8UPS | pdb_00008ups

Structure of SARS-Cov2 3CLPro in complex with Compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 
    0.268 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic.

Shurtleff, V.W.Layton, M.E.Parish, C.A.Perkins, J.J.Schreier, J.D.Wang, Y.Adam, G.C.Alvarez, N.Bahmanjah, S.Bahnck-Teets, C.M.Boyce, C.W.Burlein, C.Cabalu, T.D.Campbell, B.T.Carroll, S.S.Chang, W.de Lera Ruiz, M.Dolgov, E.Fay, J.F.Fox, N.G.Goh, S.L.Hartingh, T.J.Hurzy, D.M.Kelly 3rd, M.J.Klein, D.J.Klingler, F.M.Krishnamurthy, H.Kudalkar, S.Mayhood, T.W.McKenna, P.M.Murray, E.M.Nahas, D.Nawrat, C.C.Park, S.Qian, D.Roecker, A.J.Sharma, V.Shipe, W.D.Su, J.Taggart, R.V.Truong, Q.Wu, Y.Zhou, X.Zhuang, N.Perlin, D.S.Olsen, D.B.Howe, J.A.McCauley, J.A.

(2024) J Med Chem 67: 3935-3958

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02248
  • Primary Citation Related Structures: 
    8UPS, 8UPV, 8UPW, 8UTE

  • PubMed Abstract: 

    As SARS-CoV-2 continues to circulate, antiviral treatments are needed to complement vaccines. The virus's main protease, 3CLPro, is an attractive drug target in part because it recognizes a unique cleavage site, which features a glutamine residue at the P1 position and is not utilized by human proteases. Herein, we report the invention of MK-7845, a novel reversible covalent 3CLPro inhibitor. While most covalent inhibitors of SARS-CoV-2 3CLPro reported to date contain an amide as a Gln mimic at P1, MK-7845 bears a difluorobutyl substituent at this position. SAR analysis and X-ray crystallographic studies indicate that this group interacts with His163, the same residue that forms a hydrogen bond with the amide substituents typically found at P1. In addition to promising in vivo efficacy and an acceptable projected human dose with unboosted pharmacokinetics, MK-7845 exhibits favorable properties for both solubility and absorption that may be attributable to the unusual difluorobutyl substituent.


  • Organizational Affiliation
    • Merck & Co., Inc., West Point, Pennsylvania 19486, United States.

Macromolecule Content 

  • Total Structure Weight: 34.47 kDa 
  • Atom Count: 2,437 
  • Modeled Residue Count: 305 
  • Deposited Residue Count: 306 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5306Severe 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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I70
(Subject of Investigation/LOI)

Query on I70



Download:Ideal Coordinates CCD File
B [auth A](1R,2S,5S)-N-{(2S,3R)-4-amino-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide
C27 H46 N6 O6
PGHPGMLPXLZINT-UYYZUGKPSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free:  0.268 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.59α = 90
b = 64.09β = 90
c = 105.49γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
pointlessdata 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: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary