9R5T | pdb_00009r5t

NSP14 IN COMPLEX WITH LIGAND TDI-016037-NX-1

PDB DOI: https://doi.org/10.2210/pdb9R5T/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-05-09 Released: 2025-08-27
Deposition Author(s): Steinbacher, S., Meyer, C.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.227 (Depositor), 0.222 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of Novel Isofunctional SARS-CoV-2 NSP14 RNA Cap Methyltransferase Inhibitors by Structure-Based Virtual Screening

Meyer, C., Michino, M., Huggins, D.J., Garzia, A., Davis, J.A., Miller, M.W., Liverton, N., Hoffmann, H.H., Glickman, J.F., Nitsche, J., Ganichkin, O., Steinbacher, S., Rice, C.M., Meinke, P.T., Tuschl, T.

(2025) ACS Med Chem Lett

DOI: https://doi.org/10.1021/acsmedchemlett.5c00339

Macromolecule Content

Total Structure Weight: 123.74 kDa
Atom Count: 7,501
Modeled Residue Count: 860
Deposited Residue Count: 1,056
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, B	528	Severe acute respiratory syndrome coronavirus	Mutation(s): 2 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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JDF (Subject of Investigation/LOI) Query on A1JDF Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Y [auth B] MOL2 format, chain G [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain G [auth A] mmCIF format, chain Y [auth B]	G [auth A], Y [auth B]	~{N}-[(1-cyclopropyl-6-fluoranyl-indazol-7-yl)methyl]-1,5-dimethyl-4-[(7-methyl-2~{H}-indazol-5-yl)sulfonyl]pyrrole-2-carboxamide C₂₆ H₂₅ F N₆ O₃ S KWNCMJIBFWUTJW-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain Y [auth B] Interactions & Density Focus chain G [auth A] Focus chain Y [auth B]
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain U [auth B] mmCIF format, chain F [auth A] mmCIF format, chain U [auth B]	F [auth A], U [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain F [auth A] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain U [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain NA [auth B] SDF format, chain OA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B]	NA [auth B], OA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain NA [auth B] Focus chain OA [auth B] Interactions & Density Focus chain NA [auth B] Focus chain OA [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain IA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain IA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain IA [auth B]	IA [auth B], Q [auth A], V [auth B], W [auth B], X [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain IA [auth B] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain IA [auth B] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	BA [auth B] C [auth A] D [auth A] E [auth A] R [auth B] BA [auth B], C [auth A], D [auth A], E [auth A], R [auth B], S [auth B], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain BA [auth B] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	CA [auth B] DA [auth B] EA [auth B] FA [auth B] GA [auth B] CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B]	JA [auth B], KA [auth B], LA [auth B], MA [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Interactions & Density Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Z [auth B]	AA [auth B], H [auth A], I [auth A], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.227 (Depositor), 0.222 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.236	α = 90
b = 100.946	β = 108.12
c = 90.251	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data reduction
XDS	data reduction
autoPROC	data reduction
autoPROC	data scaling
Aimless	data scaling
REFMAC	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing