7TEK

SARS-CoV-2 3CLPro in complex with N-(4-(1H-pyrazol-4-yl)phenyl)-N-(3-chlorobenzyl)-2-(pyridin-3-yl)acetamide

PDB DOI: https://doi.org/10.2210/pdb7TEK/pdb

Classification: VIRAL PROTEIN,HYDROLASE/INHIBITOR
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-01-05 Released: 2023-01-11
Deposition Author(s): Goins, C.M., Stauffer, S.R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.274
R-Value Work: 0.208
R-Value Observed: 0.211

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

SARS-CoV-2 3CL-protease inhibitors derived from ML300: investigation of P1 and replacements of the 1,2,3-benzotriazole

Hooper, A., Macdonald, J.D., Reilly, B., Maw, J., Wirrick, A.P., Han, S.H., Lindsey, A.A., Rico, E.G., Romigh, T., Goins, C.M., Wang, N.S., Stauffer, S.R.

(2023) Med Chem Res

DOI: https://doi.org/10.1007/s00044-023-03108-9

Macromolecule Content

Total Structure Weight: 34.23 kDa
Atom Count: 2,385
Modelled Residue Count: 302
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
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	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% 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
I2D (Subject of Investigation/LOI) Query on I2D Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-[(3-chlorophenyl)methyl]-N-[4-(1H-pyrazol-4-yl)phenyl]-2-(pyridin-3-yl)acetamide C₂₃ H₁₉ Cl N₄ O LLFIKGDQQRLTFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.274
R-Value Work: 0.208
R-Value Observed: 0.211
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.843	α = 90
b = 53.561	β = 101.79
c = 44.958	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-01-11
Type: Initial release
Version 1.1: 2023-07-26
Changes: Database references
Version 1.2: 2023-10-25
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.