7D1O | pdb_00007d1o

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 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

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 Related Structures: 
  7D1O

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Organizational Affiliation: 
• Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, Beijing, 102206, China.
Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, 100101, China.
Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].

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 
• Modeled 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 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

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