9HFY | pdb_00009hfy

Crystal structure of SARS CoV-2 3CLpro (Mpro) with ALG-097078


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 
    0.190 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Discovery and Preclinical Profile of ALG-097558, a Pan-Coronavirus 3CLpro Inhibitor.

Bardiot, D.McGowan, D.C.Gupta, K.Deval, J.Chang, S.Jekle, A.Liu, C.Stevens, S.Serebryany, V.Tauchert, M.J.Maskos, K.Stoycheva, A.D.Ren, S.Jaisinghani, R.Faucher, M.O.Lin, T.I.Boland, S.Chaltin, P.Marchand, A.Wuyts, J.De Jonghe, S.Jochmans, D.Anugu, S.Baloju, V.Deta, K.Welch, M.Leyssen, P.Neyts, J.Laporte, M.Abdelnabi, R.Hu, H.Zhang, P.Le, K.Chanda, S.Smith, D.B.Raboisson, P.Beigelman, L.Symons, J.A.Blatt, L.Vandyck, K.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00088
  • Primary Citation of Related Structures:  
    9HFX, 9HFY

  • PubMed Abstract: 

    The SARS-CoV-2 outbreak of 2019 had a devastating impact on global health and economies worldwide. The viral cysteine protease (3CLpro) is responsible for viral polypeptide bond cleavages and is therefore an essential target to inhibit viral replication. Here, we report the discovery of an orally available, reversible covalent inhibitor of the SARS-CoV-2 main protease that is also highly active across other human coronaviruses and demonstrated oral efficacy in a Syrian hamster infection model at low plasma concentrations. Projection of pharmacokinetics (PK) in humans, based on PK studies in preclinical species and enhanced in vitro/in vivo efficacy of ALG-097558 ( 7 ) indicated the potential for BID dosing without the need for ritonavir, the PK boosting component of Paxlovid. After preclinical safety and pharmacological studies, ALG-097558 has progressed to phase 1 clinical trials.


  • Organizational Affiliation

    CISTIM Leuven vzw, Gaston Geenslaan 2, 3001 Leuven, Belgium.


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 
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
A1IUM (Subject of Investigation/LOI)
Query on A1IUM

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
(3~{S},3~{a}~{S},6~{a}~{R})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonyl]-~{N}-[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide
C33 H39 N5 O6
SRQDXOQIFPGVGN-FQVIVOBNSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free:  0.190 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.283α = 90
b = 99.039β = 108.19
c = 59.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release