7D1O

Crystal structure of SARS-Cov-2 main protease with narlaprevir

• PDB DOI: https://doi.org/10.2210/pdb7D1O/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-09-15 Released: 2020-09-23 
• Deposition Author(s): Fu, L.F., Feng, Y., Qi, J.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.248 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

Structural basis for the inhibition of the SARS-CoV-2 main protease by the anti-HCV drug narlaprevir.

Bai, Y., Ye, F., Feng, Y., Liao, H., Song, H., Qi, J., Gao, G.F., Tan, W., Fu, L., Shi, Y.

(2021) Signal Transduct Target Ther 6: 51-51

• PubMed: 33542181 
• DOI: https://doi.org/10.1038/s41392-021-00468-9
• Primary Citation of Related Structures:  
  7D1O

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Organizational Affiliation: 

Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.

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: 34.54 kDa 
• Atom Count: 2,512 
• Modelled Residue Count: 301 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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
NNA (Subject of Investigation/LOI)	B [auth A]	(1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl)methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropylamino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide C36 H63 N5 O7 S BZXRATSZUNDEEV-FZFXNXQRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.248 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.2	α = 90
b = 54.05	β = 101.605
c = 45.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Fu, L.F., Feng, Y., Qi, J.X.

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2021-02-24
  Changes: Database references
• Version 1.2: 2021-03-10
  Changes: Structure summary
• Version 1.3: 2021-04-14
  Changes: Derived calculations, Structure summary
• Version 1.4: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary