7NWX

SARS-COV2 NSP5 in the presence of Zn2+

PDB DOI: https://doi.org/10.2210/pdb7NWX/pdb

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

Deposited: 2021-03-17 Released: 2022-01-26
Deposition Author(s): Calderone, V., Grifagni, D., Cantini, F., Fragai, M., Banci, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.244
R-Value Work: 0.204
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design.

Grifagni, D., Calderone, V., Giuntini, S., Cantini, F., Fragai, M., Banci, L.

(2021) Chem Commun (Camb) 57: 7910-7913

PubMed: 34278402 Search on PubMed
DOI: https://doi.org/10.1039/d1cc02956h
Primary Citation of Related Structures:
7NWX, 7NXH

PubMed Abstract:
Structural data on the SARS-CoV-2 main protease in complex with a zinc-containing organic inhibitor are already present in the literature and gave hints on the presence of a zinc binding site involving the catalytically relevant cysteine and histidine residues. In this paper, the structural basis of ionic zinc binding to the SARS-CoV-2 main protease has been elucidated by X-ray crystallography. The zinc binding affinity and its ability to inhibit the SARS-CoV-2 main protease have been investigated. These findings provide solid ground for the design of potent and selective metal-conjugated inhibitors of the SARS-CoV-2 main protease.

Organizational Affiliation

Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino, 50019, Italy. francesca.cantini@unifi.it marco.fragai@unifi.it lucia.banci@unifi.it.

Macromolecule Content

Total Structure Weight: 33.89 kDa
Atom Count: 2,447
Modelled Residue Count: 306
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]