8R7B

SARS-CoV-2 NSP14 in complex with SAH and TDI-015051

PDB DOI: https://doi.org/10.2210/pdb8R7B/pdb

Classification: VIRAL PROTEIN
Organism(s): SARS-CoV-2 pseudovirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-24 Released: 2024-10-23
Deposition Author(s): Meyer, C., Garzia, A., Miller, M., Huggins, D.J., Myers, R.W., Liverton, N., Kargman, S., Nitsche, J., Ganichkin, O., Steinbacher, S., Meinke, P.T., Tuschl, T.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.244
R-Value Work: 0.190
R-Value Observed: 0.192

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

Small-molecule inhibition of SARS-CoV-2 guanine-N7 RNA cap methyltransferase

Meyer, C., Garzia, A., Miller, M., Huggins, D.J., Myers, R.W., Hoffmann, H.H., Ashbrook, A.W., Jannath, S., Liverton, N., Kargman, S., Zimmerman, M., Nelson, A.M., Cangialosi, J., Penalva-Lopez, S., Sharma, V., Ramos-Espiritu, L., Menezes, M.R., Larson, C., Nitsche, J., Alwaseem, H., Molina, H., Steinbacher, S., Glickman, J.F., Perlin, D.S., Rice, C., Meinke, P.T., Tuschl, T.

To be published.

Macromolecule Content

Total Structure Weight: 122.53 kDa
Atom Count: 7,252
Modelled Residue Count: 858
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine-N7 methyltransferase nsp14	A, B	528	SARS-CoV-2 pseudovirus	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YDT (Subject of Investigation/LOI) Query on YDT Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain X [auth B] MOL2 format, chain J [auth A] MOL2 format, chain X [auth B] mmCIF format, chain J [auth A] mmCIF format, chain X [auth B]	J [auth A], X [auth B]	N-[(5-fluoranyl-1-benzofuran-4-yl)methyl]-1,5-dimethyl-4-(1,4,6,7-tetrahydropyrazolo[4,3-c]pyridin-5-ylsulfonyl)pyrrole-2-carboxamide C₂₂ H₂₂ F N₅ O₄ S YVXDXTXKLFZFOI-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain X [auth B] Interactions & Density Focus chain J [auth A] Focus chain X [auth B]
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Q [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth B]	F [auth A], Q [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain F [auth A] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain Q [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain W [auth B] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain W [auth B] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain W [auth B]	I [auth A], N [auth B], O [auth B], P [auth B], W [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth B] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain V [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain V [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain V [auth B]	C [auth A] D [auth A] E [auth A] K [auth B] L [auth B] C [auth A], D [auth A], E [auth A], K [auth B], L [auth B], M [auth B], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain V [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain V [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	R [auth B], S [auth B], T [auth B], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]