9BBU | pdb_00009bbu

SARS-CoV-2 Mpro in complex with compound 6h inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9BBU/pdb

• Classification: VIRAL PROTEIN, Hydrolase
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-04-07 Released: 2025-04-16 
• Deposition Author(s): Nayak, A., Afsar, M., Nayak, D., Olsen, S.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.220 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

SARS-CoV-2 Mpro in complex with compound 6h inhibitor

Nayak, A., Afsar, M., Nayak, D., Olsen, S.K.

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: 68.87 kDa 
• Atom Count: 4,882 
• Modeled Residue Count: 606 
• 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 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
A1ALK (Subject of Investigation/LOI)	C [auth A], E [auth B]	N~2~-[4-(5-chloropyridin-3-yl)benzoyl]-N-{(1Z,2S)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide C25 H30 Cl N5 O3 UXWHDTJOXYLLFG-CUEBCNBESA-N
EDO (Subject of Investigation/LOI)	D [auth A], F [auth B], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.220 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.31	α = 90
b = 99.123	β = 107.73
c = 59.324	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Nayak, A., Afsar, M., Nayak, D., Olsen, S.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM115568
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM128731
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR200030

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release
  
• Version 1.1: 2025-05-14
  Changes: Derived calculations