8AJ0

Mpro of SARS COV-2 in complex with the RK-90 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8AJ0/pdb

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


• Deposited: 2022-07-27 Released: 2023-08-16 
• Deposition Author(s): El Kilani, H., Hilgenfeld, R.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.266 
• R-Value Work: 0.186 

Literature

Main Protease SARS-COV-2 in complex with the inhibitor RK-90

EL Kilani, H., Hilgenfeld, R.

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)

Macromolecule Content

• Total Structure Weight: 67.86 kDa 
• Atom Count: 4,827 
• Modelled Residue Count: 603 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A [auth AAA], B [auth BBB]	302	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
MJ0 (Subject of Investigation/LOI)	C [auth AAA], F [auth BBB]	(2R,3S)-3-[[(2S)-3-cyclopropyl-2-[2-oxidanylidene-3-(3-phenylpropanoylamino)pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide C29 H37 N5 O6 ZZWBXRBGXJAYNA-ALJFMCDRSA-N
CL	D [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.266 
• R-Value Work: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.253	α = 90
b = 54.376	β = 101.38
c = 114.192	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): El Kilani, H., Hilgenfeld, R.

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Funding Organization	Location	Grant Number
European Commission	European Union	--

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary