7SH8

Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI88


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of the SARS-CoV-2 main protease in complex with inhibitors

Yang, K.S.Sankaran, B.Liu, W.R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GJ3 (Subject of Investigation/LOI)
Query on GJ3

Download Ideal Coordinates CCD File 
B [auth A]benzyl [(2S,3R)-1-{[(2S)-1-(2-acetyl-2-{[(3S)-2-oxopyrrolidin-3-yl]methyl}hydrazinyl)-3-cyclohexyl-1-oxopropan-2-yl]amino}-3-tert-butoxy-1-oxobutan-2-yl]carbamate (non-preferred name)
C32 H49 N5 O7
LQGMWKMFHKDJKF-FBZFJNBBSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.704α = 90
b = 83.413β = 96.7
c = 86.416γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Welch FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection