7ILS | pdb_00007ils

Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z2443429438 (Nprot-x0180)

PDB DOI: https://doi.org/10.2210/pdb7ILS/pdb
Deposition Group: G_1002353 (changed state) | Explore G_1002353

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

Deposited: 2025-08-11 Released: 2026-08-26
Deposition Author(s): Aschenbrenner, J.C., Luptak, J., Balcomb, B.H., Marples, P.G., Bellini, D., Yu, C.W., Douangamath, A., Dias, A., Powell, A., Fearon, D., James, L., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.267 (Depositor), 0.297 (DCC)
R-Value Work:
0.197 (Depositor), 0.242 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD)

Luptak, J., Aschenbrenner, J.C., Balcomb, B.H., Marples, P.G., Bellini, D., Yu, C.W., Douangamath, A., Dias, A., Powell, A., Fearon, D., James, L., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 13.57 kDa
Atom Count: 1,084
Modeled Residue Count: 116
Deposited Residue Count: 117
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A	117	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9 Go to UniProtKB: P0DTC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WNM (Subject of Investigation/LOI) Query on WNM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	(3S)-1-(phenylsulfonyl)pyrrolidin-3-amine C₁₀ H₁₄ N₂ O₂ S ABNRKDROCBKFEH-VIFPVBQESA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.267 (Depositor), 0.297 (DCC)
R-Value Work: 0.197 (Depositor), 0.242 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.388	α = 90
b = 88.388	β = 90
c = 40.732	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Aschenbrenner, J.C.

Douangamath, A.

Revision History (Full details and data files)

Version 1.0: 2026-08-26
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.