6Y2F

Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)

• PDB DOI: https://doi.org/10.2210/pdb6Y2F/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-15 Released: 2020-03-04 
• Deposition Author(s): Zhang, L., Lin, D., Sun, X., Hilgenfeld, R.
• Funding Organization(s): German Federal Ministry for Education and Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.219 
• R-Value Work: 0.178 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors.

Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., Hilgenfeld, R.

(2020) Science 368: 409-412

• PubMed: 32198291 
• DOI: https://doi.org/10.1126/science.abb3405
• Primary Citation of Related Structures:  
  6Y2E, 6Y2F, 6Y2G, 6Y7M


• PubMed Abstract: 
  

  The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a global health emergency. An attractive drug target among coronaviruses is the main protease (M ^pro , also called 3CL ^pro ) because of its essential role in processing the polyproteins that are translated from the viral RNA. We report the x-ray structures of the unliganded SARS-CoV-2 M ^pro and its complex with an α-ketoamide inhibitor. This was derived from a previously designed inhibitor but with the P3-P2 amide bond incorporated into a pyridone ring to enhance the half-life of the compound in plasma. On the basis of the unliganded structure, we developed the lead compound into a potent inhibitor of the SARS-CoV-2 M ^pro The pharmacokinetic characterization of the optimized inhibitor reveals a pronounced lung tropism and suitability for administration by the inhalative route.

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Organizational Affiliation: 

Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23562 Lübeck, Germany.

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: 34.5 kDa 
• Atom Count: 2,565 
• Modelled Residue Count: 303 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O6K (Subject of Investigation/LOI)	C [auth A]	~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate C31 H41 N5 O7 FRACPXUHUTXLCX-BELIEFIBSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.219 
• R-Value Work: 0.178 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.085	α = 90
b = 80.926	β = 114.838
c = 51.659	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Zhang, L., Lin, D., Sun, X., Hilgenfeld, R.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	DZIF-TTU01 grant 8011801806

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Database references
• Version 1.2: 2020-04-01
  Changes: Database references
• Version 2.0: 2020-04-08
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Structure summary
• Version 2.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 2.2: 2021-04-28
  Changes: Source and taxonomy, Structure summary
• Version 2.3: 2023-03-08
  Changes: Database references, Derived calculations, Structure summary
• Version 2.4: 2023-08-23
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 2.5: 2024-02-07
  Changes: Refinement description