8EOY

Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI37


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.299 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted WOHClick on this verticalbar to view details

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
A, B
306Severe 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WOH
Query on WOH

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
benzyl {(2S)-1-[2-(3-amino-3-oxopropyl)-2-(chloroacetyl)hydrazinyl]-4-methyl-1-oxopentan-2-yl}carbamate (non-preferred name)
C19 H27 Cl N4 O5
SEDQMDCLDZNPIX-HNNXBMFYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.299 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.234α = 91.08
b = 60.751β = 108.98
c = 67.65γ = 107.79
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted WOHClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Welch FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection
  • Version 1.2: 2024-10-23
    Changes: Structure summary