8QDC | pdb_00008qdc

Deposited: 2023-08-28 Released: 2024-07-03
Deposition Author(s): Strater, N., Claff, T., Sylvester, K., Mueller, C.E., Guetschow, M.
Funding Organization(s): Volkswagen Foundation

Experimental Data Snapshot

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

(2024) Acta Pharm Sin B 14: 2349-2357

PubMed Abstract:
A titrant for the SARS-CoV-2 main protease (M ^pro) was developed that enables, for the first time, the exact determination of the concentration of the enzymatically active M ^pro by active-site titration. The covalent binding mode of the tetrapeptidic titrant was elucidated by the determination of the crystal structure of the enzyme-titrant complex. Four fluorogenic substrates of M ^pro, including a prototypical, internally quenched Dabcyl-EDANS peptide, were compared in terms of solubility under typical assay conditions. By exploiting the new titrant, key kinetic parameters for the M ^pro-catalyzed cleavage of these substrates were determined.

Organizational Affiliation

Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany.

Macromolecule Content

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XV9 (Subject of Investigation/LOI) Query on XV9 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	(phenylmethyl) ~{N}-[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-1-[[iminomethyl-(phenylmethyl)amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate C₃₆ H₄₆ N₆ O₅ NHQUTJQVPJWESZ-YEPDJPBYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]