8PH4 | pdb_00008ph4

Co-Crystal structure of the SARS-CoV2 main protease Nsp5 with an Uracil-carrying X77-like inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8PH4/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-18 Released: 2024-01-31 
• Deposition Author(s): Barthel, T., Altincekic, N., Jores, N., Wollenhaupt, J., Weiss, M.S., Schwalbe, H.
• Funding Organization(s): Hessian Ministry of Science, Higher Education and Art (HMWK), European Union (EU)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Targeting the Main Protease (M pro , nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies.

Altincekic, N., Jores, N., Lohr, F., Richter, C., Ehrhardt, C., Blommers, M.J.J., Berg, H., Ozturk, S., Gande, S.L., Linhard, V., Orts, J., Abi Saad, M.J., Butikofer, M., Kaderli, J., Karlsson, B.G., Brath, U., Hedenstrom, M., Grobner, G., Sauer, U.H., Perrakis, A., Langer, J., Banci, L., Cantini, F., Fragai, M., Grifagni, D., Barthel, T., Wollenhaupt, J., Weiss, M.S., Robertson, A., Bax, A., Sreeramulu, S., Schwalbe, H.

(2024) ACS Chem Biol 19: 563-574

• PubMed: 38232960 
• DOI: https://doi.org/10.1021/acschembio.3c00720
• Primary Citation Related Structures: 
  8PH4


• PubMed Abstract: 
  

  The main protease M ^pro , nsp5, of SARS-CoV-2 (SCoV2) is one of its most attractive drug targets. Here, we report primary screening data using nuclear magnetic resonance spectroscopy (NMR) of four different libraries and detailed follow-up synthesis on the promising uracil-containing fragment Z604 derived from these libraries. Z604 shows time-dependent binding. Its inhibitory effect is sensitive to reducing conditions. Starting with Z604, we synthesized and characterized 13 compounds designed by fragment growth strategies. Each compound was characterized by NMR and/or activity assays to investigate their interaction with M ^pro . These investigations resulted in the four-armed compound 35b that binds directly to M ^pro . 35b could be cocrystallized with M ^pro revealing its noncovalent binding mode, which fills all four active site subpockets. Herein, we describe the NMR-derived fragment-to-hit pipeline and its application for the development of promising starting points for inhibitors of the main protease of SCoV2.

---

Organizational Affiliation: 
• Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany.
Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany.
Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany.
Department of Biochemistry, University of Zurich, 8093 Zurich, Switzerland.
SavernaTherapeutics, 4105 Biel-Benken, Switzerland.
Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zürich, Switzerland.
Swedish NMR Centre, Department of Chemistry and Molecular Biology, University of Gothenburg, SE40530 Göteborg, Sweden.
SciLifeLab, University of Gothenburg, SE40530 Göteborg, Sweden.
Swedish NMR Centre, Department of Chemistry, University of Umeå, SE-90187 Umeå, Sweden.
Protein Production Sweden, Department of Chemistry, University of Umeå, SE-90187 Umeå, Sweden.
Oncode Institute and Division of Biochemistry, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands.
Max Planck Institute of Biophysics, D-60438 Frankfurt am Main, Germany.
Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
Consorzio Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany.
NIH, LCP NIDDK, Bethesda, Maryland 20892, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.89 kDa 
• Atom Count: 5,138 
• Modeled Residue Count: 602 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YQN (Subject of Investigation/LOI)	D [auth A], E [auth A], G [auth B], H [auth B]	~{N}-(4-~{tert}-butylphenyl)-~{N}-[(1~{S})-2-(cyclohexylamino)-2-oxidanylidene-1-pyridin-3-yl-ethyl]-2,6-bis(oxidanylidene)-5~{H}-pyrimidine-5-carboxamide C28 H33 N5 O4 IZDUHWAQOVIQDS-GOTSBHOMSA-N
MLI	C [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
DMS	I [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA	F [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.69	α = 90
b = 100.04	β = 90
c = 103.37	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Barthel, T., Altincekic, N., Jores, N., Wollenhaupt, J., Weiss, M.S., Schwalbe, H.

---

Funding Organization	Location	Grant Number
Hessian Ministry of Science, Higher Education and Art (HMWK)	Germany	20007375
European Union (EU)	European Union	871037

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Database references