9BBV | pdb_00009bbv

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

• PDB DOI: https://doi.org/10.2210/pdb9BBV/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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.258 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

SARS-CoV-2 Mpro in complex with compound 6j 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: 34.33 kDa 
• Atom Count: 2,411 
• Modeled Residue Count: 304 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ALD (Subject of Investigation/LOI)	B [auth A]	N-{(1E,2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-[4-(2-methyl-2H-indazol-4-yl)benzoyl]-L-leucinamide C28 H34 N6 O3 TVVGUBYSXPRERN-KSHAZORZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.258 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.454	α = 90
b = 63.933	β = 90
c = 105.904	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.

---

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