7D1O | pdb_00007d1o

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1038/s41392-021-00468-9
  • Primary Citation of Related Structures:  
    7D1O
    • Organizational Affiliation: 
    • Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NNA (Subject of Investigation/LOI)
Query on NNA
Download Ideal Coordinates CCD File 
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), 0.250 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.2α = 90
b = 54.05β = 101.605
c = 45.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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