7IME | pdb_00007ime

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 Z1407672867 (Nprot-x0389)

PDB DOI: https://doi.org/10.2210/pdb7IME/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: 1.63 Å
R-Value Free:
0.255 (Depositor), 0.283 (DCC)
R-Value Work:
0.192 (Depositor), 0.233 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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: 13.73 kDa
Atom Count: 1,121
Modeled Residue Count: 116
Deposited Residue Count: 117
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GWP (Subject of Investigation/LOI) Query on GWP 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]	2-cyclopropyl-1~{H}-imidazole-4-carboxamide C₇ H₉ N₃ O ZIJDZTAYMWKMQH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS (Subject of Investigation/LOI) Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
IPA (Subject of Investigation/LOI) Query on IPA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]