6WCO

Structure of SARS main protease bound to inhibitor X47


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19)

Mesecar, A.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Main protease306SARS coronavirus UrbaniMutation(s): 0 
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X47 (Subject of Investigation/LOI)
Query on X47

Download Ideal Coordinates CCD File 
D [auth A]N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclopentylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
C26 H31 N5 O2
GYSUWMLOWVCSQJ-HSZRJFAPSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
X47 BindingDB:  6WCO IC50: 1700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.763α = 90
b = 81.896β = 103.855
c = 53.672γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description