9NFP | pdb_00009nfp

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

• PDB DOI: https://doi.org/10.2210/pdb9NFP/pdb

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


• Deposited: 2025-02-21 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.17 kDa 
• Atom Count: 3,614 
• Modeled Residue Count: 420 
• Deposited Residue Count: 523 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BXZ (Subject of Investigation/LOI)	G [auth A]	N-[(4-cyclopropyl-1,3-thiazol-2-yl)methyl]-1H-pyrazole-3-carboxamide C11 H12 N4 O S JGYUOEDSKCUYRY-UHFFFAOYSA-N
PO4	E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.727	α = 90
b = 68.427	β = 90
c = 138.082	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Coker, J.A., Sun, R., Polzer, P.M., Jung, J., Stauffer, S.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release