LPHOPBHVSA-N
DMS	B [auth A], C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FMT	E [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.229 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.168 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.64	α = 90
b = 53.58	β = 102.72
c = 44.83	γ = 90

Software Package:

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

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