9NHU | pdb_00009nhu

Structure of SARS-CoV-2 NSP14 bound to 5-(((cyclopropylmethyl)amino)methyl)-N-((4-cyclopropylthiazol-2-yl)methyl)-1H-pyrazole-3-carboxamide

PDB DOI: https://doi.org/10.2210/pdb9NHU/pdb

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

Deposited: 2025-02-25 Released: 2025-12-03
Deposition Author(s): Coker, J.A., Sun, R., Polzer, P.M., Jung, J., Stauffer, S.R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.272 (Depositor), 0.273 (DCC)
R-Value Work:
0.232 (Depositor), 0.232 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Fragment-Based Development of NSP14 Exonuclease Inhibitors Confounded by Batch-to-Batch Variability

Coker, J.A., Sun, R., Polzer, P.M., Jung, J., Stauffer, S.R.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.11.21.689747

Macromolecule Content

Total Structure Weight: 60.25 kDa
Atom Count: 3,518
Modeled Residue Count: 423
Deposited Residue Count: 523
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BYF (Subject of Investigation/LOI) Query on A1BYF 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]	5-{[(cyclopropylmethyl)amino]methyl}-N-[(4-cyclopropyl-1,3-thiazol-2-yl)methyl]-1H-pyrazole-3-carboxamide C₁₆ H₂₁ N₅ O S SFATUIRQTKFPPJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]