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)


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.5 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    German Center for Infection Research (DZIF), Marburg-Gießen-Langen Site, University of Marburg, 35043 Marburg, Germany.


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 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O6K (Subject of Investigation/LOI)
Query on O6K

Download Ideal Coordinates CCD File 
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
Query on DMS

Download Ideal Coordinates CCD File 
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 = 98.085α = 90
b = 80.926β = 114.838
c = 51.659γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermanyDZIF-TTU01 grant 8011801806

Revision History  (Full details and data files)

  • 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