8AIZ

Mpro of SARS-CoV-2 in complex with the RK-68 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Main Protease SARS-CoV-2 in complex with the inhibitor RK-68

EL Kilani, H.Hilgenfeld, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replicase polyprotein 1abA [auth AAA]306Severe acute respiratory syndrome coronavirusMutation(s): 0 
Gene Names: rep1a-1b
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MIJ
Query on MIJ

Download Ideal Coordinates CCD File 
B [auth AAA](2~{R},3~{S})-3-[[(2~{S})-3-cyclopropyl-2-[2-oxidanylidene-3-(2-phenylethanoylamino)pyridin-1-yl]propanoyl]amino]-~{N}-methyl-2-oxidanyl-4-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butanamide
C28 H35 N5 O6
QZDBNMWKNRLEHS-NRTAZHGZSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.8α = 90
b = 52.8β = 103.08
c = 45.35γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionEuropean Union--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary