6WCO | pdb_00006wco

Structure of SARS main protease bound to inhibitor X47

• PDB DOI: https://doi.org/10.2210/pdb6WCO/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): SARS coronavirus Urbani
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-30 Released: 2020-08-05 
• Deposition Author(s): Mesecar, A.D., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.79 kDa 
• Atom Count: 3,123 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Main protease	A	306	SARS coronavirus Urbani	Mutation(s): 0
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X47 (Subject of Investigation/LOI)	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	B [auth A], C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.763	α = 90
b = 81.896	β = 103.855
c = 53.672	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Mesecar, A.D., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2024-12-25
  Changes: Atomic model, Data collection, Derived calculations, Structure summary