9CSY

SARS-CoV-2 papain-like protease (PLpro) bound to PF-07957472


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery of SARS-CoV-2 papain-like protease (PL pro ) inhibitors with efficacy in a murine infection model.

Garnsey, M.R.Robinson, M.C.Nguyen, L.T.Cardin, R.Tillotson, J.Mashalidis, E.Yu, A.Aschenbrenner, L.Balesano, A.Behzadi, A.Boras, B.Chang, J.S.Eng, H.Ephron, A.Foley, T.Ford, K.K.Frick, J.M.Gibson, S.Hao, L.Hurst, B.Kalgutkar, A.S.Korczynska, M.Lengyel-Zhand, Z.Gao, L.Meredith, H.R.Patel, N.C.Polivkova, J.Rai, D.Rose, C.R.Rothan, H.Sakata, S.K.Vargo, T.R.Qi, W.Wu, H.Liu, Y.Yurgelonis, I.Zhang, J.Zhu, Y.Zhang, L.Lee, A.A.

(2024) Sci Adv 10: eado4288-eado4288

  • DOI: https://doi.org/10.1126/sciadv.ado4288
  • Primary Citation of Related Structures:  
    9CSY

  • PubMed Abstract: 

    Vaccines and first-generation antiviral therapeutics have provided important protection against COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there remains a need for additional therapeutic options that provide enhanced efficacy and protection against potential viral resistance. The SARS-CoV-2 papain-like protease (PL pro ) is one of the two essential cysteine proteases involved in viral replication. While inhibitors of the SARS-CoV-2 main protease have demonstrated clinical efficacy, known PL pro inhibitors have, to date, lacked the inhibitory potency and requisite pharmacokinetics to demonstrate that targeting PL pro translates to in vivo efficacy in a preclinical setting. Here, we report the machine learning-driven discovery of potent, selective, and orally available SARS-CoV-2 PL pro inhibitors, with lead compound PF-07957472 ( 4 ) providing robust efficacy in a mouse-adapted model of COVID-19 infection.


  • Organizational Affiliation

    Pfizer Global Research and Development, Cambridge, MA 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease
A, B, C
318Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
EC: 3.4.19.12
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AZ1 (Subject of Investigation/LOI)
Query on A1AZ1

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
I [auth C]
2-methyl-5-(4-methylpiperazin-1-yl)-N-{1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]cyclopropyl}benzamide
C29 H32 N6 O
MMVYUHFDLZLNDJ-UHFFFAOYSA-N
TFA
Query on TFA

Download Ideal Coordinates CCD File 
E [auth A]trifluoroacetic acid
C2 H F3 O2
DTQVDTLACAAQTR-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.866α = 90
b = 99.662β = 90
c = 188.682γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release