9QRC | pdb_00009qrc

SARS-CoV-2 nsp14 with 6-methyl-2-[(4-methylphenyl)methyl]pyridazin-3-one

PDB DOI: https://doi.org/10.2210/pdb9QRC/pdb

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

Deposited: 2025-04-03 Released: 2026-04-15
Deposition Author(s): Shi, X., Kozielski, F., Wang, Q., Dong, D.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (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

Fragment-based screening reveals novel SARS-CoV-2 nsp14 targeting fragments.

Shi, X., Wang, Q., Dong, D., Xu, M., Al Busaidi, F., Bowler, M., Haider, S., Kozielski, F.

To be published.

Macromolecule Content

Total Structure Weight: 60.37 kDa
Atom Count: 3,606
Modeled Residue Count: 445
Deposited Residue Count: 523
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine-N7 methyltransferase nsp14	A	523	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 2.1.1.56 (PDB Primary Data), 3.1.13 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1I9I (Subject of Investigation/LOI) Query on A1I9I Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	6-methyl-2-[(4-methylphenyl)methyl]pyridazin-3-one C₁₃ H₁₄ N₂ O CQCUMPFQORSELD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]