7CA8 | pdb_00007ca8

The crystal structure of COVID-19 main protease in complex with an inhibitor Shikonin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.279 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of SARS-CoV-2 main protease in complex with the natural product inhibitor shikonin illuminates a unique binding mode.

Li, J., Zhou, X., Zhang, Y., Zhong, F., Lin, C., McCormick, P.J., Jiang, F., Luo, J., Zhou, H., Wang, Q., Fu, Y., Duan, J., Zhang, J.

(2021) Sci Bull (Beijing) 66: 661-663

  • DOI: https://doi.org/10.1016/j.scib.2020.10.018
  • Primary Citation of Related Structures:  
    7CA8
    • Organizational Affiliation: 
    • College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
298Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep, 1a-1b
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FNO
Query on FNO
Download Ideal Coordinates CCD File 
C [auth A]2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione
C16 H16 O5
NEZONWMXZKDMKF-SNVBAGLBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.96α = 90
b = 102.37β = 90
c = 103.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description