7M01

Deposited: 2021-03-10 Released: 2021-03-24
Deposition Author(s): Lovell, S., Kashipathy, M.M., Battaile, K.P., Chamandi, S.D., Rathnayake, A.D., Kim, Y., Perera, K.D., Jesri, A.R.M., Nguyen, H.N., Baird, M.A., Miller, M.J., Groutas, W.C., Chang, K.O.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

(2021) J Med Chem 64: 17846-17865

PubMed: 34865476 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.1c01037
Primary Citation of Related Structures:
7LZT, 7LZU, 7LZV, 7LZW, 7LZX, 7LZY, 7LZZ, 7M00, 7M01, 7M02, 7M03, 7M04

PubMed Abstract:
The COVID-19 pandemic is having a major impact on public health worldwide, and there is an urgent need for the creation of an armamentarium of effective therapeutics, including vaccines, biologics, and small-molecule therapeutics, to combat SARS-CoV-2 and emerging variants. Inspection of the virus life cycle reveals multiple viral- and host-based choke points that can be exploited to combat the virus. SARS-CoV-2 3C-like protease (3CLpro), an enzyme essential for viral replication, is an attractive target for therapeutic intervention, and the design of inhibitors of the protease may lead to the emergence of effective SARS-CoV-2-specific antivirals. We describe herein the results of our studies related to the application of X-ray crystallography, the Thorpe-Ingold effect, deuteration, and stereochemistry in the design of highly potent and nontoxic inhibitors of SARS-CoV-2 3CLpro.

Organizational Affiliation

Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States.

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	309	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YKS Query on YKS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	(1R,2S)-2-((S)-2-((((S)-1-(4,4-difluorocyclohexyl)-2-phenylethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid C₂₈ H₄₁ F₂ N₃ O₈ S PDAAZWNVPCMYBL-NRAAZAKSSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
YKV Query on YKV Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	(1S,2S)-2-((S)-2-((((S)-1-(4,4-difluorocyclohexyl)-2-phenylethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid C₂₈ H₄₁ F₂ N₃ O₈ S PDAAZWNVPCMYBL-KQWWLPFYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]