8UHO

Crystal structure of SARS CoV-2 3CL protease in complex with GSK4365096A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


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Literature

Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement.

Barton, L.S.Callahan, J.F.Cantizani, J.Concha, N.O.Cotillo Torrejon, I.Goodwin, N.C.Joshi-Pangu, A.Kiesow, T.J.McAtee, J.J.Mellinger, M.Nixon, C.J.Padron-Barthe, L.Patterson, J.R.Pearson, N.D.Pouliot, J.J.Rendina, A.R.Buitrago Santanilla, A.Schneck, J.L.Sanz, O.Thalji, R.K.Ward, P.Williams, S.P.King, B.W.

(2024) Bioorg Med Chem 100: 117618-117618

  • DOI: https://doi.org/10.1016/j.bmc.2024.117618
  • Primary Citation of Related Structures:  
    8UHO, 8UIA, 8UIF, 8ULD

  • PubMed Abstract: 

    The virally encoded 3C-like protease (3CL pro ) is a well-validated drug target for the inhibition of coronaviruses including Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Most inhibitors of 3CL pro are peptidomimetic, with a γ-lactam in place of Gln at the P1 position of the pseudopeptide chain. An effort was pursued to identify a viable alternative to the γ-lactam P1 mimetic which would improve physicochemical properties while retaining affinity for the target. Discovery of a 2-tetrahydrofuran as a suitable P1 replacement that is a potent enzymatic inhibitor of 3CL pro in SARS-CoV-2 virus is described herein.


  • Organizational Affiliation

    GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States. Electronic address: linda.s.barton@gsk.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WTE (Subject of Investigation/LOI)
Query on WTE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-[(benzyloxy)carbonyl]-4-fluoro-L-phenylalanyl-N-[(2S,3Z)-1-[(2S)-oxolan-2-yl]-3-(2-oxooxolan-3-ylidene)propan-2-yl]-L-leucinamide
C34 H42 F N3 O7
MSFOIQNYTTYSCY-JIXKKDCZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.724α = 90
b = 100.404β = 90
c = 103.116γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release