8Y4F | pdb_00008y4f

Crystal structure of HCoV 229E main protease in complex with Bofutrelvir

PDB DOI: https://doi.org/10.2210/pdb8Y4F/pdb

Classification: VIRAL PROTEIN
Organism(s): Human coronavirus 229E
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-30 Released: 2025-01-08
Deposition Author(s): Zeng, P., Wang, W.W., Zhang, J., Li, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.222 (Depositor), 0.223 (DCC)
R-Value Work:
0.183 (Depositor), 0.184 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of HCoV 229E main protease in complex with Bofutrelvir

Zeng, P., Wang, W.W., Zhang, J., Li, J.

To be published.

Macromolecule Content

Total Structure Weight: 66.33 kDa
Atom Count: 5,025
Modeled Residue Count: 596
Deposited Residue Count: 596
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	298	Human coronavirus 229E	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22
UniProt
Find proteins for P0C6X1 (Human coronavirus 229E) Explore P0C6X1 Go to UniProtKB: P0C6X1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6X1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FHR (Subject of Investigation/LOI) Query on FHR Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide C₂₅ H₃₂ N₄ O₄ HPKJGHVHQWJOOT-ZJOUEHCJSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002347 (FHR) Query on PRD_002347	C [auth A], D [auth B]	~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide	Peptide-like / Inhibitor		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.222 (Depositor), 0.223 (DCC)
R-Value Work: 0.183 (Depositor), 0.184 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.631	α = 90
b = 77.028	β = 91.335
c = 77.6	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-01-08
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.