7VH8

Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

Starting Model: experimental
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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 4WIClick on this verticalbar to view details

This is version 3.2 of the entry. See complete history


Literature

Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332.

Zhao, Y.Fang, C.Zhang, Q.Zhang, R.Zhao, X.Duan, Y.Wang, H.Zhu, Y.Feng, L.Zhao, J.Shao, M.Yang, X.Zhang, L.Peng, C.Yang, K.Ma, D.Rao, Z.Yang, H.

(2022) Protein Cell 13: 689-693


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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4WI
Query on 4WI

Download Ideal Coordinates CCD File 
B [auth A](1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
C23 H34 F3 N5 O4
WDVIRQQKRMIXGS-XIFHJVQQSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.341α = 90
b = 63.256β = 90
c = 105.953γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

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 4WIClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 2.0: 2021-12-22
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2022-07-06
    Changes: Database references
  • Version 3.0: 2023-07-05
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
  • Version 3.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 3.2: 2024-11-06
    Changes: Structure summary